Reference alignment for KilA-N domains (MUSCLE, reference species)
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Aligned KilA-N domain family
Alignment of KilA-N domains in selected genome sequenced fungi, generated with the MUSCLE webserver.
This is a MUSCLE alignment for KilA-N domains found in genome-sequenced fungi by PSI-BLAST. Gene names have been revised to name genes to their most similar counterparts in Saccharomyces cerevisiae. The gene names now either correspond to the orthologuous Saccharomyces cerevisiae gene (Mbp1, Swi4, Phd1, Sok2 or Xbp1) if they fulfill RBM, or use the first three letters of the most similar yeast orthologue's gene name plus A, B, C ... if they are paralogues. In addition, the yeast Xbp1 gene has been added to the alignment (bold). In BLAST scans, Saccharomyces cerevisiae Xbp1 often gives only partial matches to HSPs. It turns out that an entire KilA-N domain can be defined for Xbp1; it has one 84 amino acid insertion and another 17 amino acid insertion relative to the consensus KilA-N domains and is therefore split into separate HSPs. I have included the sequence here, but removed all residues that are inserted relative to the closely related Debaryomyces hansenii orthologue. Failure to recognize domain similarity when one or more long indels are present is a frequently encountered problem that automatic algorithms do not address well.
The output is sorted in the same order as the input file. Some residues that were proposed to be important for DNA binding were manually highlighted in red (-) and blue (+) in the Mbp1_SACCE sequence. Two structurally important residues have been colored green.
MUSCLE (3.6) multiple sequence alignment Mbp1_SACCE SIMKRKKDDWVNATHILKAA--------NFA------KAKRTRILEKEV--LKETHEKVQGG----FGKYQ--------GTWVPLNIAKQLAEK--FSVYD-QLKPLFDF Mbp1_ASHGO SIMKRKADDWVNATHILKAA--------KFA------KAKRTRILEKEV--IKDTHEKVQGG----FGKYQ--------GTWVPLDIARRLAQK--FEVLE-ELRPLFDF Mbp1_ASPFU --MRRRGDDWINATHILKVA--------GFD------KPARTRILEREV--QKGTHEKVQGG----YGKYQ--------GTWIPLHEGRLLAER--NNIID-KLRPIFDY Mbp1_ASPNI SVMRRRSDDWINATHILKVA--------GFD------KPARTRILEREV--QKGVHEKVQGG----YGKYQ--------GTWIPLQEGRQLAER--NNILD-KLLPIFDY Mbp1_ASPTE SVMRRRADDWINATHILKVA--------GFD------KPARTRILEREV--QKGVHEKVQGG----YGKYQ--------GTWIPLPEGRLLAER--NNIID-KLRPIFDY Mbp1_CANAL -IMRRKKDSWINATHILKIA--------KFP------KAKRTRILEKDV--QTGIHEKVQGG----YGKYQ--------GTYVPLDLGAAIARN--FGVYD-VLKPIFEF Mbp1_CANGL SIMKRKNDGWVNATHILKAA--------NFA------KAKRTRILEKEV--LKEMHEKVQGG----FGKYQ--------GTWVPLNIAINLAEK--FDVYQ-DLKPLFDF Mbp1_COPCI AVMRRRSDSWLNATQILKVA--------GFD------KPQRTRVLEREV--QKGEHEKVQGG----YGKYQ--------GTWIPLERGMQLAKQ--YNCEH-LLRPIIEF Mbp1_CRYNE SVMRRASDSWVNATQILKVA--------GVH------KSARTKILEKEV--LNGIHEKIQGG----YGKYQ--------GTWVPLDRGRDLAEQ--YGVGS-YLSSVFDF Mbp1_DEBHA -IMRRKLDSWINATHILKIA--------KFP------KAKRTRILEKDV--QTGVHEKVQGG----YGKYQ--------GTYVPLDLGADIAKN--FGVFD-SLRPIFEF Mbp1_GIBZE -VMRRRSDDWINATHILKAA--------GFD------KPARTRILERDV--QKDVHEKIQGG----YGKYQ--------GTWIPLESGQALAER--HSVID-RLRPIFEY Mbp1_KLULA SIMKRKADNWVNATHILKAA--------KFP------KAKRTRILEKEV--ITDTHEKVQGG----FGKYQ--------GTWIPLELASKLAEK--FEVLD-ELKPLFDF Mbp1_MAGGR -VMRRRVDDWINATHILKAA--------GFD------KPARTRILEREV--QKDQHEKVQGG----YGKYQ--------GTWIPLEAGEALAHR--NNIFD-RLRPIFEF Mbp1_NEUCR -VMRRRHDDWVNATHILKAA--------GFD------KPARTRILEREV--QKDTHEKIQGG----YGRYQ--------GTWIPLEQAEALARR--NNIYE-RLKPIFEF Mbp1_PICST -IMRRKLDSWINATHILKIA--------KFP------KAKRTRILEKDV--QTGVHEKVQGG----YGKYQ--------GTYVPLELGRDIAKN--FGVFD-ILKPIFDF MbpA_SCHPO --MKRCHDNWLNATQILKIA--------ELD------KPRRTRILEKFA--QKGLHEKIQGG----CGKYQ--------GTWVPSERAVELAHE--YNVFD-LIQPLIEY Mbp1_USTMA AVMRRRSDDWLNATQILKVV--------GLD------KPQRTRVLEREI--QKGIHEKVQGG----YGKYQ--------GTWIPLDVAIELAER--YNIQG-LLQPITSY Mbp1_YARLI AVMRRKSDGWVNATHILKVA--------GFD------KPQRTRILEKEV--QKGVHEKVQGG----YGKYQ--------GTWVPLERAREIATL--YDVDS-HLAPIFNY Swi4_ASHGO -VMRRLHDDWVNITQVFKVA--------TFS------KTQRTKILEKES--ADISHEKIQGG----YGRFQ--------GTWIPLDSAKGLVAK--YEITD-IVV----- Sok2_ASHGO SVVRRADNDMINGTKLLNVA--------KMT------RGRRDGILKAEK-----VRHVVKIG----SMHLK--------GVWIPFERALALAQR--EKIVD-MLFPLF-- Xbp1_ASPFU -VMWDYNIGLVRTTHLFKCN--------DYS-----------KMLNANP-GLREICHSITGG----ALAAQ--------GYWMPYEAAKAVAATFCWKIRH-ALTPLFG- MbpA_ASPFU AVMKRRSDSWLNATQILKVA--------GVV------KARRTKTLEKEI--AAGEHEKVQGG----YGKYQ--------GTWVNYQRGVELCRE--YHVEE-LLRPLLEY Sok2_ASPFU -VARREDNHMINGTKLLNVA--------GMT------RGRRDGILKSEK-----VRHVVKIG----PMHLK--------GVWIPFERALEFANK--EKITD-LLYPLF-- XbpA_ASPNI -ISWDYNVGLVLTRSLFKCN--------GHP------KTAPAKVLKMNP-GLGDISHSITGG----ALVGQ--------GYWMPFRAAKALATTFCWNIRF-VLTPMFG- Xbp1_ASPNI TVMWDYNIGLVRTTHLFKCN--------DYS------KTTPAKMLNQNP-GLRDICHSITGG----ALAAQ--------GYWMPYEAAKAIAATFCWKIRF-ALTPLFG- MbpA_ASPNI AVMKRRSDSWLNATQILKVA--------GVV------KARRTKTLEKEI--AAGEHEKVQGG----YGKYQ--------GTWVNYQRGVELCRE--YHVEE-LLRPLLEY SokA_ASPNI -VARREDNGMINGTKLLNVA--------GMT------RGRRDGILKSEK-----VRNVVKIG----PMHLK--------GVWIPFDRALEFANK--EKITD-LLYPLF-- Sok2_ASPNI -VARREDNHMINGTKLLNVA--------GMT------RGRRDGILKSEK-----VRHVVKIG----PMHLK--------GVWIPFERALEFANK--EKITD-LLYPLF-- Xbp1_ASPTE -IMWDYNIGLVRTTPLFRSQ--------NYS------KTTPAKVLDANP-GLREISHSITGG----AIVAQDKP-----GYWIPFEAAKAVAATFCWRIRY-ALTPIFG- MbpA_ASPTE AVMKRRSDSWLNATQILKVA--------GVV------KARRTKTLEKEI--AAGEHEKVQGG----YGKYQ--------GTWVNYQRGVDLCRE--YHVEE-LLRPLLEY Sok2_ASPTE -VARREDNSMINGTKLLNVA--------GMT------RGRRDGILKSEK-----IRHVVKIG----PMHLK--------GVWIPFERALEFANK--EKITD-LLYPLF-- MbpC_CANAL -VLRRVQDSFVNVTQLFQILIKLE----VLP------TSQVDNYFDNEI--LSNLKYFGSSSNTPQYLDLRKHQNIYLQGIWIPYDKAVNLALK--FDIYE-ITKKLF-- Xbp1_CANAL -VIWDYETGWVHLTGIWKASLTID----GSNVSPSHLKADIVKLLESTPKEYQQYIKRIRGG----FLKIQ--------GTWLPYKLCKILARRFCYYLRY-SLIPIFG- MbpA_CANAL SIMRRCKDDWVNATQILKCC--------NFP------KAKRTKILEKGV--QQGLHEKVQGG----FGRFQ--------GTWIPLEDARKLAKT--YGVTE-ELAPVL-- Sok2_CANAL -VSRREDTNYINGTKLLNVI--------GMT------RGKRDGILKTEK-----IKNVVKVG----SMNLK--------GVWIPFDRAYEIARN--EGVDS-LLYPLF-- Phd1_CANAL SVVRRADNNMINGTKLLNVA--------QMT------RGRRDGILKSEK-----VRHVVKIG----SMHLK--------GVWIPFERALAMAQR--EQIVD-MLYPLF-- SokA_CANGL TVVRRADNDMVNGTKLLNVT--------GMT------RGRRDGILKNEP-----VRDVVKGG----PMTLK--------GVWIPIDRARAIARQ--EGIEQ-WLYPLF-- Swi4_CANGL -VMRRTMDDWVNVTQVFKIA--------QFS------KTQRTKILEKES--TNMKHEKVQGG----YGRFQ--------GTWVPLEAAKFMTTK--YNIDNPVVNTILSF Sok2_CANGL SVVRRADNDMINGTKLLNVT--------KMT------RGKRDGILRSEK-----YRKVVKIG----SMHLK--------GVWIPFERALFIAKR--EKIVD-LLYPLF-- Xbp1_COPCI -IMMDIDDGYILWTGIWKAL--------GNS------KADIVKMIDSQP-DLAPLIRRVRGG----YLKIQ--------GTWMPYEVALKLSRRVAWPIRH-DLVPLFGF MbpA_CRYNE AVMRRRSDAYLNATQILKVA--------GFD------KPQRTRVLEREV--QKGEHEKVQGG----YGKYQ--------GTWIPIERGLALAKQ--YGVED-ILRPIIDY Xbp1_DEBHA -IIWDYETGFVHLTGIWKASINDEVNTHRNL------KADIVKLLESTPKQYHQHIKRIRGG----FLKIQ--------GTWLPFDLCKMLAKRFCYHIRF-QLIPIFG- MbpB_DEBHA -ILRRVQDSYINISQLFSILLKIG----HLS------EAQLTNFLNNEI--LTNTQYLSSGGSNPQFNDLRNHEVRDLRGLWIPYDRAVSLALK--FDIYE-LAKSLF-- MbpA_DEBHA -IMRRCKDDWVNATQILKCC--------NFP------KAKRTKILEKGV--QQGLHEKIQGG----YGRFQ--------GTWIPLADAQRLAAS--YGVTP-DLAPVL-- SokA_DEBHA -VSRREDTNYVNGTKLLNVA--------GMT------RGKRDGILKTEK-----TKSVVKVG----AMNLK--------GVWIPFERASEIARN--EGIDG-LLYPLF-- Sok2_DEBHA SVVRRADNNMINGTKLLNVA--------QMT------RGRRDGILKSEK-----VRHVVKIG----SMHLK--------GVWIPFERALAMAQR--EGIVD-LLYPLF-- Xbp1_GIBZE AVMWDYNIGLVRMTPFFKCR--------GYG------KTIPAKMLGLNP-GLKEITHSITGG----SIAAQ--------GYWMPYRCAKAICATFCHPIAG-ALIPIFG- MbpA_GIBZE AVMRRRNDSWLNATQILKVA--------GVD------KGKRTKILEKEI--QTGEHEKVQGG----YGKYQ--------GTWIKFERGLQVCRQ--YGVEE-LLRPLLTY Sok2_GIBZE -VARREDNHMINGTKLLNVA--------GMT------RGRRDGILKSEK-----VRHVVKIG----PMHLK--------GVWIPYDRALDFANK--EKITE-LLYPLF-- Swi4_KLULA -IMRRCNDNWLNITQVFKAG--------SFT------KAQRTKILEKEA--NEIKHEKIQGG----YGRFQ--------GTWIPWESTKYLVEK--YNINNKVVKRIVEF Sok2_KLULA SVVRRADNDMINGTKLLNVT--------RMT------RGRRDGILKAEK-----IRHVVKIG----SMHLK--------GVWIPFERALVMAQR--EKIVD-LLYALF-- Xbp1_MAGGR TVMWDYGCGLVRMTHFFKCR--------GYT------KTVPGKVLNQNH-GLKDITYSITGG----SISAQ--------GYWMPFACARAVCATFCHPIAG-ALIPIFG- MbpA_MAGGR AVMKRIGDSKLNATQILKVA--------GVE------KGKRTKILEKEI--QTGEHEKVQGG----YGKYQ--------GTWIKYERALEVCRQ--YGVEE-LLRPLLEY Sok2_MAGGR -VARREDNHMINGTKLLNVA--------GMT------RGRRDGILKSEK-----MRHVVKIG----PMHLK--------GVWIPFERALDFANK--EKITE-LLYPLF-- MbpA_NEUCR AVMRRQKDGWVNATQILKVA--------NID------KGRRTKILEKEI--QIGEHEKVQGG----YGKYQ--------GTWIPFERGLEVCRQ--YGVEE-LLSKLL-- MbpA_PICST -IMRRCKDDWVNATQILKCC--------NFP------KAKRTKILEKGV--QQGLHEKVQGG----FGRFQ--------GTWIPLPDAQRLATM--YGVTA-DAAPVL-- SokA_PICST -VSRREDTNFVNGTKLLNVI--------GMT------RGKRDGILKTEK-----TRNVVKVG----SMNLK--------GVWIPFDRAFEIARN--EGVDE-ALHPLF-- Sok2_PICST SVVRRADNNMINGTKLLNVA--------QMT------RGRRDGILKSEK-----VRHVVKIG----SMHLK--------GVWIPFERALAMAQR--EGIVD-LLYPLF-- Sok2_SACCE SVVRRADNDMVNGTKLLNVT--------KMT------RGRRDGILKAEK-----IRHVVKIG----SMHLK--------GVWIPFERALAIAQR--EKIAD-YLYPLF-- Phd1_SACCE SVVRRADNNMINGTKLLNVT--------KMT------RGRRDGILRSEK-----VREVVKIG----SMHLK--------GVWIPFERAYILAQR--EQILD-HLYPLF-- Swi4_SACCE -VMRRTKDDWINITQVFKIA--------QFS------KTKRTKILEKES--NDMQHEKVQGG----YGRFQ--------GTWIPLDSAKFLVNK--YEIIDPVVNSILTF Xbp1_SACCE CVIWSHDSGYVFMTGIWRLYQDVMKGLINLPRGDSNIKPELRDLICQSYKDFANFTKRIRGG----YIKIQ--------GTWLPMEISRLLCLRFCFPIRY-FLVPIFG- MbpB_SCHPO --LRRCPDSYFNISQILRLA--------GTS------SSENAKELDDII--ESGDYENVDSK----HPQID--------GVWVPYDRAISIAKR--YGVYE-ILQPLISF Mbp1_SCHPO SVMRRRRDSWLNATQILKVA--------DFD------KPQRTRVLERQV--QIGAHEKVQGG----YGKYQ--------GTWVPFQRGVDLATK--YKVDG-IMSPILS- MbpA_USTMA TMMIDVDTSFVRFTSITQAL--------GKN------KVNFGRLVKTCP-ALDPHITKLKGG----YLSIQ--------GTWLPFDLAKELSRRIAWEIRD-HLVPLFGY MbpB_USTMA AVMRRRGDGWLNATQILKIA--------GIE------KTRRTKILEKSI--LTGEHEKIQGG----YGKFQ--------GTWIPLQRAQQVAAE--YNVSH-LLQPILEF MbpB_YARLI -IIWDYHTGYVHLTGLWKAI--------GNS------KADIVKLIDNSP-DLEAVIRRVRGG----YLKIQ--------GTWVPYDIARALASRTCYFIRF-ALIPLFG- Xbp1_YARLI AVMRRRTDSSLNATQILKVA--------GVE------KSKRTKILEKEI--LTGAHEKVQGG----YGKYQ--------GTWIPYERGVDLCRQ--YSVYD-VLQPLLAF SokA_YARLI -VARREDNDMINGTKLLNVA--------GMT------RGRRDGILKGEK-----LRHVVKAG----AMHLK--------GVWIPYDRALEFANK--EKIID-LLFPLF-- Sok2_YARLI -VARREDNNMINGTKLLNVV--------GMT------RGRRDGILKTEK-----IRHVVKIG----AMHLK--------GVWIPYERALAFAQR--ERIVD-VLYPLF-- . . . * :: .
