Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1geqa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1u0sy_ | CheY protein | CheY-like | Flavodoxin-like | α/β |
Query <-- 0.983 --> IntermediateDALI alignment (Z-score: 9.7 Raw score:956.80) query 1 mietpyylidkakltrnmeriahvreksGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 ::::::::: ::::::::::::::: d1geqa_ 1 -------------------------mfkDGSLIPYLTagdpdkqsTLNFLLALDEYAGAI 35 query 56 TSSS--------------------------lFEVRLGRER---fGKETHAYSVA------ 80 :::: ::::::::: :::::::::: d1geqa_ 36 ELGIpfsdpiadgktiqeshyralkngfklrEAFWIVKEFrrhsSTPIVLMTYYnpiyra 95 query 81 yGDNEIDEVVS-HADKIIFNSIS--QLERFADKAA--GIARGLRLNPQrlgeWDVPKVER 135 :::::::::: ::::::::::: :::::::::: ::::::::::: :::::::: d1geqa_ 96 gVRNFLAEAKAsGVDGILVVDLPvfHAKEFTEIAReeGIKTVFLAAPN----TPDERLKV 151 query 136 VMDRIN-GFMIHNNCenkdfgLFDRMLGEIEERFGALIarVDWVSLGGGIHFtgddypvD 194 :::::: :::::::: ::::::::::::::::: :::::::::::: : d1geqa_ 152 IDDMTTgFVYLVSLY------EIPKTAYDLLRRAKRIC--RNKVAVGFGVSK-------R 196 query 195 AFSARLRAFSdrygvqIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldll 254 :::::::::: :::::::::::::: d1geqa_ 197 EHVVSLLKEG-----aNGVVVGSALVKIIG------------------------------ 221 query 255 iyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknw 314 :::: d1geqa_ 222 ------------------------------------------------EKGR-------- 225 query 315 fngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1geqa_ 226 ------------------eateflkkkveellgi 241 FAST alignment (Normalized score: 5.72 Raw score:1657.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG----AKALLALKCFA----------TWSVFD 46 :::::: :::::: d1geqa_ 1 -----------------------------MFKDGSLIPY-----LTAGDPDKQSTLNFLL 26 query 47 LMRDYMDGTTSS------------------------------SLFEVRLGRERFGKETHA 76 ::::::::::: :::::::::::::::::: d1geqa_ 27 ALDEYAGAIEL-GIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVL 85 query 77 YSVAY---------GDNEIDEVVS-HADKIIFN--SISQLERFADKA---AGIARGLRLN 121 :: :::::::::: :::::::: ::::::::::: :::::::::: d1geqa_ 86 MT---YYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEI-AREEGIKTVFLAA 141 query 122 PQRLGE-WDVPKVERVMDR-INGFMIHNNCENKD------FGLFDRMLGEIEERFGALIA 173 : :::::::::::: :::::: :::::::::::::: d1geqa_ 142 P-----NTPDERLKVIDDMTTGFVYL--------VSLYEIPKTAYDLLRRAKRI------ 182 query 174 RV--DWVSLGGGIHFTGDDYPVDA-----FSARLRAFSDRYGVQIYLEPGEASITKSTTL 226 ::::: :::::::::: ::: ::::::::: d1geqa_ 183 --CRNKVAV---------------GFGVSKREHVVSLLK-EGA-NGVVVGSAL------- 216 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1geqa_ 217 ------------------------------------------------------------ 217 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1geqa_ 217 ------------------------------------------------------------ 217 query 347 LS------------------------- 348 d1geqa_ 217 --VKIIGEKGREATEFLKKKVEELLGI 241 TMalign alignment (TM-score: 0.43 Raw score:149.14) query 1 --MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF--A-T-WSVFDLMRDYMDG 54 : :::::::::::: : : ::::::::::::: d1geqa_ 1 MF-------------------------K-DGSLIPYLTAGDPDKQSTLNFLLALDEYAGA 34 query 55 TTSSS-------------------------LFEVRLGRERF---G-KETHAYSVA--YG- 82 ::::: ::::::::::: : ::::::::: :: d1geqa_ 35 IELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYR 94 query 83 --D-NEIDEVVS-HADKIIFN-S-ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVE 134 : :::::::: :::::::: : :::::::::::: ::::::::::: ::::::: d1geqa_ 95 AGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPN----TPDERLK 150 query 135 RVMDRIN-GFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPV 193 ::::::: :::::::: :::::::::::::::: ::::::::::::: : d1geqa_ 151 VIDDMTTGFVYLVSLY------EIPKTAYDLLRRAKRI--CRNKVAVGFGVSK------R 196 query 194 DAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::::::: ::::: :::::::: : : d1geqa_ 197 -EHVVSLLKEG----ANGVV-VGSALVKI-I-------------------------G--- 221 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 ::: d1geqa_ 222 -------------------------------------------------EKG-------- 224 query 314 WFNGVKMPAIAIRE------------LDGSVRTVREFTYADYEQSLS 348 ::::: d1geqa_ 225 ---------REATEFLKKKVEELLGI--------------------- 241 HHsearch alignment (Probability: 0.07 E-value:0.12) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRD---------YMDGTTSSSLFEVRLGRER 69 :::::::::::::::::::::::::::::::: ::::::::::::::::::: d1geqa_ 123 KEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRI 182 query 70 FGKETHAYSVAYGDNEIDEVVS-HADKIIFNS 100 :::::::::::::::::::::: ::::::::: d1geqa_ 183 CRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 214
Intermediate <-- 1.135 --> HitDALI alignment (Z-score: 4.8 Raw score:439.20) d1geqa_ 1 mfkdGSLIPYLT---------------------agdPDKQSTLNFLLALDeyAGAIELGI 39 :::::::: :::::::::::::: :::::::: d1u0sy_ 1 ----GKRVLIVDdaafmrmmlkdiitkagyevageaTNGREAVEKYKELK--PDIVTMDI 54 d1geqa_ 40 PFsdpiadgktiqeshyralkngfKLREAFWIVKEFRRHS-STPIVLMTYYNPIyragvr 98 :: :::::::::::::::: ::::::::::::: d1u0sy_ 55 TM----------------------PEMNGIDAIKEIMKIDpNAKIIVCSAMGQQ------ 86 d1geqa_ 99 NFLAEAKASGVDGILVVDlpvfhakefteiareegiktvFLAApntpderlkviddmTTG 158 :::::::::::::::::: :::: ::: d1u0sy_ 87 AMVIEAIKAGAKDFIVKP---------------------FQPS------------rvVEA 113 d1geqa_ 159 FVylvslyeipktaydllrrakricrnkvavgfgvskrehvvsllkegangvvvgsalvk 218 :: d1u0sy_ 114 LN---------------------------------------------------------- 115 d1geqa_ 219 iigekgreateflkkkveellgi 241 d1u0sy_ 116 --------------------kvs 118 FAST alignment (Normalized score: 4.90 Raw score:826.30) d1geqa_ 1 MFKDGSLIPYLTAG-------------------------DPDKQSTLNFLLALDE-YAGA 34 :::::: ::::::::::::: :::: d1u0sy_ 1 ----GKRVLI----VDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKE---LKPDI 49 d1geqa_ 35 IELGIPFSDPIADGKTIQESHYRALKNGFKLR------EAFWIVKEFRRHS-STPIVLMT 87 :::: ::::::::::::: :::::::: d1u0sy_ 50 VTMD----------------------------ITMPEMNGIDAIKEIMKIDPNAKIIVCS 81 d1geqa_ 88 YYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDE 147 ::: ::::::::::::::::::: d1u0sy_ 82 AMG------QQAMVIEAIKAGAKDFIVK-------------------------------- 103 d1geqa_ 148 RLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGA 207 d1u0sy_ 104 ------------------------------------------------------------ 104 d1geqa_ 208 NGVVVGSALVKIIGEKGREATEFLKKKVEELLGI--------------- 241 d1u0sy_ 104 ----------------------------------PFQPSRVVEALNKVS 118 TMalign alignment (TM-score: 0.31 Raw score:74.29) d1geqa_ 1 M--------FKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQ 52 : :::: :: d1u0sy_ 1 GKRVLIVDD-------------------------------------------AAFM--RM 15 d1geqa_ 53 ESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTY-YNPIYRAGVRNFLAEAKASGVDG 111 : :::: : : ::: d1u0sy_ 16 --M-----------------------------LKDII------------T--K----AGY 26 d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLA-APNTPDERLKVIDDMTTGFVYLVSLYEIPK 170 :: :::: :::::::::::: : :: :::::: ::::: d1u0sy_ 27 EV-----------------------AGEATNGREAVEKYKEL-K-PD-IVTMDI-TMPEM 59 d1geqa_ 171 TAYDLLRRAKRIC-RNKVAVGFGVSK-REHVVSLLKEGANGVVVGSALV----------- 217 ::::::::::::: ::::::: :::: ::::::::::::::::::: :: d1u0sy_ 60 NGIDAIKEIMKIDPNAKIIVC-SAMGQQAMVIEAIKAGAKDFIVKP-FQPSRVVEALNKV 117 d1geqa_ 218 -KIIGEKGREATEFLKKKVEELLGI 241 d1u0sy_ 118 S------------------------ 118 HHsearch alignment (Probability: 0.84 E-value:0.00) d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLY-EIPK 170 ::::::::::::::::::::::::::::: :::::::::::::::::::::::: :::: d1u0sy_ 4 VLIVDDAAFMRMMLKDIITKAGYEVAGEA--TNGREAVEKYKELKPDIVTMDITMPEMNG 61 d1geqa_ 171 TAYDLLRRAKR-ICRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 214 ::::::::: ::::::::::::::::::::::::::::::::: d1u0sy_ 62 --IDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKP 104