========= Reference ========= M Gerstein, E Sonnhammer, C Chothia (1994). "Volume Changes in Protein Evolution," J. Mol. Biol. (in press) ===== Notes ===== This alignment contains 24 dihydrofolate reductase sequences based on 4 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 '$' 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 core postions were determined from surface area calculations on the structures. The '1' and '0's in the four 'xxxx surf' lines give the surface area at each sequence position in the four key structures: 0=0-9 Square Angstroms, 1=10-19 Sq. Angstrom, and so on. The numbers to the right of each sequence are the weights assigned to the sequence by the tree weighting procedure described in the paper. To simplify the presentation of the alignment -- i.e. so it would not take up too many columns -- the tails of two of the sequences were clipped. DYR_HSVSC: Add at end LFKSHAGLTCSVKPKEASYDFELS DYR_BACSU: Add at end VGGF Likewise, to lower the number of columns, sections were clipped out of the middle of two sequences. DYR_PNECA: PHGKINEDGF insert at '+' in WVGTKV+D DYR_YEAST: SEQDPAQLKEFLPPKV insert at '&' in LEEVF&ELPETD =============================================================================== #SEQ 0 1 1 1 1 1 1 1 1 1 1 2 2 2 2 #SEQ 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 #SEQ 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890 #CHC 1 1 1 1 1 1 1 1 1 #CHC 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 #CHC 123 456789012 34567890123456 78901234567 8901234567 8901234567890 1234567890 123456 78901234567 89012345678901 234567890 123456789012345 67890 123456789012345678901234567 8901234567890123456 7890123456789 #CORE $$$$$$$ $$$ $ $ $ $$ $ $$$$$ $$ $ $ $ $$$$$ $ $ $ $ $ $ $$$$$$ $$ $ $$$$ $ $ $ $ $ $$ #SS ********* *********** ************* ****** *** ********** ***** ********* ********** * * ******** # 1dh1 surf 1000000 0 1 10 0 0 00 0 000001 10 0 0 0 100010 1 1 0 0 01 2 2 1 20000 10 0 0 0000 0 1 4 0 0 1 1 0 01 # 8dfr surf 01000000 000 11 1 2 04 0 000000 00 2 2 1 000000 1 1 0 0 01 0 0 1 000000 00 01 0 0000 0 2 1 1 0 2 3 0 01 # 3dfr surf 1000010 1100 0 01 0 0 00000 00 0 0 00000 1 1 1 3 06 2 91000001 00 09 0 6 0100 0 0 2 22 1 0200 3 # 4dfr surf 0000100 00 0 0 00 0 00000 1 1 0 000 1 3 1 1 2 05 0 11000020 10 02 0 9 0000 1 0 3 01 1 0 0105 1 DYR_HUMAN ===VGS==LncIvavsQ==NMgigKNGDLPwPP=lRNeFRyfQRM=tTTSSVEGKQ=====NlvimgKKtwFSi==PEKNRPlKGr==Inlvls======RELKEPpQGaH==FLsRSlDDaLKLtE==QPELANKVD=====MvwivggSSvyKEaM==NHPGH===LKlfvtRiMQDFESDTFfPEIDLEKyK=LLPEYPGVLSDVQEEKGIK====yKfEvyEKND===== 0.6056 DYR_CHICK ===VRS==LnsIvavcQ==NMgigKDGNLPwPP=lRNeYKyfQRM=tSTSHVEGKQ=====NavimgKKtwFSi==PEKNRPlKDr==Inivls======RELKEApKGaH==YLsKSlDDaLALlD==SPELKSKVD=====MvwivggTAvyKAaM==EKPIN===HRlfvtRiLHEFESDTFfPEIDYKDfK=LLTEYPGVPADIQEEDGIQ====yKfEvyQKSVLAQ== 0.8080 DYR_BOVIN ---VRP--LncIvavsQ--NMgigKNGDLPwPP-lRNeFQyfQRM-tTVSSVEGKQ-----NlvimgRKtwFSi--PEKNRPlKDr--Inivls------RELKEPpKGaH--FLaKSlDDaLELiQ--DPELTNKVD-----VvwivggSSvyKEaM--NKPGH---VRlfvtRiMQEFESDAFfPEIDFEKyK-LLPEYPGVPLDVQEEKGIK----yKfEvyEKNN----- 0.6148 DYR_PIG ---VRP--LncIvavsQ--NMgigKNGDLPwPP-lRNeYKyfQRM-tTTSSVEGKQ-----NlvimgRKtwFSi--PEKNRPlKDr--Inivls------RELKEPpQGaH--FLaKSlDDaLKLtE--QPELKDKVD-----MvwivggSSvyKEaM--NKPGH---IRlfvtRiMKEFESDTFfPEIDLEKyK-LLSECSGVPSDVQEEKGIK----yKfEvyEKNN----- 0.5920 DYR_MOUSE ---VRP--LncIvavsQ--NMgigKNGDLPwPP-lRNeFKyfQRM-tTTSSVEGKQ-----NlvimgRKtwFSi--PEKNRPlKDr--Inivls------RELKEPpRGaH--FLaKSlDDaLRLiE--QPELASKVD-----MvwivggSSvyEQaM--NEPGH---LRlfvtRiMQEFESDTFfPEIDLGKyK-LLPEYPGVLSEVQEEDGIK----yKfEvyEKKD----- 0.5651 DYR_MESAU ---VRP--LncIvavsQ--NHgigKNGDFPwPM-lRNeFKyfQRM-tTTSSVEGKQ-----NlvimgRKtwFSi--PEKNRPlKDr--Inivls------RELKEPpQGaH--FLaKSlDDaLKLiE--QPELADKVD-----MvwivggSSvyKEaM--NQPGH---LRlfvtRiMQEFESDTFfPEIDLEKyK-LLPEYPGVLSEVQEEKGIK----yKfEvyEKKG----- 0.5651 DYR_HSVS7 ---MVLL-LncIvavdQ--NMgigKNGYLPwPL-lTNdFKyfQRM-tT-SSVKNKQ-----NlvimgKNtwFSi--PEKNRPlKDr--Inlvls------KKLKEIpHGaH--FLaRSlNDaLKLiE--QPEFVNKVD-----MvwiiggSSvyKDaM--NYSSH---LKlfvtRiMQSFETDTFfPEIDLKKyK-PLIEYPGVPSNTQEEKGIR----yKfEvyEKNY----- 0.6070 DYR_HSVSA ---MVQA-LncIvavaQ--NMgigKQGNLPwPR-lMNdFKhfQRM-tTTSSVPDKQ-----NlvimgKKtwFSi--PEKNRPlKGr--Invvls------KELKELpHRaH--FLaKSlDDaLKLtE--QPELANKVD-----MvwiiggSSvyKEaM--SYPCD---LKlfvtRiMQDFECDTFfPEFDLEKyK-LLIEYPSVLSNVQEEKSIK----yKfEvyEKNH----- 0.7216 DYR_HSVSC ---MVLL-LncIvavdQ--NMgigKKGHLPwPL-lINdFKyfQRM-tT-SSVKNKQ-----NlvimgKNtwFSi--PEKNRPlKDr--Inlvls------KKLKEIpHGaH--FLaRSlNDaLKLiE--QPELVNKVD-----RvwiiggSSvyKDaM--NYSSH---LKlfvtRiMQSFETDTFfPEIDLKNyK-LLIEYPGVPSNTQEEKGIK----yKfEvyEKIVNTF-- 0.6070 DYR_AEDAL ---MKK--FslIvavcA--NGgigIKGDLPwR--lRQeLKyfSRM-tKKIQDSGKR-----NaiimgRKtyFGv--PESKRPlPEr--Lniilt---------RDPsANaY--PSeVMvCTsMQEaL--KKLDEAPLVNEIE-NvwivggNAvyKEaM--QSDRC---HRiyltEiKETFECDAFfPEITSDFqL--VKNDDDVPEDIQEENGIQ----yQyRiyEKVPK---- 1.2095 DYR_PNECA -MNQQKS-LtlIvaltT--SYgigRSNSLPwK--lKKeISyfKRV-tSFVPTFDSFESM--NvvlmgRKtwESi--PLQFRPlKGr--Invvit-----RNESLDLgNGi---HSaKSlDHaLELlY--RTYGSESSVQIN--RifviggAQlyKAaM--DHPKL---DRimatIiYKDIHCDVFfPLKFRDKeW-SSVWKKEKHSDLESWVGTKV-D-yEfEmwTRDL----- 1.2703 DYR_YEAST MAGGKIP-IvgIvaclQ-PEMgigFRGGVPwR--lPSeMKyfRQV-tSLTKDPNKK-----NalimgRKtwESi--PPKFRPlPNr--Mnviis-RSFKDDFVHDKeRSi---VQsNSlANaIMNlE--SNFKEHLE------RiyviggGEvySQiF-SITDHWLI-TKinplDkNATPAMDTFlDAKKLEEvF-ELPETDCDQRYSLEEKG------yCfEftLYNRK---- 1.3062 DYR_LACCA ========TafLwaqdR==DGligKDGHLPwH==lPDdLHyfRAQ=tV============GKimvvgRRtyESf====PKRPlPEr==Tnvvlt======HQEDYQaQGa===VVvHDvAAvFAYaK==QHLDQ=========ElviaggAQifTAfK==DDV=====DTllvtRlAGSFEGDTKmIPLNWDDfT====KVSSRT===VEDTNPALT==hTyEvwQKKA===== 1.3334 DYRA_ECOLI =====M==IslIaalaV==DRvigMENAMPwN==lPAdLAwfKRN=tL============NKpvimgRHtwESi====G=RPlPGr==Kniils=======SQPGTdDRv===TWvKSvDEaIAAcG==DVP===========EimviggGRvyEQfL==PKA=====QKlyltHiDAEVEGDTHfPDYEPDDwE====SVFSEF===HDADAQNSHS=yCfEilERR====== 1.0774 DYRB_ECOLI -----MK-LslMvaisK--NGvigNGPDIPwS--aKGeQLlfKAI-tY------------NQwllvgRKtfESm------GAlPNr--Kyavvt-----RSSFTSDnENv---LIfPSiKDaLTNlK--KITD----------HvivsggGEiyKSlI--DQV-----DTlhisTiDIEPEGDVYfPEIPSNFrP----VFTQDF---ASNIN------ySyQiwQKG------ 1.0518 DYRC_ECOLI -----MK-VslMaakaK--NGvigCGPHIPwS--aKGeQLlfKAL-tY------------NQwllvgRKtfESm------GAlPNr--Kyavvt-----RSAWTADnDNv---IVfPSiEEaMYGlA--ELTD----------HvivsggGEiyREtL--PMA-----STlhisTiDIEPEGDVFfPNIPNTFeV----VFEQHF---SSNIN------yCyQiwQKG------ 1.0518 DYR7_ECOLI -----MK-IslIsatsE--NGvigNGPDIPwS--aKGeQLlfKAL-tY------------NQwllvgRKtfDSm------GVlPNr--Kyavvs-----RKGISSSnENv---LVfPSiEIaLQElS--KITD----------HlyvsggGQiyNSlI--EKA-----DIihlsTvHVEVEGDINfPKIPENFnL----VFEQFF---LSNIN------yTyQiwKKG------ 1.0973 DYR_NEIGO ----MLK-ItiIaacaE--NLcigAGNAMPwH--iPEdFAffKVY-tL------------GKpvimgRKtwESl----PVKPlPGr--Rnivis------RQADYCaAGa---ETvASlEVaLALcA--GAE-----------EavimggAQiyGQaM--PLA-----TDlritEvDLSVEGDAFfPEIDRTHwR----EAERTE--RRVSSKGVA---yTfVhyLGK------ 1.2848 DYR3_SALTY ---ML---IslIaalaH--NNligKDNLIPwH--lPAdLRhfKAV-tL------------GKpvvmgRRtfESi-----GRPlPGr--Rnvvvs----RNPQWQAEgVEv---APsLDaALaLLTdC--E-------------EamiiggGQlyAEaL--PRA-----DRlyltYiDAQLNGDTHfPDYLSLGwQ----ELERST--HPADDKNS----yAcEfvTLSRQR--- 1.2252 DYRA_KLEAE ----M---IslIaalrV--DRvigMENAMPwN--lNEdLAwfKRN-tL------------NKpvvmgRLtwESi-----GRPlPGr--Knivis----SKPGSDDRvQWv---SSvEEaIAaCGDvE----------------EimviggGRvyDEfL--PKA-----QKlyltHiDAEVEGDTHfPDYDPDEwE----SVFSEF--HDADAQNSHS--yCfEilERR------ 1.0774 DYRA_STAAU ----MT--LsiIvahdK--QRvigYQNQLPwH--lPNdLKhiKQL-tT------------GNtlvmaRKtfNSi-----GKPlPNr--Rnvvlt-------NQASFhHEg---VDvINsLDeIKElS----------------HvfifggQTlyEAmI--DQV-----DDmyitViDGKFQGDTFfPPYTFENwE-VESSVEGQL--DEKNTIP-----hTfLhlVRRKGK--- 1.2815 DYR_BACSU ----M---IsfIfamdA--NRligKDNDLPwH--lPNdLAyfKKI-tS------------GHsiimgRKtfESi-----GRPlPNr--Knivvt----SAPDSEFQgCTv---TVvSSlKDvLDIcS--GPE-----------EcfviggAQlyTDlF--PYA-----DRlymtKiHHEFEGDRHfPEFDESNwK-LVSSEQGTK--DEKNPYD-----yEfLmyEKKNSSK-- 1.2815 DYR_HALVO ----ME--LvsVaalaE--NRvigRDGELPwPS-iPAdKKqyRSR-iA------------DDpvvlgRTtfESm-----RDDlPGs--Aqivms--RSERSFSVDTaHRa---ASvEEaVDiAASlD--AE------------TayviggAAiyALfQ--PHL-----DRmvlsRvPGEYEGDTYyPEWDAAEwE------LDAETDHEG---------fTlQewVRSASSR-- 1.4325 DYR_ENTFC ----MF--Ism-waqdK--NGligKDGLLPwR--lPNdMRffREH-tM------------DKilvmgRKtyEGm----GKLSlPYr--Hiivlt-----TQKDFKVeKNa---EVlHSiDElLAYaK--DIPE----------DiyvsggSRifQAlL--PET-----KIiwrtLiDAEFEGDTFiGEIDFTSfE----LVEEHEGI-VNQENQYP---hRfQkwQKMSKVV-- 1.3334 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