sibA - dictyBase/community-annotations GitHub Wiki
SibA Protein sequence supplied by Pierre Cosson, containing a signal sequence
MNRILTLFILFISLFIVCEATHFRFGTMSWMPMGSHNTIKFSSNYAFRIGFFKKFNKGCN VGDVVKVGDLDLGDDKTKVDVNLVVTSVNQADDWFTGEFSYTHTYNPIKLGGKAVTYKVV FTDCCRIKSLLNNAEGSWYISTSVVVDPNQGSDVSTFNRSPVSGMVPIITLNRDKNNQFL IAASDPNGDTLTYSLSNAYTMNQPSGLSIDSSKGIVSFKPTVSGFYSTQIMIKDTKGAYV VVDFLINSVIEPGVCHPSCSNGGNTCNGNSGCKSCKGTDSNGNTCSSFPPVFVYPPTPTD GSLLAYEVNKTNSFSIQCKTEEKSKTVFIQPANIPLAATLTSSDQNKQVSTLTYSMLPQL KHIGVYVISAYCTDNKGLVSTITSFSISVEKPICGHGTNKPGGGCNCETGWDPEKNCYEC LKGHYGEKCDPVDPCVNGESNEGSQGNGKCTCYYGWEGKNCDIKVNQVCNANKENVVLDS SVAKSSYINPNFAQVYLNTDPSKQALTLSSKLSIPETIDKFEVLVLVDSQPSIVEYWDNF KKYSSDLTKNLQDISETVSIGLGLFSDAKTNGYSFVLKKSIGNGLSGLDDKDKAPASSYS TKNSLIALTSAAEFPAGWSTGSIKIIVLLTDNDYSATAQEVSKFTSTLISKSILPVVVSF NDNQNWDTLFKNQGFGSTKKTSNAKGNDWVSVATSAIKDVLSKAVVKAIDDTKGFLTLPS ATTISIEDSKDYTIPIQIKYPQGQSDIPQNPSVSYSVVGFGITRIVINYNSAPTALGYSI ETKQNVNYNFKLSGSDVDGNTLTIKFKTIPAASVGVIQADGVTIEQGDSFSIEKTFTFKP ATNYYTKSTNDKFTFVANDGCLDSNEATVEIKITHVNQAPSCSSLSGSAISVTGLNTPKS FSLQGSDIETDSNLKIVFGDLTAISAYGNIKSGSNVVSTGSSVQLSSGSASLTFTQTKDI ANDKEITVDFKVNDGSLDSSSSCSFKVKFVHFNKPPVAFAVTPLTIRQNSELKITISASD SDSDSVIFTLDDLKLGGGDSFFKCDDRSQLTAPFTTQPVSISGGVASFSEICYSSPLVNA NSYASLVFFANDGQLSSDKFKVLININGDRPNAPPVVNQIPNFTMNEDDISNELVIDGID PDELDQGKLKGIIIQKPTNGVILVKSGSSTSEAPIIGNAPYKIFYKPNPLYYGTDSFSYT VEDSMGERDATPKTTQITVQHVNHAPTLSIDPYDFTSQTSEKTLELTPKDIDLIDTVFHC TIVKLPATAIIKTSAGKVIDTVPTDLSDNKYIITSNNNIYNDFSDSFDAKCYDSSNAVSN IATGPITFRYINVPPKAESSDETLNQDSSVSFSVKATDLEDNSNVRAVIRSLPAKGTLTI KSTGKAAEISSTYAIDDFVYTPVAGYSNWDKPGHVGPADSFNFVAKDSKNDISSNIGTVS FFIEPRNPPTYEGLAVLYTKENTDLPFSISGIVGNGGSNVFLRIKSIVSRGSLYATHCMG TEGCMSEPNPVDININFTSQPYTFSFTPIEYENGDNYAIIEFVLYDKFNGQEVESQKYTI IINVIPVNQAPEVILIEHTLSTLPNNVIAFDKFKTVKMETNSYVIIKYDGTDIDDPKEKL KSYIVSPPLRGLLYVYDKDAKDGLGKLIKKDDTFVPVAQDGFWYIVFVPTPGSSGDGYVR IPISMVDFLGDISVPVTVAVDVSKKNIPPFITIENKNYTSLANTSIVVTGVSFDDPDSKY NDVELILSLVNKDGDLVSNKIATFSLSQQSKAKCTKHSEFAQFTCRSNKKTLNALISTMY VNHQGGGSYRLKVFVNDLGYSSPASIRDKNHMTATDYVELDVTKPEVTTTKENNNKTVLT GAIAGAAAGAGLLAAGAWFLLKKSAPPTDAFFGEGAFADGAVSTNPMYEESGRSAINPLY EASSENL
sibA cDNA supplied by Pierre Cosson
ATGAATAGAATTTTAACTTTATTTATATTGTTTATAAGTTTATTTATAGTTTGTGAAGCA ACACATTTCCGTTTTGGTACTATGTCATGGATGCCGATGGGATCACATAATACTATAAAA TTTTCTTCAAATTATGCATTTCGTATAGGTTTTTTCAAAAAATTTAACAAAGGGTGCAAT GTTGGTGATGTTGTTAAAGTGGGTGATTTGGACCTTGGAGATGATAAAACTAAAGTTGAT GTTAATTTAGTAGTAACATCAGTTAATCAGGCCGATGATTGGTTTACCGGAGAGTTTTCA TACACACACACTTATAACCCAATAAAATTAGGTGGAAAAGCCGTCACATATAAAGTAGTC TTTACTGATTGTTGCAGAATTAAATCATTGTTAAACAATGCAGAAGGTAGTTGGTATATT TCCACATCAGTGGTTGTTGATCCAAATCAAGGTAGTGATGTATCTACTTTCAATCGTTCA CCAGTTTCAGGTATGGTCCCAATTATCACTTTAAATAGAGATAAAAATAATCAATTCCTT ATCGCAGCATCTGATCCAAATGGTGATACACTCACATATTCTCTCAGTAATGCCTACACC ATGAACCAACCATCAGGTTTAAGTATCGATAGCAGCAAAGGCATAGTATCATTTAAACCA ACCGTTTCTGGTTTTTATTCTACTCAAATTATGATCAAAGATACCAAGGGTGCTTACGTT GTAGTTGATTTCCTCATTAATTCAGTCATAGAGCCAGGTGTTTGTCATCCATCTTGTAGC AATGGTGGAAATACTTGCAATGGTAACTCGGGCTGTAAATCATGTAAAGGAACAGACTCA AACGGTAACACTTGTTCTTCTTTCCCACCAGTTTTTGTTTATCCACCAACTCCGACAGAT GGTTCTCTCCTTGCATATGAAGTAAACAAAACAAATTCTTTTTCAATTCAATGTAAAACT GAAGAAAAATCTAAAACTGTATTTATTCAACCTGCAAATATTCCACTTGCTGCTACTCTT ACTTCATCAGATCAAAATAAACAAGTTTCAACTCTTACTTATTCAATGTTACCACAATTA AAACATATTGGTGTTTATGTTATTTCAGCTTATTGTACTGATAATAAGGGTTTAGTCTCA ACTATTACTTCTTTTTCAATTTCAGTTGAAAAACCAATTTGTGGTCATGGTACTAATAAA CCAGGTGGTGGTTGTAATTGTGAAACAGGTTGGGATCCAGAAAAGAATTGTTATGAATGT TTAAAAGGACATTATGGTGAAAAATGTGACCCAGTAGATCCATGTGTAAATGGTGAGTCC AATGAAGGCAGCCAAGGTAATGGTAAATGTACATGCTACTATGGTTGGGAAGGTAAAAAT TGTGATATTAAAGTTAACCAAGTTTGTAATGCAAACAAAGAAAATGTTGTTCTCGATTCA TCAGTAGCTAAATCAAGTTATATCAATCCAAACTTTGCTCAAGTTTACTTAAATACCGAT CCATCAAAACAAGCTTTAACTCTTTCATCTAAACTTAGTATTCCAGAAACAATTGATAAA TTTGAAGTTTTGGTTCTTGTTGATTCTCAACCAAGTATCGTTGAATATTGGGATAATTTT AAAAAGTATTCATCTGATTTAACTAAAAACCTCCAAGATATTAGTGAAACTGTTTCAATT GGTTTAGGTTTATTCTCAGATGCCAAAACCAATGGTTATTCATTCGTTTTAAAGAAATCA ATTGGTAATGGTCTTAGTGGTTTGGATGATAAAGATAAAGCACCTGCTTCATCGTACTCT ACTAAAAATTCACTCATTGCACTTACAAGTGCTGCAGAATTTCCAGCTGGTTGGAGCACA GGTTCAATTAAAATCATTGTTCTTTTAACTGATAATGATTATTCAGCCACTGCTCAAGAA GTTTCTAAATTTACATCCACTTTAATCAGTAAATCCATTTTACCAGTTGTTGTTAGTTTT AATGATAATCAAAATTGGGATACCCTTTTCAAAAACCAAGGCTTTGGTTCAACTAAAAAA ACTTCAAACGCTAAAGGTAATGACTGGGTATCAGTAGCTACTAGTGCTATCAAGGATGTT TTAAGCAAAGCAGTTGTTAAAGCAATCGATGATACCAAAGGATTTTTAACACTTCCATCA GCAACTACAATTAGTATCGAAGATTCAAAAGATTACACTATTCCAATTCAAATCAAATAT CCACAAGGTCAATCAGATATTCCTCAAAACCCATCTGTATCTTACTCTGTTGTAGGTTTT GGTATAACTAGAATTGTTATCAACTATAATAGTGCTCCAACTGCTTTAGGCTATTCAATT GAAACCAAACAAAATGTAAACTATAACTTTAAATTATCAGGTAGTGATGTTGATGGAAAT ACTTTAACTATTAAATTTAAAACTATTCCAGCCGCATCTGTTGGTGTAATTCAAGCTGAT GGTGTAACCATTGAACAAGGTGATTCATTCTCAATTGAAAAAACCTTTACCTTTAAACCA GCCACCAATTATTACACTAAATCTACCAATGATAAATTTACATTTGTAGCTAATGATGGT TGTTTAGATAGTAATGAAGCAACCGTTGAAATTAAAATTACCCATGTAAATCAAGCACCA TCTTGTTCAAGTCTTTCAGGTTCTGCAATTTCAGTTACTGGATTAAATACACCAAAATCT TTCTCATTACAAGGTAGTGATATTGAAACCGATTCAAATTTAAAAATTGTATTTGGTGAC TTAACTGCTATTTCAGCTTATGGTAACATTAAAAGTGGTAGCAATGTAGTCTCCACTGGA TCAAGTGTACAACTTTCCTCTGGTTCTGCATCTCTTACATTCACACAAACTAAAGATATT GCAAATGACAAAGAAATTACCGTTGATTTCAAAGTTAATGATGGTTCATTAGATTCTTCA TCTTCATGTTCTTTCAAGGTTAAATTTGTTCATTTCAATAAACCACCAGTTGCATTCGCT GTAACACCACTTACAATTAGACAAAATTCAGAACTTAAAATTACTATTTCAGCCTCTGAT TCCGACTCTGATAGTGTTATTTTTACTTTAGACGACCTCAAATTGGGTGGAGGTGATAGT TTCTTTAAATGTGATGATAGATCACAACTCACCGCACCATTTACAACCCAACCAGTTTCA ATTTCTGGTGGTGTAGCATCATTCTCTGAAATCTGTTATTCATCCCCACTCGTAAATGCA AATTCATATGCAAGTTTAGTATTCTTTGCCAATGATGGCCAGTTATCTAGTGATAAATTT AAAGTTTTAATCAATATCAATGGTGATCGTCCAAATGCCCCACCAGTTGTAAATCAAATT CCAAATTTCACAATGAATGAAGATGATATTTCCAATGAATTGGTAATTGATGGTATCGAC CCAGATGAATTAGATCAAGGTAAACTTAAAGGTATTATAATACAAAAACCAACGAATGGA GTTATCTTAGTTAAATCAGGTAGTTCAACAAGTGAAGCACCAATTATTGGTAATGCACCA TACAAGATTTTCTATAAACCAAATCCATTATACTATGGTACAGATAGTTTTTCTTATACT GTTGAGGATAGTATGGGTGAGAGAGATGCAACTCCAAAGACTACTCAAATCACAGTCCAA CATGTTAATCATGCACCAACCCTTTCAATTGATCCATATGATTTCACCTCTCAAACTTCT GAAAAAACTTTAGAATTAACACCAAAAGATATTGATTTAATAGATACTGTATTCCATTGC ACTATCGTTAAATTACCAGCAACTGCCATTATTAAAACCTCTGCTGGTAAAGTAATCGAT ACTGTACCAACTGATTTATCAGATAATAAATACATCATAACTTCAAATAATAATATCTAT AATGATTTCAGTGATTCATTCGATGCAAAATGTTATGATTCAAGTAATGCAGTTTCAAAT ATTGCAACTGGCCCAATCACCTTTAGATATATTAATGTTCCACCAAAAGCAGAATCATCA GATGAAACCTTAAATCAAGATAGTTCCGTTAGTTTCTCAGTAAAAGCCACCGATCTTGAA GATAATTCAAATGTTAGGGCTGTAATTAGATCCCTTCCAGCAAAAGGTACCCTTACAATT AAATCAACAGGAAAAGCAGCTGAAATCTCTTCAACCTATGCAATTGATGATTTTGTTTAT ACTCCAGTTGCAGGTTATTCCAATTGGGATAAACCAGGCCATGTTGGACCAGCCGATTCT TTCAATTTTGTTGCAAAAGATAGTAAAAATGATATCTCTTCAAATATTGGTACTGTTTCA TTCTTTATTGAACCAAGAAATCCACCAACCTATGAGGGTTTAGCTGTTTTATACACTAAA GAAAATACTGATCTTCCATTCAGTATTTCTGGTATCGTTGGTAATGGTGGTTCAAATGTT TTCCTAAGAATTAAATCGATCGTTTCCAGGGGTTCATTATATGCCACTCATTGTATGGGT ACTGAAGGTTGTATGTCTGAACCAAATCCAGTTGATATTAACATAAACTTCACATCTCAA CCATATACCTTTAGTTTTACACCAATTGAATATGAAAATGGTGATAATTATGCCATTATT GAATTTGTACTCTATGATAAATTTAATGGTCAAGAAGTTGAATCCCAAAAATATACCATT ATCATCAATGTTATCCCAGTAAATCAAGCACCAGAGGTCATCTTAATTGAACATACTCTT TCAACTCTACCAAATAATGTTATAGCATTCGATAAATTTAAGACTGTTAAAATGGAAACT AACTCTTATGTCATTATTAAATATGATGGCACTGATATTGACGATCCAAAAGAAAAATTA AAATCTTATATTGTCAGTCCTCCACTTCGTGGTTTACTCTATGTCTATGATAAAGATGCT AAGGATGGTTTGGGTAAATTAATAAAAAAGGATGATACATTTGTTCCTGTAGCTCAAGAT GGTTTTTGGTATATCGTTTTTGTACCAACTCCAGGTTCATCTGGTGATGGTTATGTTCGT ATTCCAATTTCAATGGTAGATTTCTTGGGTGATATCTCTGTTCCAGTCACAGTTGCAGTT GATGTTTCAAAAAAGAATATTCCACCATTCATTACCATTGAAAATAAAAACTATACTTCA CTCGCCAATACTTCAATCGTTGTTACAGGTGTCTCATTTGATGATCCAGACAGTAAATAT AATGATGTTGAATTAATTCTCTCATTGGTTAACAAGGATGGCGATTTAGTTTCAAATAAA ATTGCAACATTCTCTTTATCTCAACAAAGTAAAGCAAAATGCACCAAACATTCTGAATTC GCTCAATTCACTTGTAGATCAAATAAAAAGACACTCAATGCTTTAATTTCCACAATGTAT GTAAATCACCAAGGTGGTGGTTCTTATCGTCTCAAAGTATTCGTTAATGATTTAGGTTAT AGTTCACCAGCATCAATTAGAGATAAAAATCATATGACTGCAACTGATTATGTTGAATTG GATGTAACAAAACCTGAAGTTACTACCACCAAAGAAAATAATAATAAAACAGTATTAACT GGTGCAATTGCTGGTGCTGCCGCTGGTGCAGGTTTACTTGCCGCTGGTGCTTGGTTCTTA TTAAAGAAATCTGCTCCACCAACAGATGCATTCTTTGGTGAAGGAGCTTTTGCTGATGGT GCTGTCTCTACAAATCCAATGTATGAAGAAAGTGGTAGATCTGCTATCAATCCATTATAT GAAGCTTCTTCTGAAAATTTATAA
Is SibA phylogenetically related to mammalian integrin beta chains?
In Cornillon et al.,EMBO Reports 6, (2006) we report the identification of a new adhesion molecule with integrin beta features.
There are many features present in mammalian integrin beta chains and also found in Dictyostelium Sib proteins, in particular a highly conserved cytoplasmic domain interacting with talin, a glycine-rich transmembrane domain, and an extracellular domain containing a VWA domain. In metazoas it is believed that integrin beta chains were among the first extracellular domains exhibiting a VWA domain, and interestingly in Dictyostelium Sib proteins are the only proteins in the genome that comprise an extracellular VWA domain. Furthermore Sib VWA domains seem closely related to mammalian integrin beta VWA domains.
There are also some clear differences between Dictyostelium Sib proteins and mammalian integrin beta chains, in particular the presence of an additional repeated motif in Dictyostelium Sibs, and several unique features of integrin beta VWA domains. However given the early evolutionary divergence of Dictyostelium, one would expect some differences to emerge in these distinct lineages.
Personally, having to choose between a phylogenetic link between Sib proteins and mammalian beta integrins or convergent evolution, I find the second hypothesis rather unlikely.
So how can we decide if Sibs are integrin beta chains or not? Maybe the most clear answer would be to identify a partner showing similarity to an alpha integrin? We are working on it. Time will tell...
Pierre Cosson June 2006
dictyBase Comments
Created new gene model. Genomic DNA has an insertion of a C at position 17 Gareth's AX4 sequence supports P. Cosson's sequence in the critical regions of the C nt insertion and the splice donor at the first intron. At other discrepancies, Gareth's sequence has nnn or is less clear. The new gene model is the best available from the genomic sequence, however, an artificial gap needed to be inserted and its N-terminal protein sequence still differs in several positions to GenBank DQ793219 (A) and does not have a predicted signal sequence (SignalP), whereas DQ793219 (B) contains a predicted signal sequence:
A: MDRILTLFIWFKSLFKVGKATHFRFGTMSWMPMGSHNTIKFSSNYAFR 48 M+RILTLFI F SLF V +ATHFRFGTMSWMPMGSHNTIKFSSNYAFR B: MNRILTLFILFISLFIVCEATHFRFGTMSWMPMGSHNTIKFSSNYAFR 48
pfey January 2012
cDNA from P. Cosson on top and from genomic DNA; genDNA) at bottom; note the 5' differences including the C residue insertion resulting in an artificial gap to prevent a frame shift in the curated model, and the amino acid changes seen above.
cDNA: 1 atgaatagaattttaac-tttatttatattgtttataagtttatttatagtttgtgaagc 60
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genDNA: 1 atggatagaattttaacctttatttatttggtttaaaagtttatttaaagttgggaaagc 60
cDNA: 65 aacacatttccgttttggtactatgtcatggatgccgatgggatcacataatactataaa 120
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genDNA: 65 aacacatttccgttttggtactatgtcatggatgccaatgggatcacataatactataaa 120
pfey August 2022
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