========= Reference ========= M Gerstein, E Sonnhammer, C Chothia (1994). "Volume Changes in Protein Evolution," J. Mol. Biol. (in press) ===== Notes ===== This alignment contains 40 plastocyanin-azurin family sequences based on 2 key structures. It is based on sequences in PIR-36 and SwissProt-24. The sequences corresponding to the key structures are highlighted with '=' . The alignment is only accurate in the "Core" regions. These are indicated by the 'x' above each of the 56 core sequence positions. Outside of the core, particularly in regions not below '*'s, residues were positioned arbitrarily. The core positions are also indicated by lower case letters. The numbers to the right of each sequence are the weights assigned to the sequence by the tree weighting procedure described in the paper. The pseudo-azurin sequence was not used. It is shown at bottom. =============================================================================== 1 2 3 4 5 6 7 8 9 1234567890123456789012 34567890123 4567890123456789012345 6789012345678 901234567 8901234567 890123456789 |||||||||||||||||||||| ||||||||||| |||||||||||||||||||||| |||||||||||||---||||||||| |||||||||| |||||||||||| ***** *********** ********** ******* ** ******* ******** ********* SELECT: x x x x x x x x x x xxxxx x x x x x x x x x CUPX ====iDvLlGADDGSLAfVPSEfSiS===PGEKiVfKnNa=====GFPhnivfDEDSIPSGVDASKI==============SMSZZBLLNAKGE===TFEvAlSNK=====GEySfYcSpH=QGAGmVgKvTVN====== 1.0253 CULC ----aEvLlGSSDGGLVfEPSTfSvA---SGEKiVfKnNa-----GFPhnvvfDEDEIPAGVDASKI--------------SMSEEDLLNAPGE---TYAvTlTEK-----GTySfYcApH-QGAGmVgKvTVN------ 0.9523 A24404 ----aEvLlGSSDGGLAfVPSDlSiA---SGEKiTfKnNa-----GFPhnvvfDEDEVPAGVDVTKI--------------SMPEEDLLNAPGE---EYSvTlTEK-----GTyKfYcApH-AGAGmVgKvTVN------ 1.0306 CUVF ----vEvLlGASDGGLAfVPNSfEvS---AGDTiVfKnNa-----GFPhnvvfDEDEIPSGVDAAKI--------------SMPEEDLLNAPGE---TYSvKlDAK-----GTyKfYcSpH-QGAGmVgQvTVN------ 1.0560 CUSP ----vEvLlGGGDGSLAfLPGDfSvA---SGEEiVfKnNa-----GFPhnvvfDEDEIPSGVDAAKI--------------SMSEEDLLNAPGE---TYKvTlTEK-----GTyKfYcSpH-QGAGmVgKvTVN------ 0.9414 CUSP2? ----iEvLlGGGDGSLAfVPNDfSiA---KGEKiVfKnNa-----GFPhnvvfDEDEIPSGVDASKI--------------SMDENDLLNAAGE---TYEvAlTEA-----GTySfYcApH-QGAGmVgKvTVN------ 0.9631 CUED ----vEiLlGGEDGSLAfIPSNfSvP---SGEKiTfKnNa-----GFPhnvvfDEDEVPSGVDSAKI--------------SMSEDDLLNAPGE---TYSvTlTES-----GTyKfYcSpH-QGAGmVgKvTVN------ 1.0101 S00210 ----vDvLlGADDGSLAfVPSEfSvP---AGEKiVfKnNa-----GFPhnvlfDEDAVPSGVDVSKI--------------SMSEEDLLNAKGE---TFEvAlSDK-----GEyTfYcSpH-QGAGmVgKvIVN------ 1.0253 CUVM ----iEvLlGGDDGSLAfIPNDfSvA---AGEKiVfKnNa-----GFPhnvvfDEDEIPSGVDAGKI--------------SMNEEDLLNAPGE---VYKvNlTEK-----GSySfYcSpH-QGAGmVgKvTVN------ 0.9414 CUKV ----iEiLlGGDDGSLAfVPNNfTvA---SGEKiTfKnNa-----GFPhnvvfDEDEIPSGVDSGKI--------------SMNEEDLLBAPGZ---VYZvZlTZK-----GSySfYcSpH-QGAGmVgKvTVN------ 1.0423 CUFB ----lEvLlGSGDGSLVfVPSEfSvP---SGEKiVfKnNa-----GFPhnvvfDEDEIPAGVDAVKI--------------SMPEEELLNAPGE---TYVvTlDTK-----GTySfYcSpH-QGAGmVgKvTVN------ 0.9523 CUDM ----lDvLlGSDDGELAfVPNNfSvP---SGEKiTfKnNa-----GFPhnvvfDEDEIPSGVDASKI--------------SMDEADLLNAPGE---TYAvTlTEK-----GSySfYcSpH-QGAGmVgKvTVN------ 0.9554 CUPO ----lDvLlGGDDGSLAfIPGNfSvS---AGEKiTfKnNa-----GFPhnvvfDEDEIPAGVDASKI--------------SMAEEDLLNAAGE---TYSvTlSEK-----GTyTfYcApH-QGAGmVgKvTVN------ 0.9207 CUUA ----iEvLlGSDDGGLAfVPGNfSiS---AGEKiTfKnNa-----GFPhnvvfDEDEIPAGVDASKI--------------SMPEEDLLNAPGE---TYSvTlSEK-----GTySfYcSpH-QGAGmVgKvTVN------ 0.9207 CURX ----iEiKlGGDDGALAfVPGSfTvA---AGEKiVfKnNa-----GFPhnivfDEDEVPAGVDASKI--------------SMSEEDLLNAPGE---TYAvTlSEK-----GTySfYcSpH-QGAGmVgKvTVQ------ 1.0164 JA0065 ----mEvLlGSDDGSLAfVPSEfTvA---KGEKiVfKnNa-----GFPhnvvfDEDEIPSGVDASKI--------------SMDETALLNGAGE---TYEvTlTEP-----GSyGfYcApH-QGAGmVgKlTVK------ 1.0760 S00206 ----qDvLlGANGGVLVfEPNDfSvK---AGETiTfKnNa-----GYPhnvvfDEDAVPSGVDVSKI--------------S--QEEYLTAPGE---TFSvTlTVP-----GTyGfYcEpH-AGAGmVgKvTVN------ 1.0055 RICE ----qEvLlGANGGVLVfEPNDfTvK---SGETiTfKnNa-----GFPhnvvfDEDAVPSGVDVSKI--------------S--QEEYLNAPGE---TFSvTlTVP-----GTyGfYcEpH-AGAGmVgKvTVN------ 1.0055 PARS ----aEvKlGSDDGGLVfSPSSfTvA---AGEKiTfKnNa-----GFPhnivfDEDEVPAGVNAEKI--------------S--QPEYLNGAGE---TYEvTlTEK-----GTyKfYcEpH-AGAGmKgEvTVN------ 1.0897 CARROT ----aEvKlGADDGALVfSPSSfSvA---KGEGiSfKnNa-----GFPhnivfDEDEVPAGVDVSKI--------------S--QEDYLDGAGE---SFTvTlTEK-----GTyKfYcEpH-AGAGmKgEvTVN------ 1.0897 SCOB ----aNvKlGADSGALVfEPATvTiK---AGDSvTwTnNa-----GFPhnivfDEDAVPAGVNADAL--------------S--HDDYLNAPGE---SYTaKfDTA-----GEyGyFcEpH-QGAGmVgKvIVQ------ 1.1994 CUKL ---DvTvKlGADSGALVfEPSSvTiK---AGETvTwVnNa-----GFPhnivfDEDEVPSGANAEAL--------------S--HEDYLNAPGE---SYSaKfDTA-----GTyGyFcEpH-QGAGmKgTiTVQ------ 1.1994 A25055 ---AaIvKlGGDDGSLAfVPNNiTvG---AGESiEfInNa-----GFPhnivfDEDAVPAGVDADAI--------------S--AEDYLNSKGQ---TVVrKlTTP-----GTyGvYcDpH-SGAGmKmTiTVQ------ 1.1743 ULAR ---AqIvKlGGDDGALAfVPSKiSvA---AGEAiEfVnNa-----GFPhnivfDEDAVPAGVDADAI--------------S--YDDYLNSKGE---TVVrKlSTP-----GVyGvYcEpH-AGAGmKmTiTVG------ 1.1743 CUAI --ETyTvKlGSDKGLLVfEPAKlTiK---PGDTvEfLnNk-----VPPhnvvfDAALNPAKSADLAK--------------SLSHKQLLMSPGQSTSTTFpAdAPA-----GEyTfYcEpH-RGAGmVgKiTVAG----- 1.5867 AZALCO AQCEaTiEsNDA===MQyNLKEmVvDKSCKQFTvHlKhVgKMAKVAMGhnwvlTKEADKEGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGE===SDSvTfDVSKLTPGEAyAyFcSfPGHWAMmKgTlKLSN===== 1.0061 AZBR AECSvDiAgTDQ---MQfDKKAiEvSKSCKQFTvNlKhTgKLPRNVMGhnwvlTKTADMQAVEKDGIAAGLDNQYLKAGDTRVLAHTKVLGGGE---SDSvTfDVAKLAAGDDyTfFcSfPGHGALmKgTlKLVD----- 0.7861 AZALCX AECSvDiAgNDQ---MQfDKKEiTvSKSCKQFTvNlKhPgKLAKNVMGhnwvlTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGE---TDSvTfDVSKLAAGEDyAyFcSfPGHFALmKgVlKLVD----- 0.7861 AZALCF A-CDvSiEgNDS---MQfNTKSiVvDKTCKEFTiNlKhTgKLPKAAMGhnvvvSKKSDESAVATDGMKAGLNNDYVKAGDERVIAHTSVIGGGE---TDSvTfDVSKLKEGEDyAfFcSfPGHWSImKgTiELGS----- 1.0061 AZPSCA AECSvDiQgNDQ---MQfNTNAiTvDKSCKQFTvNlShPgNLPKNVMGhnwvlSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGE---KDSvTfDVSKLKEGEQyMfFcTfPGHSALmKgTlTLK------ 0.7204 6 AECSvDiQgNDQ---MQfSTNAiTvDKACKTFTvNlShPgSLPKNVMGhnwvlTTAADMQGVVTDGMAAGLDKNYVKDGDTRVIAHTKIIGSGE---KDSvTfDVSKLKAGDAyAfFcSfPGHSAMmKgTlTLK------ 0.7204 AZPSBF AECKtTiDsTDQ---MSfNTKAiEiDKACKTFTvElThSgSLPKNVMGhnlviSKQADMQPIATDGLSAGIDKNYLKEGDTRVIAHTKVIGAGE---KDSlTiDVSKLNAAEKyGfFcSfPGHISMmKgTvTLK------ 0.7472 8 AECKvTvDsTDQ---MSfDTKAiEiDKSCKTFTvDlKhSgNLPKNVMGhnwvlTTQADMQPVATDGMAAGIDKNYLKEGDTRIIAHTKIIGAGE---TDSvTfDVSKLKADGKyMfFcSfPGHIAMmKgTvTLK------ 0.6149 AZPSDF AECKvDvDsTDQ---MSfNTKEiTiDKSCKTFTvNlThSgSLPKNVMGhnwvlSKSADMAGIATDGMAAGIDKDYLKPGDSRVIAHTKIIGSGE---KDSvTfDVSKLTAGESyEfFcSfPGHNSMmKgAvVLK------ 0.7045 A2 AECKvTvDsTDQ---MSfNTKEiTiDKSCKQFTvElThSgNLPKNVMGhnwvlTTQADMQPVATDGMAAGIDKDYLKAGDERIIAHTKIIGAGE---KDSvTfDVSKLKADEKySfFcSfPGHISMmKgAvV-------- 0.6149 A4 AECKvTvDsTDQ---MSfNTKEiTiDKSCKTFTvElThSgSLPKNVMGhnwvvSTDALMQPVATDGMAAGIDKNYLKEGDDIAIAHTKIIGAGE---KDSvTfDVSKLAAGTDyAfFcSfPGHISMmKgTvVI------- 0.5944 A8 AECKvTvDsTDQ---MSfNTKAiEiDKSCKTFTvElThSgNLPKNVMGhnwvlTSAANMQPVATDGMAAGIDKDYLKPGDDRIIAHTKIIGAGE---KDSvTfDVSKLAAGTDyAfFcSfPGHISMmKgTvTVK------ 0.5944 A16 AGCSvDvEaNDA---MQyNTKNiDvEKSCKEFTvNlKhTgSLPKNVMGhnlviTKTADFKAVMNDGVAAGEAGNFVKAGDARVVAHTKLVGGGE---KDSvKvDVSKLAAGEKyTfFcSfPGHATMmRgTvT-------- 1.1023 A17 ASCEtTvTsGDT---MTySTRSiSvPASCAEFTvNfEhKgHMPKTGMGhnwvlAKSADVGDVAKEGAHAGADNNFVTPGDKRVIAFTPIIGGGE---KTSvKfKVSALSKDEAyTyFcSyPGHFSMmRgTlK-------- 1.3360 A18 GNCAaTvEsNDN---MFqNTKDiQvSKACKEFTiTlKhTgTQPKASMGhnlviAKAEDMDGVFKDGVGAA-DTDYVKPDDARVVAHTKLIGGGE---ESSlTlDPAKLADGD-yKfAcTfPGHGALmNgKvT-------- 1.3054 ***** *********** ********** ******* ** ******* ******** ********* 1 2 3 4 5 6 7 8 9 0 1 2 3 1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| 1 2 3 4 5 6 7 8 9 0 1 2 123456789012 3456789012345678901234567890123456789012345678901234567890123456789012345678901 23456789012345678901234567890123456789 pseudoa ENIEVHMLNKGGAMVFEPAYIKAN PGDTVTFIPVD KGHNVESIKDMIPEGAEKFKS KINENYVLTVTQPGAYLVKCTPHYA MGMIALIAVG DSPANLDQIVSAKKP KIVQERLEKVIA