Difference between revisions of "Reference annotation yeast Mbp1"
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<div id="BIO"> | <div id="BIO"> | ||
<div class="b1"> | <div class="b1"> | ||
| − | Mbp1 protein reference annotation | + | Yeast Mbp1 protein reference annotation |
</div> | </div> | ||
| − | + | ||
| + | | ||
| + | |||
| + | __TOC__ | ||
| + | |||
| + | |||
| + | <section begin=contents_summary /> | ||
| + | A reference annotation of the ''Saccharomyces cerevisiae'' Mbp1 protein sequence that integrates annotation sources we encounter throughout the course. | ||
| + | <section end=contents_summary /> | ||
| − | |||
| Line 23: | Line 30: | ||
| − | * see also: [[ | + | * see also: [[Reference APSES domains (reference species)]] |
| + | * see also: [[Reference APSES proteins (reference species)]] | ||
| Line 68: | Line 76: | ||
==Annotations== | ==Annotations== | ||
| − | ===NCBI CDD APSES | + | ===NCBI CDD APSES and KilA-Ndomain boundaries=== |
<section begin=CDD_APSES /> | <section begin=CDD_APSES /> | ||
| − | APSES domain boundaries can be derived from the results of a [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04383 '''CDD search'''] with the ID <tt>1BM8_A</tt>. The KilA-N superfamily domain alignment is returned. | + | The APSES domain is a well-defined type of DNA-binding domain that is ubiquitous in fungi and unique in that kingdom. Structurally it is a member of the Winged Helix-Turn-Helix family. Recently it was found that it is homologous to the somewhat shorter, prokaryotic KilA-N domain; thus the APSES domain was retired from [http://pfam.xfam.org/family/PF02292 '''pFam'''] and instances were merged into the [http://pfam.xfam.org/family/PF04383 '''KilA-N'''] family. However InterPro has a [http://www.ebi.ac.uk/interpro/entry/IPR018004 KilA-N] entry but still recognizes the [http://www.ebi.ac.uk/interpro/entry/IPR003163 APSES domain]. |
| + | |||
| + | |||
| + | KilA-N domain boundaries in Mbp1 can be derived from the results of a [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04383 '''CDD search'''] with the ID <tt>1BM8_A</tt> (the Mbp1 DNA binding domain crystal structure). The KilA-N superfamily domain alignment is returned. | ||
| + | |||
:<small>(pfam 04383): KilA-N domain; The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease.</small> | :<small>(pfam 04383): KilA-N domain; The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease.</small> | ||
| Line 88: | Line 100: | ||
</div> | </div> | ||
| + | Note that CDD and SMART are '''not consistent''' in how they apply <code>pFam 04383</code> to the Mbp1 sequence. See [[#Consolidated Annotation|annotation]] below. | ||
| − | + | The CDD KilA-N domain definition begins at position 16 of the 1BM8 sequence. But virtually all fungal APSES domains have a longer, structurally defined, conserved N-terminus. Blindly applying the KilA-N domain definition to these proteins would lose important information. '''For most purposes we will prefer the sequence spanned by the <tt>1BM8_A</tt> structure.''' The sequence is given below, the <span style="color: #005522;">KilA-N domain is coloured dark green</span>. By this definition the APSES domain is 99 amino acids long and comprises residues 4 to 102 of the <code>NP_010227</code> sequence. | |
<div style="line-height: 0; white-space: pre; border: solid 1px #445577; background-color: #F4F6FF; font-family: 'Courier New', Courier, monospace; padding: 10px;"> | <div style="line-height: 0; white-space: pre; border: solid 1px #445577; background-color: #F4F6FF; font-family: 'Courier New', Courier, monospace; padding: 10px;"> | ||
| Line 100: | Line 113: | ||
<p style="line-height:0.3;">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&doptcmdl=GenPept&db=Protein&term=1BM8A 1BM8A] <span style="color: #888888"> 81 </span><span style="color: #005522">KQLAEKFSVY</span><span style="color: #2233CC;">DQLKPLFDF</span> <span style="color: #888888">99</span></p> | <p style="line-height:0.3;">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&doptcmdl=GenPept&db=Protein&term=1BM8A 1BM8A] <span style="color: #888888"> 81 </span><span style="color: #005522">KQLAEKFSVY</span><span style="color: #2233CC;">DQLKPLFDF</span> <span style="color: #888888">99</span></p> | ||
</div> | </div> | ||
| + | |||
| + | |||
| + | | ||
| + | ;Yeast APSES domain sequence in FASTA format | ||
| + | |||
| + | >APSES_MBP1 Residues 4-102 of S. cerevisiae Mbp1 | ||
| + | QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI | ||
| + | LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF | ||
| + | |||
| + | |||
| + | | ||
| + | |||
| + | ;Synopsis of ranges | ||
| + | <table> | ||
| + | |||
| + | <tr class="sh"> | ||
| + | <td><b>Domain</b></td> | ||
| + | <td><b>Link</b></td> | ||
| + | <td><b>Length</b></td> | ||
| + | <td><b>Boundary</b></td> | ||
| + | <td><b>Range (Mbp1)</b></td> | ||
| + | <td><b>Range (1BM8)</b></td> | ||
| + | </tr> | ||
| + | |||
| + | <tr><td colspan="6" class="sp"> </td></tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td>KilA-N: pfam04383 (CDD)</td> | ||
| + | <td>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?ascbin=8&maxaln=10&seltype=2&uid=252556&querygi=6320147&aln=4,18,2,29,48,31,19,67,65,20,87,89,6 CDD alignment]</td> | ||
| + | <td>72</td> | ||
| + | <td><tt>STGSI ... KFSVY</tt></td> | ||
| + | <td>21 - 93</td> | ||
| + | <td>18 - 90</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s1"> | ||
| + | <td>KilA-N: pfam04383 (SMART)</td> | ||
| + | <td>[http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1 Smart main page]</td> | ||
| + | <td>79</td> | ||
| + | <td><tt>IHSTG ... YDQLK</tt></td> | ||
| + | <td>19 - 97</td> | ||
| + | <td>16 - 94</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td>KilA-N: SM01252 (SMART)</td> | ||
| + | <td>[http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1 Smart main page]</td> | ||
| + | <td>84</td> | ||
| + | <td><tt>TGSIM ... DFTQT</tt></td> | ||
| + | <td>22 - 105</td> | ||
| + | <td>19 - 99...</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s1"> | ||
| + | <td>APSES: Interpro IPR003163</td> | ||
| + | <td>[http://www.ebi.ac.uk/interpro/protein/P39678 (Interpro)]</td> | ||
| + | <td>130</td> | ||
| + | <td><tt>QIYSA ... IRSAS</tt></td> | ||
| + | <td>3 - 133</td> | ||
| + | <td>1 - 99...</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td>APSES (1BM8)</td> | ||
| + | <td>–</td> | ||
| + | <td>99</td> | ||
| + | <td><tt>QIYSA ... PLFDF</tt></td> | ||
| + | <td>4 - 102</td> | ||
| + | <td>1 - 99</td> | ||
| + | </tr> | ||
| + | </table> | ||
<section end=CDD_APSES /> | <section end=CDD_APSES /> | ||
| Line 242: | Line 326: | ||
== Orthologs == | == Orthologs == | ||
| − | The Mbp1 orthologs in the | + | The Mbp1 orthologs in the [[Reference_species_for_fungi|ten fungal reference species]]. |
| − | + | ||
* ''Aspergillus nidulans'' (ASPNI) | * ''Aspergillus nidulans'' (ASPNI) | ||
| − | * '' | + | * ''Bipolaris oryzae'' (BIPOR) |
| + | * ''Coprinopsis cinerea'' (COPCI) | ||
| + | * ''Cryptococcus neoformans'' (CRYNE) | ||
* ''Neurospora crassa'' (NEUCR) | * ''Neurospora crassa'' (NEUCR) | ||
| + | * ''Puccinia Graminis'' (PUCGR) | ||
| + | * '''''Saccharomyces cerevisiae'' (SACCE)''' | ||
* ''Schizosaccharomyces pombe'' (SCHPO) | * ''Schizosaccharomyces pombe'' (SCHPO) | ||
* ''Ustilago maydis'' (USTMA) | * ''Ustilago maydis'' (USTMA) | ||
| + | * ''Wallemia mellicola'' (WALME) | ||
| + | Orthologs were determined by [[BLAST scripting|RBM]] to [http://www.ncbi.nlm.nih.gov/protein/NP_010227 '''NP_010227'''], residues 4 to 102. Uniprot accession numbers were obtained from the [http://www.uniprot.org/uploadlists/ Uniprot mapping service]. | ||
| − | + | <table width="80%"> | |
| − | <table width=" | ||
<tr class="sh"> | <tr class="sh"> | ||
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<tr class="s1"> | <tr class="s1"> | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
<td class="sc">''Aspergillus nidulans''</td> | <td class="sc">''Aspergillus nidulans''</td> | ||
<td class="sc">ASPNI</td> | <td class="sc">ASPNI</td> | ||
| Line 278: | Line 359: | ||
</tr> | </tr> | ||
| + | <tr class="s2"> | ||
| + | <td class="sc">''Bipolaris orizae''</td> | ||
| + | <td class="sc">BIPOR</td> | ||
| + | <td class="sc">COCMIDRAFT_338</td> | ||
| + | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_007682304 XP_007682304] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_007682304?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
| + | <td class="sc">[http://www.uniprot.org/uniprot/W6ZM86 W6ZM86]</td> | ||
| + | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td class="sc">'' | + | <td class="sc">''Coprinopsis cinerea''</td> |
| − | <td class="sc"> | + | <td class="sc">COPCI</td> |
| − | <td class="sc"> | + | <td class="sc">CC1G_01306</td> |
| − | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/ | + | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_001837394 XP_001837394] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_001837394?report=fasta&log$=seqview&format=text (FASTA)]</small></td> |
| − | <td class="sc">[http://www.uniprot.org/uniprot/ | + | <td class="sc">[http://www.uniprot.org/uniprot/A8NYC6 A8NYC6]</td> |
</tr> | </tr> | ||
<tr class="s2"> | <tr class="s2"> | ||
| + | <td class="sc">''Cryptococcus neoformans''</td> | ||
| + | <td class="sc">CRYNE</td> | ||
| + | <td class="sc">CND05520</td> | ||
| + | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_570545 XP_570545] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_570545?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
| + | <td class="sc">[http://www.uniprot.org/uniprot/Q5KHS0 Q5KHS0]</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s1"> | ||
<td class="sc">''Neurospora crassa''</td> | <td class="sc">''Neurospora crassa''</td> | ||
<td class="sc">NEUCR</td> | <td class="sc">NEUCR</td> | ||
| − | <td class="sc"> NCU07246 </td> | + | <td class="sc">NCU07246</td> |
<td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_955821 XP_955821] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_955821?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_955821 XP_955821] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_955821?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
<td class="sc">[http://www.uniprot.org/uniprot/Q7RW59 Q7RW59]</td> | <td class="sc">[http://www.uniprot.org/uniprot/Q7RW59 Q7RW59]</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td class="sc">''Puccinia graminis''</td> | ||
| + | <td class="sc">PUCGR</td> | ||
| + | <td class="sc">PGTG_08863</td> | ||
| + | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_003327086 XP_003327086] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_003327086?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
| + | <td class="sc">[http://www.uniprot.org/uniprot/E3KED4 E3KED4]</td> | ||
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| + | <td class="sc">''Saccharomyces cerevisiae''</td> | ||
| + | <td class="sc">SACCE</td> | ||
| + | <td class="sc">Mbp1</td> | ||
| + | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/NP_010227 NP_010227] <small>[http://www.ncbi.nlm.nih.gov/protein/NP_010227?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
| + | <td class="sc">[http://www.uniprot.org/uniprot/P39678 P39678]</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
<td class="sc">''Schizosaccharomyces pombe''</td> | <td class="sc">''Schizosaccharomyces pombe''</td> | ||
<td class="sc">SCHPO</td> | <td class="sc">SCHPO</td> | ||
| − | <td class="sc"> | + | <td class="sc">Res2</td> |
<td class="sc">[http://www.ncbi.nlm.nih.gov/protein/NP_593032 NP_593032] <small>[http://www.ncbi.nlm.nih.gov/protein/NP_593032?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/NP_593032 NP_593032] <small>[http://www.ncbi.nlm.nih.gov/protein/NP_593032?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
<td class="sc">[http://www.uniprot.org/uniprot/P41412 P41412]</td> | <td class="sc">[http://www.uniprot.org/uniprot/P41412 P41412]</td> | ||
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="s1"> |
<td class="sc">''Ustilago maydis''</td> | <td class="sc">''Ustilago maydis''</td> | ||
<td class="sc">USTMA</td> | <td class="sc">USTMA</td> | ||
| − | <td class="sc"> | + | <td class="sc">UM06196</td> |
<td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_762343 XP_762343] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_762343?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_762343 XP_762343] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_762343?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
<td class="sc">[http://www.uniprot.org/uniprot/Q4P117 Q4P117]</td> | <td class="sc">[http://www.uniprot.org/uniprot/Q4P117 Q4P117]</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td class="sc">''Wallemia mellicola''</td> | ||
| + | <td class="sc">WALME</td> | ||
| + | <td class="sc">WALSEDRAFT_59726</td> | ||
| + | <td class="sc">[http://www.ncbi.nlm.nih.gov/protein/XP_006957051 XP_006957051] <small>[http://www.ncbi.nlm.nih.gov/protein/XP_006957051?report=fasta&log$=seqview&format=text (FASTA)]</small></td> | ||
| + | <td class="sc">[http://www.uniprot.org/uniprot/I4YGC0 I4YGC0]</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
| + | |||
| + | |||
| + | |||
| + | ;FASTA formatted sequences | ||
| + | (Header lines were edited to begin with a code identifying the sequence as orthologous to Mbp1, and including the species shorthand code.) | ||
| + | |||
| + | |||
| + | <source lang="text"> | ||
| + | >MBP1_ASPNI XP_660758 AN3154.2 [Aspergillus nidulans FGSC A4] | ||
| + | MAAVDFSNVYSATYSSVPVYEFKIGTDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKV | ||
| + | QGGYGKYQGTWIPLQEGRQLAERNNILDKLLPIFDYVAGDRSPPPAPKHTSAASKPRAPKINKRVVKEDV | ||
| + | FSAVNHHRSMGPPSFHHEHYDVNTGLDEDESIEQATLESSSMIADEDMISMSQNGPYSSRKRKRGINEVA | ||
| + | AMSLSEQEHILYGDQLLDYFMTVGDAPEATRIPPPQPPANFQVDRPIDDSGNTALHWACAMGDLEIVKDL | ||
| + | LRRGADMKALSIHEETPLVRAVLFTNNYEKRTFPALLDLLLDTISFRDWFGATLFHHIAQTTKSKGKWKS | ||
| + | SRYYCEVALEKLRTTFSPEEVDLLLSCQDSVGDTAVLVAARNGVFRLVDLLLSRCPRAGDLVNKRGETAS | ||
| + | SIMQRAHLAERDIPPPPSSITMGNDHIDGEVGAPTSLEPQSVTLHHESSPATAQLLSQIGAIMAEASRKL | ||
| + | TSSYGAAKPSQKDSDDVANPEALYEQLEQDRQKIRRQYDALAAKEAAEESSDAQLGRYEQMRDNYESLLE | ||
| + | QIQRARLKERLASTPVPTQTAVIGSSSPEQDRLLTTFQLSRALCSEQKIRRAAVKELAQQRADAGVSTKF | ||
| + | DVHRKLVALATGLKEEELDPMAAELAETLEFDRMNGKGVGPESPEADHKDSASLPFPGPVVSVDA | ||
| + | |||
| + | >MBP1_BIPOR XP_007682304 COCMIDRAFT_338 [Bipolaris oryzae ATCC 44560] | ||
| + | MPPAPDGKIYSATYSNVPVYECNVNGHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKV | ||
| + | QGGYGKYQGTWIPLEEGRGLAERNGVLDKMRAIFDYVPGDRSPPPAPKHATAASNRMKPPRQTAAAVAAA | ||
| + | AVAAAAAAAAVANHNALMSNSRSQASEDPYENSQRSQIYREDTPDNETVISESMLGDADLMDMSQYSADG | ||
| + | NRKRKRGMDQMSLLDQQHQIWADQLLDYFMLLDHEAAVSWPEPPPSINLDRPIDEKGHAAMHWAAAMGDV | ||
| + | GVVKELIHRGARLDCLSNNLETPLMRAVMFTNNFDKETMPSMVKIFQQTVHRTDWFGSTVFHHIAATTSS | ||
| + | SNKYVCARWYLDCIINKLSETWIPEEVTRLLNAADQNGDTAIMIAARNGARKCVRSLLGRNVAVDIPNKK | ||
| + | GETADDLIRELNQRRRMHGRTRQASSSPFAPAPEHRLNGHVPHFDGGPLMSVPVPSMAVRESVQYRSQTA | ||
| + | SHLMTKVAPTLLEKCEELATAYEAELQEKEAEFFDAERVVKRRQAELEAVRKQVAELQSMSKGLHIDLND | ||
| + | EEAERQQEDELRLLVEEAESLLEIEQKAELRRLCSSMPQQNSDSSPVDITEKMRLALLLHRAQLERRELV | ||
| + | REVVGNLSVAGMSEKQGTYKKLIAKALGEREEDVESMLPEILQELEEAETQERAEGLDGSPV | ||
| + | |||
| + | >MBP1_COPCI XP_001837394 CC1G_01306 [Coprinopsis cinerea okayama7#130] | ||
| + | MPEAQIFKATYSGIPVYEMMCKGVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGG | ||
| + | YGKYQGTWIPLERGMQLAKQYNCEHLLRPIIEFTPAAKSPPLAPKHLVATAGNRPVRKPLTTDLSAAVIN | ||
| + | TRSTRKQVADGVGEESDHDTHSLRGSEDGSMTPSPSEASSSSRTPSPIHSPGTYHSNGLDGPSSGGRNRY | ||
| + | RQSNDRYDEDDDASRHNGMGDPRSYGDQILEYFISDTNQIPPILITPPPDFDPNMAIDDDGHTSLHWACA | ||
| + | MGRIRIVKLLLSAGADIFKVNKAGQTALMRSVMFANNYDVRKFPELYELLHRSTLNIDNSNRTVFHHVVD | ||
| + | VAMSKGKTHAARYYMETILTRLADYPKELADVINFQDEDGETALTMAARCRSKRLVKLLIDHGADPKINN | ||
| + | HDGKNAEDYILEDERFRSSPAPSSRVAAMSYRNAQVAYPPPGAPSTYSFAPANHDRPPLHYSAAAQKAST | ||
| + | RCVNDMASMLDSLAASFDQELRDKERDMAQAQALLTNIQAEILESQRTVLQLRQQAEGLSQAKQRLADLE | ||
| + | NALQDKMGRRYRLGFEKWIKDEETREKVIRDAANGDLVLTPATTSYTVDEDGDSDSGSNGDKNKGKRKAQ | ||
| + | VQQEEVSDLVELYSNIPTDPEELRKQCEALREEVSQSRKRRKAMFDELVTFQAEAGTSGRMSDYRRLIAA | ||
| + | GCGGLEPLEIDSVLGMLLETLEAEDPSSTSATWSGSKGQQTG | ||
| + | |||
| + | >MBP1_CRYNE XP_570545 CND05520 [Cryptococcus neoformans var. neoformans JEC21] | ||
| + | MEPPSNPIQPPVTPSHHSLLSAISPALSEQTPAPIHTLPPHLRPSIPQPHIAPPRPSSVQPTMEEQQRMH | ||
| + | HIQQHQQQQHFQQQQNDENVFGSVMGAPGHVPGHEAPMSTQPKVYASVYSGVPVFEAMIRGISVMRRASD | ||
| + | SWVNATQILKVAGVHKSARTKILEKEVLNGIHEKIQGGYGKYQGTWVPLDRGRDLAEQYGVGSYLSSVFD | ||
| + | FVPSASVIAALPVIRTGTPDRSGQQTPSGLPGHPNQRVISPFANHGQTTPHMPPPQFIHQGNEQMMNLPP | ||
| + | HPSSLAYPTQPKPYFSMPLQHTVGPQYDERHEGMTMTPTMSMDGLAPPADIARMGFPYNPSDIYIDQYGQ | ||
| + | PHATYQASPYGKESGHPSKRQRSDAEGSYIESGAAVQQHVEQDEEADDGLDNDSTASDDARDPPPLPSSM | ||
| + | LLPHKPIRPKATPANGRIKSRLVQIFNVEGQVNLRSVFGLAPDQLPNFDIDMVIDDQGHSALHWACALAR | ||
| + | LSIVQQLIELGADIHRGNYAGETPLIRAVLTSNHAEAGSFTDLLHLLSPSIRTLDHAYRTVLHHIALVAG | ||
| + | VKGRVPAARTYMASVLEWVAREQQANNTHSITNPPNPADRNELAPINLRTLVDVQDVHGDTALNVAARVG | ||
| + | NKGLVGLLLDAGADKTRANKLGLRPENFGLEIEALKISNGEAVMANLKSEVSKPERKSRDVQKNIATIFE | ||
| + | SISSTFSSEMLAKQTKLNATEASVRHATRALADKRQHLHRAQEKLATMQLFEQRSENVRRIMDAIAAGTL | ||
| + | LTPAEFTGRTQTMHEKSTGQLPPLAFRHVPGLALDASSQSQLNGAPPSTPLSVEDQEDIALPERDDPECL | ||
| + | VKLRRMALWEDRIAEVLEDKIRAMEGEGVDRAVKYRKLVSVCAKVPVDKVDSMLDGLVAAVESEGQGLDF | ||
| + | SRASNFVNRIKATKS | ||
| + | |||
| + | >MBP1_NEUCR XP_955821 NCU07246 [Neurospora crassa OR74A] | ||
| + | MVKENVGGNPEPGIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREV | ||
| + | QKDTHEKIQGGYGRYQGTWIPLEQAEALARRNNIYERLKPIFEFQPGNESPPPAPRHASKPKAPKVKPAV | ||
| + | PTWGSKSAKNANPPQPGTFLPPGRKGLPAQAPDYNDADTHMHDDDTPDNLTVASASYMAEDDRYDHSHFS | ||
| + | TGHRKRKRDELIEDMTEQQHAVYGDELLDYFLLSRNEQPAVRPDPPPNFKPDWPIDNERHTCLHWASAMG | ||
| + | DVDVMRQLKKFGASLDAQNVRGETPFMRAVNFTNCFEKQTFPQVMKELFSTIDCRDLSGCTVIHHAAVMK | ||
| + | IGRVNSQSCSRYYLDIILNRLQETHHPEFVQQLLDAQDNDGNTAVHLAAMRDARKCIRALLGRGASTDIP | ||
| + | NKQGIRAEELIKELNASISKSRSNLPQRSSSPFAPDTQRHDAFHEAISESMVTSRKNSQPNYSSDAANTV | ||
| + | QNRITPLVLQKLKDLTATYDSEFKEKDDAEKEARRILNKTQSELKALTASIDDYNSRLDTDDVAAKTAAE | ||
| + | MATARHKVLAFVTHQNRISVQEAVKQELAALDRANAVTNGTSTKSKSSSPSKKPKLSPIPDQKDKPPKDE | ||
| + | NETESEAEHPDPPAAQAHQQQPGPSSQDTEVEDQDREEEEDDYTHRLSLAAELRSILQEQRSAENDYVEA | ||
| + | RGMLGTGERIDKYKHLLMSCLPPDEQENLEENLEEMIKLMEQEDESVTDLPAGAVGGGGGGNAADGSGGG | ||
| + | GQPSNGRRESVLPALRGGNGDGEMSRRGSRTAAAAAAQVDGEREINGRAGAERTERIQEIAAV | ||
| + | |||
| + | >MBP1_PUCGR XP_003327086 PGTG_08863 [Puccinia graminis f. sp. tritici CRL 75-36-700-3] | ||
| + | MAYGGSIQPLRPPSRESATLHLHQPDLTVTSPPLSLTHCPPCVYSHFTHTPTSLIVIQVSLHSLLDQETY | ||
| + | HLLPSRSPPTVSVRMGTTTIYKATYSGVPVLEMPCEGIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLE | ||
| + | REIQKGTHEKIQGGYGKYQGTWVPLDRGIDLAKQYGVDHLLSALFNFQPSSNESPPLAPKHVTALSTRVK | ||
| + | VSKVSAASAARAARAVVPSLPSTSGLGGRNTNNSWSNFDSDNEPGLPPAASSRESNGNWATQSKLARSSN | ||
| + | LARARANINNSHPEDLPVPAPDQLQASPLPSMQTADPENDNSLTPSELSLPSRTPSPIEDLPLTVNTASS | ||
| + | QSTRNKGKSRDLPDDEDLSRGQKRKYDTSLVEDTSYSDGADDQYINGNPSNAASAKYAKLILDYFVSESS | ||
| + | QIPNFLNDPPSDFDPNVVIDDDGHTALHWACAMGRIKIIKLLLTCGADIFRANNAGQTALMRAVMFTNNH | ||
| + | DLRTFPELFESFSGSVINIDRTDRTVFHYVIDIALTKGKVPAARYYLETILSQLSEYPKELIDILNFQDE | ||
| + | DGETALTLAARCRSKKLVKILLDHGANPKTANRDGKSAEDYILEDDKFRALSPTPCSSGPIRQLDQNSPG | ||
| + | GTSNRSDFVDLVDPVPIDSNLIPQRSPNASPPHYSETGQRVTKQLLPEVTSMIELLATTFDTELQDKERD | ||
| + | LDHAVGLLSNIEKEYLEGQRKILNYERMLSDFGEKKLALGDLEKELNDKLGKRYRFGWEKYVRDEEERAR | ||
| + | RITEQRSKYLQELSIEDRKLLDSSNLRFADPSKQEVLMKLQADERENSDLLNLIRTNSTDVESECDLLRE | ||
| + | SVQKLSEERERLFKEFINLSSENTGGENEEDDGANHTSANTSRLNNYRKLISLGCGGIGLDEVDEVIESL | ||
| + | NEGIDVNELNDNGFLTEQDEELGNHQNYHNIHTQGR | ||
| + | |||
| + | >MBP1_SACCE NP_010227 Mbp1p [Saccharomyces cerevisiae S288c] | ||
| + | MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF | ||
| + | GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET | ||
| + | KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL | ||
| + | PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ | ||
| + | QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV | ||
| + | NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS | ||
| + | IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL | ||
| + | SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM | ||
| + | MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ | ||
| + | MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK | ||
| + | KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS | ||
| + | LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA | ||
| + | |||
| + | >MBP1_SCHPO NP_593032 Res2 [Schizosaccharomyces pombe 972h-] | ||
| + | MAPRSSAVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQ | ||
| + | GGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSLDIDEGKAIAPKKKQTKQKKPSVRGRRGRKPSSLSS | ||
| + | STLHSVNEKQPNSSISPTIESSMNKVNLPGAEEQVSATPLPASPNALLSPNDNTIKPVEELGMLEAPLDK | ||
| + | YEESLLDFFLHPEEGRIPSFLYSPPPDFQVNSVIDDDGHTSLHWACSMGHIEMIKLLLRANADIGVCNRL | ||
| + | SQTPLMRSVIFTNNYDCQTFGQVLELLQSTIYAVDTNGQSIFHHIVQSTSTPSKVAAAKYYLDCILEKLI | ||
| + | SIQPFENVVRLVNLQDSNGDTSLLIAARNGAMDCVNSLLSYNANPSIPNRQRRTASEYLLEADKKPHSLL | ||
| + | QSNSNASHSAFSFSGISPAIISPSCSSHAFVKAIPSISSKFSQLAEEYESQLREKEEDLIRANRLKQDTL | ||
| + | NEISRTYQELTFLQKNNPTYSQSMENLIREAQETYQQLSKRLLIWLEARQIFDLERSLKPHTSLSISFPS | ||
| + | DFLKKEDGLSLNNDFKKPACNNVTNSDEYEQLINKLTSLQASRKKDTLYIRKLYEELGIDDTVNSYRRLI | ||
| + | AMSCGINPEDLSLEILDAVEEALTREK | ||
| + | |||
| + | >MBP1_USTMA XP_762343 UM06196 [Ustilago maydis 521] | ||
| + | MSGDKTIFKATYSGVPVYECIINNVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQG | ||
| + | GYGKYQGTWIPLDVAIELAERYNIQGLLQPITSYVPSAADSPPPAPKHTISTSNRSKKIIPADPGALGRS | ||
| + | RRATSIETESEVIGAAPNNVSEGSMSPSPSDISSSSRTPSPLPADRAHPLHANHALAGYNGRDANNHARY | ||
| + | ADIILDYFVTENTTVPSLLINPPPDFNPDMSIDDDEHTALHWACAMGRIRVVKLLLSAGADIFRVNSNQQ | ||
| + | TALMRATIFPNSLSSFTDPSLNIDRNDRTVFHHVVDLALSRGKPHAARYYMETMINRLADYGDQLADILN | ||
| + | FQDDEGETPLTMAARARSKRLVRLLLEHGADPKIRNKEGKNAEDYIIEDERFRSSPSRTGPAGIELGADG | ||
| + | LPVLPTSSLHTSEAGQRTAGRAVTLMSNLLHSLADSYDSEINTAEKKLTQAHGLLKQIQTEIEDSAKVAE | ||
| + | ALHHEAQGVDEERKRVDSLQLALKHAINKRARDDLERRWSEGKQAIKRARLQAGLEPGALSTSNATNAPA | ||
| + | TGDQKSKDDAKSLIEALPAGTNVKTAIAELRKQLSQVQANKTELVDKFVARAREQGTGRTMAAYRRLIAA | ||
| + | GCGGIAPDEVDAVVGVLCELLQESHTGARAGAGGERDDRARDVAMMLKAFPVYSRCIVMNRQLAVTRYPC | ||
| + | CRLLFYSLPCRTNMISGLWMQSDSVAAVLARSNAVLRISPCPKCARMSKLQAHLYEASAARLCGGKMLRR | ||
| + | TLALFSEAARSSSSSSASAAASSSASILTSHLSKAHLPPSLARSAKPHKNLYQMLSTLPKDGVGARVRQR | ||
| + | RWAAKGLDVSHDVDLKAHLAKLHHTGATKTNKDEGHLCYWEITKVRLKDGGNHGKAWGRFVWRERNAGVV | ||
| + | KQGQAQAKLTKVCLSMVVAHPGKPITKAESGERIPGALKYCWDLAH | ||
| + | |||
| + | >MBP1_WALME XP_006957051 [Wallemia mellicola CBS 633.66] | ||
| + | MSAPPIYKACYSGVPVYEFNCKNVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGG | ||
| + | YGKYQGTWIPMERSVELARQYRIELLLDPIINYLPGPQSPPLAPKHATNVGSRARKSTAPAAQTLPSTSK | ||
| + | VFHPLSSTKHPAKLAAATNAKAEISDGEDASIPSSPSFKSNSSRTPSPIRINARKRKLEDEATIPSSAID | ||
| + | GSISYEDIILDYFISESTQIPALLIHPPSDFNPNMSIDDEGHTAMHWACAMGKVRVVKLLLSAGADIFRV | ||
| + | NHSEQTALMRSVMFSNNYDIRKFPQLYELLHRSTLNLDKHDRTVLHHIVDLALTKSKTHAARYYMECVLS | ||
| + | KLANYPDELADVINFQDDEGESALTLAARARSKRLVKLLLEHGADSKLPNKDGKTAEDYILEDERFRQSP | ||
| + | LLNSNHLRLHPPDTSIYAPPAHLFNSETSQNIANTSMSSVANLLESLAQSYDKEITQKERDYQQAQVILR | ||
| + | NIKTDIVEAKSNIEKMTIDSSEFEHLKHKLRELEMKLEEHSNDVYNKGWEEYSRNVDDPAIDAPSDNVQE | ||
| + | ECASLRNKIKDLQEKRISSMQELIKRQKEVGTGKKMSEYRKLISVGCGIPTTEIDAVLEMLLESLESENA | ||
| + | NKKAALASGISGALSSTSSAPSQATTSAPTGVATPGAPVPASSEKAGLLPPAPVMQ | ||
| + | |||
| + | </source> | ||
===Ortholog APSES domains=== | ===Ortholog APSES domains=== | ||
| − | The ortholog APSES domains can be aligned without gaps. They comprise the following sequences: | + | The ortholog APSES domains can be aligned (nearly) without gaps. They comprise the following sequences: |
| − | + | <source lang="text"> | |
| − | + | CLUSTAL format alignment by MAFFT L-INS-i (v6.850b) | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| + | MBP1_ASPNI NVYSATYSSVPVYEFKIG---TDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLQEGRQLAERNNILDKLLPIFDY | ||
| + | MBP1_BIPOR KIYSATYSNVPVYECNVN---GHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLEEGRGLAERNGVLDKMRAIFDY | ||
| + | MBP1_NEUCR GIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREVQKDTHEKIQGGYGRYQGTWIPLEQAEALARRNNIYERLKPIFEF | ||
| + | MBP1_COPCI QIFKATYSGIPVYEMMCK---GVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGGYGKYQGTWIPLERGMQLAKQYNCEHLLRPIIEF | ||
| + | MBP1_WALME PIYKACYSGVPVYEFNCK---NVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGGYGKYQGTWIPMERSVELARQYRIELLLDPIINY | ||
| + | MBP1_PUCGR TIYKATYSGVPVLEMPCE---GIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREIQKGTHEKIQGGYGKYQGTWVPLDRGIDLAKQYGVDHLLSALFNF | ||
| + | MBP1_USTMA TIFKATYSGVPVYECIIN---NVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQGGYGKYQGTWIPLDVAIELAERYNIQGLLQPITSY | ||
| + | MBP1_SCHPO AVHVAVYSGVEVYECFIK---GVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL | ||
| + | MBP1_SACCE QIYSARYSGVDVYEFIHS---TGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF | ||
| + | MBP1_CRYNE KVYASVYSGVPVFEAMIR---GISVMRRASDSWVNATQILKVAGVHKSARTKILEKEVLNGIHEKIQGGYGKYQGTWVPLDRGRDLAEQYGVGSYLSSVFDF | ||
| + | :. : **.: * * :*:* *.*:***:***... *. **::**::: ***:***:*:*****:*:: . ** : : .: . | ||
| + | </source> | ||
| + | |||
| + | When considering the relatively high degree of conservation – e.g. there are 34 '''fully conserved''' positions (<code>*</code>) in this alignment of 103 positions – keep in mind that this collection of species represents [http://www.timetree.org/index.php?taxon_a=saccharomyces+cerevisiae&taxon_b=cryptococcus+neoformans&submit=Search on the order of '''a billion years'''] of divergent evolution from a common ancestor. | ||
| | ||
| + | ===Distant Homologs=== | ||
| − | + | APSES domains are a subfamily of [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04383 Kil-A N domains]; the latter include examples: | |
| + | * in Protists (e.g. [http://www.ncbi.nlm.nih.gov/protein/XP_001289194 ''Trichomonas vaginalis'' <code>XP_001289194</code>]) | ||
| + | * in DNA viruses (e.g. [http://www.ncbi.nlm.nih.gov/protein/NP_955235 ''Canarypox virus'' <code>NP_955235</code>]) | ||
| + | * in Gammaproteobacteria (e.g. [http://www.ncbi.nlm.nih.gov/protein/WP_032936777 ''Escherichia coli'' <code>WP_032936777</code> (KilA)]) | ||
| + | |||
| + | {{Vspace}} | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
</div> | </div> | ||
Latest revision as of 01:31, 9 October 2016
Yeast Mbp1 protein reference annotation
Contents
A reference annotation of the Saccharomyces cerevisiae Mbp1 protein sequence that integrates annotation sources we encounter throughout the course.
Links
- NP_010227.1 at Genbank
- P39678 at UniProtKB
- 1MB1 at PDB
- 1BM8 at PDB
- 1L3G at PDB
- 1SW6 at PDB
- cd00204 (Ankyrin domain) at CDD
- cl04494 (KilA-N superfamily domain) at CDD
- see also: Reference APSES domains (reference species)
- see also: Reference APSES proteins (reference species)
FASTA sequences
>gi|6320147|ref|NP_010227.1| Mbp1p [Saccharomyces cerevisiae S288c] MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA
>1BM8_A QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIA KQLAEKFSVYDQLKPLFDF
>1MB1_A MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDHHHHHH
Note: the sequence segments colored grey are disorderd in the protein structure. This generally means they do not contribute significant energy to the fold of the domain. The six histidines at the C-terminus colored in firebrick were added for purification and are not part of the Mbp1 sequence.
>1L3G_A SNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLN IAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDKLAAALEHHHHHH
Note: here too the C-terminus is disordered and colored grey and the protein has a purification tag colored in firebrick. However, this being an NMR file, disordered segments are included in the PDB coordinate file and defining the extent of disorder required evaluating the superposed set of models. There are no more structured residues than in the 1MB1 structure, even though the sequence used in the experiment was longer.
>1SW6_A NDDINKGPSGDNENNGTDDNDRTAGPIITFTHDLTSDFLSSPLKIMKALPSPVVNDNEQKMKLEAFLQRLLFPEIQEMPT SLNNDSSNRNSEGGSSNQQQQHVSFDSLLQEVNDAFPNTQLNLNIPVDEHGNTPLHWLTSIANLELVKHLVKHGSNRLYG DNMGESCLVKAVKSVNNYDSGTFEALLDYLYPCLILEDSMNRTILHHIIITSGMTGCSAAAKYYLDILMGWIVKKQNRPI QSGTNEKESKPNDKNGERKDSILENLDLKWIIANMLNAQDSNGDTCLNIAARLGNISIVDALLDYGADPFIANKSGLRPV DFGAGLE
Note: this sequence is a part of the Saccharomyces cerevisiae Swi6 protein, which is homologous to Mbp1 but does not contain an APSES domain. Its ankyrin domains have been structurally defined in the 1SW6 PDB file, they do not conform in all details to the canonical Ankyrin domain structure. The sequence segments colored grey are disordered in the protein structure.
Annotations
NCBI CDD APSES and KilA-Ndomain boundaries
The APSES domain is a well-defined type of DNA-binding domain that is ubiquitous in fungi and unique in that kingdom. Structurally it is a member of the Winged Helix-Turn-Helix family. Recently it was found that it is homologous to the somewhat shorter, prokaryotic KilA-N domain; thus the APSES domain was retired from pFam and instances were merged into the KilA-N family. However InterPro has a KilA-N entry but still recognizes the APSES domain.
KilA-N domain boundaries in Mbp1 can be derived from the results of a CDD search with the ID 1BM8_A (the Mbp1 DNA binding domain crystal structure). The KilA-N superfamily domain alignment is returned.
- (pfam 04383): KilA-N domain; The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease.
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BM8A 16 IHSTGSIMKRKKDDWVNATHILKAANFAKaKRTRILEKEVLKETHEKVQ---------------GGFGKYQGTWVPLNIA 80
Cdd:pfam04383 3 YNDFEIIIRRDKDGYINATKLCKAAGETK-RFRNWLRLESTKELIEELSeennvdkseiiigrkGKNGRLQGTYVHPDLA 81
90
....*....|....
1BM8A 81 KQLA----EKFSVY 90
Cdd:pfam04383 82 LAIAswisPEFALK 95
Note that CDD and SMART are not consistent in how they apply pFam 04383 to the Mbp1 sequence. See annotation below.
The CDD KilA-N domain definition begins at position 16 of the 1BM8 sequence. But virtually all fungal APSES domains have a longer, structurally defined, conserved N-terminus. Blindly applying the KilA-N domain definition to these proteins would lose important information. For most purposes we will prefer the sequence spanned by the 1BM8_A structure. The sequence is given below, the KilA-N domain is coloured dark green. By this definition the APSES domain is 99 amino acids long and comprises residues 4 to 102 of the NP_010227 sequence.
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BM8A 1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIA 80
90
....*....|....*....
1BM8A 81 KQLAEKFSVYDQLKPLFDF 99
- Yeast APSES domain sequence in FASTA format
>APSES_MBP1 Residues 4-102 of S. cerevisiae Mbp1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
- Synopsis of ranges
| Domain | Link | Length | Boundary | Range (Mbp1) | Range (1BM8) |
| KilA-N: pfam04383 (CDD) | CDD alignment | 72 | STGSI ... KFSVY | 21 - 93 | 18 - 90 |
| KilA-N: pfam04383 (SMART) | Smart main page | 79 | IHSTG ... YDQLK | 19 - 97 | 16 - 94 |
| KilA-N: SM01252 (SMART) | Smart main page | 84 | TGSIM ... DFTQT | 22 - 105 | 19 - 99... |
| APSES: Interpro IPR003163 | (Interpro) | 130 | QIYSA ... IRSAS | 3 - 133 | 1 - 99... |
| APSES (1BM8) | – | 99 | QIYSA ... PLFDF | 4 - 102 | 1 - 99 |
NCBI CDD Ankyrin domain boundaries
- Derived from the results of a CDD search with the RefSeq ID (NP_010227). There are two, partially overlapping alignments with the profile, which contains 4 ANK repeats each. The aligned sequence is the consensus sequence for the profile (see the CDD output documentation for details).
- Alignment 1 - E-value = 1.69e-08
10 20 30 40 50 60 70 80 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....| MBP1_SACCE 76 IDPELHTAFHWACSMGNLPIAEALYEAGTSIRSTNSQGQTPLMRSSLFHNsytrrtfPRIFQLLHETVFDIDSQS---QT 152 Cdd:cd00204 3 RDEDGRTPLHLAASNGHLEVVKLLLENGADVNAKDNDGRTPLHLAAKNGH-------LEIVKLLLEKGADVNARDkdgNT 75 90 100 110 120 130 ....*....|....*....|....*....|....*....|....*....|....*.... MBP1_SACCE 153 VIHHIVKRKSTtpSAVYYLdvvLSKIKDfspqyriellLNTQDKNGDTALHIASKNGDV 211 Cdd:cd00204 76 PLHLAARNGNL--DVVKLL---LKHGAD----------VNARDKDGRTPLHLAAKNGHL 119
- Alignment 2 - E-value=8.66e-05
10 20 30 40 50 60 70 80 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*... MBP1_SACCE 192 NTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLT----ANEIMNQQYEQMMIQNGTNQHV--NSSNTDLNIHVNTNNIET 273 Cdd:cd00204 1 NARDEDGRTPLHLAASNGHLEVVKLLLENGADVNAKDNDGRTplhlAAKNGHLEIVKLLLEKGADVNArdKDGNTPLHLAARNGNLDV 88
SMART Annotations
A SMART search with the yeast Mbp1 protein sequence retrieved the APSES domain and three regions of similarity to ankyrin domains, annotated a number of low-complexity regions and a stretch of coiled coil. Annotations have been consolidated below.
SAS Annotations
A SAS FASTA search with yeast Mbp1 protein sequence retrieved the homologous Ankyrin sequence from Swi6 (PDB: 1SW6), together with secondary structure annotations. This structural annotation is based on homology to a protein of known structure. Annotations were consolidated into below.
While CDD, SMART and SAS all annotate the same general regions, they disagree in details of the domain boundaries and on the precise alignment.
Consolidated Annotation
MBP1_SACCE
Annotations based on
- CDD domain analysis,
- SAS structure annotation and
- literature data on binding region
Keys:
= domain annotation
C Coiled coil regions predicted by Coils2 program
x Low complexity region
* Proposed binding region
+ positively charged residues, oriented for possible DNA binding interactions
- negatively charged residues, oriented for possible DNA binding interactions
E beta strand
H alpha helix
t beta turn
Sequence that was invisible in the 1SW6 structure is listed in lowercase.
10 20 30 40 50 60
MSNQIYSARY SGVDVYEFIH STGSIMKRKK DDWVNATHIL KAANFAKAKR TRILEKEVLK
1MB1 ----EEEEEt t-EEEEEEEE t-EEEEEEtt ---EEHHHHH HH----HHHH HHHHhhhHHH
* *+**-+**** Proposed DNA binding
pfam04383 == ========== ========== ========== ========== (CDD alignment)
pfam04383 ====== ========== ========== ========== ========== (SMART alignment)
70 80 90 100 110 120
ETHEKVQGGF GKYQGTWVPL NIAKQLAEKF SVYDQLKPLF DFTQTDGSAS PPPAPKHHHA
1MB1 ---EEE---- tt--EEEE-H HHHHHHHHH- --HHHHtt-
**+*+***** **** Proposed DNA binding
pfam04383 ========== ========== ========== === (CDD alignment)
pfam04383 ========== ========== ========== ========== ========== = (SMART alignment)
130 140 150 160 170 180
SKVDRKKAIR SASTSAIMET KRNNKKAEEN QFQSSKILGN PTAAPRKRGR PVGSTRGSRR
190 200 210 220 230 240
KLGVNLQRSQ SDMGFPRPAI PNSSISTTQL PSIRSTMGPQ SPTLGILEEE RHDSRQQQPQ
Low compl. xxxxx (SMART SEG)
250 260 270 280 290 300
QNNSAQFKEI DLEDGLSSDV EPSQQLQQVF NQNTGFVPQQ QSSLIQTQQT ESMATSVSSS
Low compl.x xx xxxxxxxxxx xxxxxxxxxx (SMART SEG)
310 320 330 340 350 360
PSLPTSPGDF ADSNPFEERF PGGGTSPIIS MIPRYPVTSR PQTSDINDKV NKYLSKLVDY
xxxxxxx (SMART SEG)
Swi6 GPII TFTHDLTSDF LSSPLKIMKA LPSPVVNDNE QKM--KL-EA (SAS alignment: 1SW6)
1SW6 -EEE --tt---ttt ------EE-- ---t---HHH HHH--HH-HH (SAS 2° structure)
370 380 390 400 410 420
FISNEMK-------------------------------SNK SLPQVLLHPP PHSAPYIDAP IDPELHTAFH WACSMGNLPI AEALYEAGTS
Swi6 FLQRLLFpeiqemptslnndssnrnseggssnqqqqhvSFD SLLQEVNDAF PNTQLNLNIP VDEHGNTPLH WLTSIANLEL VKHLVKHGSN (SAS alignment: 1SW6)
1SW6 HHHHHH- -HH HHHHHHHHH- t-----t--- --t----HHH HHHH--tHHH HHHHHH---- (SAS 2° structure)
430 440 450 460 470 480
IRSTNSQGQT PLMRSSLFHN SYTRRTFPRI FQLLHETVFD IDSQSQTVIH HIVKRKSTT---P
Swi6 RLYGDNMGES CLVKAVKSVN NYDSGTFEAL LDYLYPCLIL EDSMNRTILH HIIITSGMTGCSA (SAS alignment: 1SW6)
1SW6 t---tt---- HHHHHHH--H HHH---HHHH HHHHHHHHHE E-t----HHH HHHHHH--t--HH (SAS 2° structure)
490 500 510 520 530 540
SAVYYLDVVL-------------------------------SKIKDFSPQY RIELLLNTQD KNGDTALHIA SKNGDVVFFN TLVKMGALTT
Swi6 AAKYYLDILMGWIVKKQNRPIQSGtnekeskpndkngerkDSILENLDLKW IIANMLNAQD SNGDTCLNIA ARLGNISIVD ALLDYGADPF (SAS alignment: 1SW6)
1SW6 HHHHHHHHHHHHHHHHHH--EEE- -HHHHHt-HHH HHHH------ t----HHHHH HHH--HHHHH HHHH----t- (SAS 2° structure)
550 560 570 580 590 600
ISNKEGLTAN EIMNQQYEQM MIQNGTNQHV NSSNTDLNIH VNTNNIETKN DVNSMVIMSP
Swi6 IANKSGLRPV DFGAG (SAS alignment: 1SW6)
1SW6 ---t----HH HH--- (SAS 2° structure)
610 620 630 640 650 660
VSPSDYITYP SQIATNISRN IPNVVNSMKQ MASIYNDLHE QHDNEIKSLQ KTLKSISKTK
Coiled c. CCCCCCCC CCCCCCCCCC CCCCC (SMART COILS2)
670 680 690 700 710 720
IQVSLKTLEV LKESSKDENG EAQTNDDFEI LSRLQEQNTK KLRKRLIRYK RLIKQKLEYR
Low compl. x xxxxxxxxxx xxxxxxx (SMART SEG)
730 740 750 760 770 780
QTVLLNKLIE DETQATTNNT VEKDNNTLER LELAQELTML QLQRKNKLSS LVKKFEDNAK
790 800 810 820 830
IHKYRRIIRE GTEMNIEEVD SSLDVILQTL IANNNKNKGA EQIITISNAN SHA
Orthologs
The Mbp1 orthologs in the ten fungal reference species.
- Aspergillus nidulans (ASPNI)
- Bipolaris oryzae (BIPOR)
- Coprinopsis cinerea (COPCI)
- Cryptococcus neoformans (CRYNE)
- Neurospora crassa (NEUCR)
- Puccinia Graminis (PUCGR)
- Saccharomyces cerevisiae (SACCE)
- Schizosaccharomyces pombe (SCHPO)
- Ustilago maydis (USTMA)
- Wallemia mellicola (WALME)
Orthologs were determined by RBM to NP_010227, residues 4 to 102. Uniprot accession numbers were obtained from the Uniprot mapping service.
| Species | Code | Name | RefSeq | UniProt |
| Aspergillus nidulans | ASPNI | AN3154 | XP_660758 (FASTA) | Q5B8H6 |
| Bipolaris orizae | BIPOR | COCMIDRAFT_338 | XP_007682304 (FASTA) | W6ZM86 |
| Coprinopsis cinerea | COPCI | CC1G_01306 | XP_001837394 (FASTA) | A8NYC6 |
| Cryptococcus neoformans | CRYNE | CND05520 | XP_570545 (FASTA) | Q5KHS0 |
| Neurospora crassa | NEUCR | NCU07246 | XP_955821 (FASTA) | Q7RW59 |
| Puccinia graminis | PUCGR | PGTG_08863 | XP_003327086 (FASTA) | E3KED4 |
| Saccharomyces cerevisiae | SACCE | Mbp1 | NP_010227 (FASTA) | P39678 |
| Schizosaccharomyces pombe | SCHPO | Res2 | NP_593032 (FASTA) | P41412 |
| Ustilago maydis | USTMA | UM06196 | XP_762343 (FASTA) | Q4P117 |
| Wallemia mellicola | WALME | WALSEDRAFT_59726 | XP_006957051 (FASTA) | I4YGC0 |
- FASTA formatted sequences
(Header lines were edited to begin with a code identifying the sequence as orthologous to Mbp1, and including the species shorthand code.)
>MBP1_ASPNI XP_660758 AN3154.2 [Aspergillus nidulans FGSC A4]
MAAVDFSNVYSATYSSVPVYEFKIGTDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKV
QGGYGKYQGTWIPLQEGRQLAERNNILDKLLPIFDYVAGDRSPPPAPKHTSAASKPRAPKINKRVVKEDV
FSAVNHHRSMGPPSFHHEHYDVNTGLDEDESIEQATLESSSMIADEDMISMSQNGPYSSRKRKRGINEVA
AMSLSEQEHILYGDQLLDYFMTVGDAPEATRIPPPQPPANFQVDRPIDDSGNTALHWACAMGDLEIVKDL
LRRGADMKALSIHEETPLVRAVLFTNNYEKRTFPALLDLLLDTISFRDWFGATLFHHIAQTTKSKGKWKS
SRYYCEVALEKLRTTFSPEEVDLLLSCQDSVGDTAVLVAARNGVFRLVDLLLSRCPRAGDLVNKRGETAS
SIMQRAHLAERDIPPPPSSITMGNDHIDGEVGAPTSLEPQSVTLHHESSPATAQLLSQIGAIMAEASRKL
TSSYGAAKPSQKDSDDVANPEALYEQLEQDRQKIRRQYDALAAKEAAEESSDAQLGRYEQMRDNYESLLE
QIQRARLKERLASTPVPTQTAVIGSSSPEQDRLLTTFQLSRALCSEQKIRRAAVKELAQQRADAGVSTKF
DVHRKLVALATGLKEEELDPMAAELAETLEFDRMNGKGVGPESPEADHKDSASLPFPGPVVSVDA
>MBP1_BIPOR XP_007682304 COCMIDRAFT_338 [Bipolaris oryzae ATCC 44560]
MPPAPDGKIYSATYSNVPVYECNVNGHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKV
QGGYGKYQGTWIPLEEGRGLAERNGVLDKMRAIFDYVPGDRSPPPAPKHATAASNRMKPPRQTAAAVAAA
AVAAAAAAAAVANHNALMSNSRSQASEDPYENSQRSQIYREDTPDNETVISESMLGDADLMDMSQYSADG
NRKRKRGMDQMSLLDQQHQIWADQLLDYFMLLDHEAAVSWPEPPPSINLDRPIDEKGHAAMHWAAAMGDV
GVVKELIHRGARLDCLSNNLETPLMRAVMFTNNFDKETMPSMVKIFQQTVHRTDWFGSTVFHHIAATTSS
SNKYVCARWYLDCIINKLSETWIPEEVTRLLNAADQNGDTAIMIAARNGARKCVRSLLGRNVAVDIPNKK
GETADDLIRELNQRRRMHGRTRQASSSPFAPAPEHRLNGHVPHFDGGPLMSVPVPSMAVRESVQYRSQTA
SHLMTKVAPTLLEKCEELATAYEAELQEKEAEFFDAERVVKRRQAELEAVRKQVAELQSMSKGLHIDLND
EEAERQQEDELRLLVEEAESLLEIEQKAELRRLCSSMPQQNSDSSPVDITEKMRLALLLHRAQLERRELV
REVVGNLSVAGMSEKQGTYKKLIAKALGEREEDVESMLPEILQELEEAETQERAEGLDGSPV
>MBP1_COPCI XP_001837394 CC1G_01306 [Coprinopsis cinerea okayama7#130]
MPEAQIFKATYSGIPVYEMMCKGVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGG
YGKYQGTWIPLERGMQLAKQYNCEHLLRPIIEFTPAAKSPPLAPKHLVATAGNRPVRKPLTTDLSAAVIN
TRSTRKQVADGVGEESDHDTHSLRGSEDGSMTPSPSEASSSSRTPSPIHSPGTYHSNGLDGPSSGGRNRY
RQSNDRYDEDDDASRHNGMGDPRSYGDQILEYFISDTNQIPPILITPPPDFDPNMAIDDDGHTSLHWACA
MGRIRIVKLLLSAGADIFKVNKAGQTALMRSVMFANNYDVRKFPELYELLHRSTLNIDNSNRTVFHHVVD
VAMSKGKTHAARYYMETILTRLADYPKELADVINFQDEDGETALTMAARCRSKRLVKLLIDHGADPKINN
HDGKNAEDYILEDERFRSSPAPSSRVAAMSYRNAQVAYPPPGAPSTYSFAPANHDRPPLHYSAAAQKAST
RCVNDMASMLDSLAASFDQELRDKERDMAQAQALLTNIQAEILESQRTVLQLRQQAEGLSQAKQRLADLE
NALQDKMGRRYRLGFEKWIKDEETREKVIRDAANGDLVLTPATTSYTVDEDGDSDSGSNGDKNKGKRKAQ
VQQEEVSDLVELYSNIPTDPEELRKQCEALREEVSQSRKRRKAMFDELVTFQAEAGTSGRMSDYRRLIAA
GCGGLEPLEIDSVLGMLLETLEAEDPSSTSATWSGSKGQQTG
>MBP1_CRYNE XP_570545 CND05520 [Cryptococcus neoformans var. neoformans JEC21]
MEPPSNPIQPPVTPSHHSLLSAISPALSEQTPAPIHTLPPHLRPSIPQPHIAPPRPSSVQPTMEEQQRMH
HIQQHQQQQHFQQQQNDENVFGSVMGAPGHVPGHEAPMSTQPKVYASVYSGVPVFEAMIRGISVMRRASD
SWVNATQILKVAGVHKSARTKILEKEVLNGIHEKIQGGYGKYQGTWVPLDRGRDLAEQYGVGSYLSSVFD
FVPSASVIAALPVIRTGTPDRSGQQTPSGLPGHPNQRVISPFANHGQTTPHMPPPQFIHQGNEQMMNLPP
HPSSLAYPTQPKPYFSMPLQHTVGPQYDERHEGMTMTPTMSMDGLAPPADIARMGFPYNPSDIYIDQYGQ
PHATYQASPYGKESGHPSKRQRSDAEGSYIESGAAVQQHVEQDEEADDGLDNDSTASDDARDPPPLPSSM
LLPHKPIRPKATPANGRIKSRLVQIFNVEGQVNLRSVFGLAPDQLPNFDIDMVIDDQGHSALHWACALAR
LSIVQQLIELGADIHRGNYAGETPLIRAVLTSNHAEAGSFTDLLHLLSPSIRTLDHAYRTVLHHIALVAG
VKGRVPAARTYMASVLEWVAREQQANNTHSITNPPNPADRNELAPINLRTLVDVQDVHGDTALNVAARVG
NKGLVGLLLDAGADKTRANKLGLRPENFGLEIEALKISNGEAVMANLKSEVSKPERKSRDVQKNIATIFE
SISSTFSSEMLAKQTKLNATEASVRHATRALADKRQHLHRAQEKLATMQLFEQRSENVRRIMDAIAAGTL
LTPAEFTGRTQTMHEKSTGQLPPLAFRHVPGLALDASSQSQLNGAPPSTPLSVEDQEDIALPERDDPECL
VKLRRMALWEDRIAEVLEDKIRAMEGEGVDRAVKYRKLVSVCAKVPVDKVDSMLDGLVAAVESEGQGLDF
SRASNFVNRIKATKS
>MBP1_NEUCR XP_955821 NCU07246 [Neurospora crassa OR74A]
MVKENVGGNPEPGIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREV
QKDTHEKIQGGYGRYQGTWIPLEQAEALARRNNIYERLKPIFEFQPGNESPPPAPRHASKPKAPKVKPAV
PTWGSKSAKNANPPQPGTFLPPGRKGLPAQAPDYNDADTHMHDDDTPDNLTVASASYMAEDDRYDHSHFS
TGHRKRKRDELIEDMTEQQHAVYGDELLDYFLLSRNEQPAVRPDPPPNFKPDWPIDNERHTCLHWASAMG
DVDVMRQLKKFGASLDAQNVRGETPFMRAVNFTNCFEKQTFPQVMKELFSTIDCRDLSGCTVIHHAAVMK
IGRVNSQSCSRYYLDIILNRLQETHHPEFVQQLLDAQDNDGNTAVHLAAMRDARKCIRALLGRGASTDIP
NKQGIRAEELIKELNASISKSRSNLPQRSSSPFAPDTQRHDAFHEAISESMVTSRKNSQPNYSSDAANTV
QNRITPLVLQKLKDLTATYDSEFKEKDDAEKEARRILNKTQSELKALTASIDDYNSRLDTDDVAAKTAAE
MATARHKVLAFVTHQNRISVQEAVKQELAALDRANAVTNGTSTKSKSSSPSKKPKLSPIPDQKDKPPKDE
NETESEAEHPDPPAAQAHQQQPGPSSQDTEVEDQDREEEEDDYTHRLSLAAELRSILQEQRSAENDYVEA
RGMLGTGERIDKYKHLLMSCLPPDEQENLEENLEEMIKLMEQEDESVTDLPAGAVGGGGGGNAADGSGGG
GQPSNGRRESVLPALRGGNGDGEMSRRGSRTAAAAAAQVDGEREINGRAGAERTERIQEIAAV
>MBP1_PUCGR XP_003327086 PGTG_08863 [Puccinia graminis f. sp. tritici CRL 75-36-700-3]
MAYGGSIQPLRPPSRESATLHLHQPDLTVTSPPLSLTHCPPCVYSHFTHTPTSLIVIQVSLHSLLDQETY
HLLPSRSPPTVSVRMGTTTIYKATYSGVPVLEMPCEGIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLE
REIQKGTHEKIQGGYGKYQGTWVPLDRGIDLAKQYGVDHLLSALFNFQPSSNESPPLAPKHVTALSTRVK
VSKVSAASAARAARAVVPSLPSTSGLGGRNTNNSWSNFDSDNEPGLPPAASSRESNGNWATQSKLARSSN
LARARANINNSHPEDLPVPAPDQLQASPLPSMQTADPENDNSLTPSELSLPSRTPSPIEDLPLTVNTASS
QSTRNKGKSRDLPDDEDLSRGQKRKYDTSLVEDTSYSDGADDQYINGNPSNAASAKYAKLILDYFVSESS
QIPNFLNDPPSDFDPNVVIDDDGHTALHWACAMGRIKIIKLLLTCGADIFRANNAGQTALMRAVMFTNNH
DLRTFPELFESFSGSVINIDRTDRTVFHYVIDIALTKGKVPAARYYLETILSQLSEYPKELIDILNFQDE
DGETALTLAARCRSKKLVKILLDHGANPKTANRDGKSAEDYILEDDKFRALSPTPCSSGPIRQLDQNSPG
GTSNRSDFVDLVDPVPIDSNLIPQRSPNASPPHYSETGQRVTKQLLPEVTSMIELLATTFDTELQDKERD
LDHAVGLLSNIEKEYLEGQRKILNYERMLSDFGEKKLALGDLEKELNDKLGKRYRFGWEKYVRDEEERAR
RITEQRSKYLQELSIEDRKLLDSSNLRFADPSKQEVLMKLQADERENSDLLNLIRTNSTDVESECDLLRE
SVQKLSEERERLFKEFINLSSENTGGENEEDDGANHTSANTSRLNNYRKLISLGCGGIGLDEVDEVIESL
NEGIDVNELNDNGFLTEQDEELGNHQNYHNIHTQGR
>MBP1_SACCE NP_010227 Mbp1p [Saccharomyces cerevisiae S288c]
MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF
GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET
KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL
PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ
QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV
NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS
IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL
SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM
MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ
MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK
KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS
LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA
>MBP1_SCHPO NP_593032 Res2 [Schizosaccharomyces pombe 972h-]
MAPRSSAVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQ
GGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSLDIDEGKAIAPKKKQTKQKKPSVRGRRGRKPSSLSS
STLHSVNEKQPNSSISPTIESSMNKVNLPGAEEQVSATPLPASPNALLSPNDNTIKPVEELGMLEAPLDK
YEESLLDFFLHPEEGRIPSFLYSPPPDFQVNSVIDDDGHTSLHWACSMGHIEMIKLLLRANADIGVCNRL
SQTPLMRSVIFTNNYDCQTFGQVLELLQSTIYAVDTNGQSIFHHIVQSTSTPSKVAAAKYYLDCILEKLI
SIQPFENVVRLVNLQDSNGDTSLLIAARNGAMDCVNSLLSYNANPSIPNRQRRTASEYLLEADKKPHSLL
QSNSNASHSAFSFSGISPAIISPSCSSHAFVKAIPSISSKFSQLAEEYESQLREKEEDLIRANRLKQDTL
NEISRTYQELTFLQKNNPTYSQSMENLIREAQETYQQLSKRLLIWLEARQIFDLERSLKPHTSLSISFPS
DFLKKEDGLSLNNDFKKPACNNVTNSDEYEQLINKLTSLQASRKKDTLYIRKLYEELGIDDTVNSYRRLI
AMSCGINPEDLSLEILDAVEEALTREK
>MBP1_USTMA XP_762343 UM06196 [Ustilago maydis 521]
MSGDKTIFKATYSGVPVYECIINNVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQG
GYGKYQGTWIPLDVAIELAERYNIQGLLQPITSYVPSAADSPPPAPKHTISTSNRSKKIIPADPGALGRS
RRATSIETESEVIGAAPNNVSEGSMSPSPSDISSSSRTPSPLPADRAHPLHANHALAGYNGRDANNHARY
ADIILDYFVTENTTVPSLLINPPPDFNPDMSIDDDEHTALHWACAMGRIRVVKLLLSAGADIFRVNSNQQ
TALMRATIFPNSLSSFTDPSLNIDRNDRTVFHHVVDLALSRGKPHAARYYMETMINRLADYGDQLADILN
FQDDEGETPLTMAARARSKRLVRLLLEHGADPKIRNKEGKNAEDYIIEDERFRSSPSRTGPAGIELGADG
LPVLPTSSLHTSEAGQRTAGRAVTLMSNLLHSLADSYDSEINTAEKKLTQAHGLLKQIQTEIEDSAKVAE
ALHHEAQGVDEERKRVDSLQLALKHAINKRARDDLERRWSEGKQAIKRARLQAGLEPGALSTSNATNAPA
TGDQKSKDDAKSLIEALPAGTNVKTAIAELRKQLSQVQANKTELVDKFVARAREQGTGRTMAAYRRLIAA
GCGGIAPDEVDAVVGVLCELLQESHTGARAGAGGERDDRARDVAMMLKAFPVYSRCIVMNRQLAVTRYPC
CRLLFYSLPCRTNMISGLWMQSDSVAAVLARSNAVLRISPCPKCARMSKLQAHLYEASAARLCGGKMLRR
TLALFSEAARSSSSSSASAAASSSASILTSHLSKAHLPPSLARSAKPHKNLYQMLSTLPKDGVGARVRQR
RWAAKGLDVSHDVDLKAHLAKLHHTGATKTNKDEGHLCYWEITKVRLKDGGNHGKAWGRFVWRERNAGVV
KQGQAQAKLTKVCLSMVVAHPGKPITKAESGERIPGALKYCWDLAH
>MBP1_WALME XP_006957051 [Wallemia mellicola CBS 633.66]
MSAPPIYKACYSGVPVYEFNCKNVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGG
YGKYQGTWIPMERSVELARQYRIELLLDPIINYLPGPQSPPLAPKHATNVGSRARKSTAPAAQTLPSTSK
VFHPLSSTKHPAKLAAATNAKAEISDGEDASIPSSPSFKSNSSRTPSPIRINARKRKLEDEATIPSSAID
GSISYEDIILDYFISESTQIPALLIHPPSDFNPNMSIDDEGHTAMHWACAMGKVRVVKLLLSAGADIFRV
NHSEQTALMRSVMFSNNYDIRKFPQLYELLHRSTLNLDKHDRTVLHHIVDLALTKSKTHAARYYMECVLS
KLANYPDELADVINFQDDEGESALTLAARARSKRLVKLLLEHGADSKLPNKDGKTAEDYILEDERFRQSP
LLNSNHLRLHPPDTSIYAPPAHLFNSETSQNIANTSMSSVANLLESLAQSYDKEITQKERDYQQAQVILR
NIKTDIVEAKSNIEKMTIDSSEFEHLKHKLRELEMKLEEHSNDVYNKGWEEYSRNVDDPAIDAPSDNVQE
ECASLRNKIKDLQEKRISSMQELIKRQKEVGTGKKMSEYRKLISVGCGIPTTEIDAVLEMLLESLESENA
NKKAALASGISGALSSTSSAPSQATTSAPTGVATPGAPVPASSEKAGLLPPAPVMQ
Ortholog APSES domains
The ortholog APSES domains can be aligned (nearly) without gaps. They comprise the following sequences:
CLUSTAL format alignment by MAFFT L-INS-i (v6.850b)
MBP1_ASPNI NVYSATYSSVPVYEFKIG---TDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLQEGRQLAERNNILDKLLPIFDY
MBP1_BIPOR KIYSATYSNVPVYECNVN---GHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLEEGRGLAERNGVLDKMRAIFDY
MBP1_NEUCR GIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREVQKDTHEKIQGGYGRYQGTWIPLEQAEALARRNNIYERLKPIFEF
MBP1_COPCI QIFKATYSGIPVYEMMCK---GVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGGYGKYQGTWIPLERGMQLAKQYNCEHLLRPIIEF
MBP1_WALME PIYKACYSGVPVYEFNCK---NVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGGYGKYQGTWIPMERSVELARQYRIELLLDPIINY
MBP1_PUCGR TIYKATYSGVPVLEMPCE---GIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREIQKGTHEKIQGGYGKYQGTWVPLDRGIDLAKQYGVDHLLSALFNF
MBP1_USTMA TIFKATYSGVPVYECIIN---NVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQGGYGKYQGTWIPLDVAIELAERYNIQGLLQPITSY
MBP1_SCHPO AVHVAVYSGVEVYECFIK---GVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL
MBP1_SACCE QIYSARYSGVDVYEFIHS---TGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
MBP1_CRYNE KVYASVYSGVPVFEAMIR---GISVMRRASDSWVNATQILKVAGVHKSARTKILEKEVLNGIHEKIQGGYGKYQGTWVPLDRGRDLAEQYGVGSYLSSVFDF
:. : **.: * * :*:* *.*:***:***... *. **::**::: ***:***:*:*****:*:: . ** : : .: .
When considering the relatively high degree of conservation – e.g. there are 34 fully conserved positions (*) in this alignment of 103 positions – keep in mind that this collection of species represents on the order of a billion years of divergent evolution from a common ancestor.
Distant Homologs
APSES domains are a subfamily of Kil-A N domains; the latter include examples:
- in Protists (e.g. Trichomonas vaginalis
XP_001289194) - in DNA viruses (e.g. Canarypox virus
NP_955235) - in Gammaproteobacteria (e.g. Escherichia coli
WP_032936777(KilA))
