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 | d1rcqa2 | Alanine racemase | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1u1ja2 | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
Query <-- 2.121 --> IntermediateDALI alignment (Z-score: 14.6 Raw score:1308.30) query 1 mietpyylidkAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFDLMRDYMDGTT 56 ::::::::::::::::::::::::::::: :::::::::::::::: d1rcqa2 1 -----------IDLQALRHNYRLAREATGARALAVIKADAyghgAVRCAEALAAEADGFA 49 query 57 SSSLFEVRLGRER-FGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADK--aaG 113 ::::::::::::: ::::::::::::::::::::::::::::::::::::::::: : d1rcqa2 50 VACIEEGLELREAgIRQPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERAslarP 109 query 114 IARGLRLNPQ--RLGEWDVpKVERVMDRI--------NGFMIHNNceNKDFGLfdRMLGE 163 :::::::::: ::::::: ::::::::: :::::::: :::::: ::::: d1rcqa2 110 LNVWLXMDSGmhRVGFFPE-DFRAAHERLrasgkvakIVMMSHFS-rADELDC--PRTEE 165 query 164 IEERFGALIA-RVDWVSLGGGIhftgddypvdaFSARlRAFSdrygvQIYLEPGEASI-- 220 :::::::::: ::::::::::: :::: :::: ::::::::::: d1rcqa2 166 QLAAFSAASQgLEGEISLRNSP----------aVLGW-PKVP-----SDWVRPGILLYga 209 query 221 -------------TKSTtlevtvldtlynknlaivdssieahmldlliyretakvlpneg 267 :::: d1rcqa2 210 tpferahpladrlRPVM------------------------------------------- 226 query 268 shsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaire 327 d1rcqa2 227 ------------------------------------------------------------ 227 query 328 ldgsvrtvreftyadyeqsls 348 d1rcqa2 227 --------------------- 227 FAST alignment (Normalized score: 7.57 Raw score:2124.00) query 1 MIETPYYLIDKA-KLTRNMERIAHVREKSGAKALLALKCFA---------TWSVFDLMRD 50 ::::::::::::::::::::::: :::::::::: d1rcqa2 1 ------------IDLQALRHNYRLAREATGARALAV-----IKADAYGHGAVRCAEALAA 43 query 51 YMDGTTSSSLFEVRLGRE-RFGKETHAYSVA----YGDNEIDEVVSHA--DKIIFNSISQ 103 :::::::::::::::::: :::::::: ::::::::::: :::::::::: d1rcqa2 44 EADGFAVACIEEGLELREAGIRQPILL----LEGFFEASELELIVA--HDFWCVVHCAWQ 97 query 104 LERFADKAA------GIARGLRLNP--QRLGEWDVPKVERV------MDRI--NGFMIHN 147 ::::: :::::::::: :::: ::::::::: :::: ::::: : d1rcqa2 98 LEAIE----RASLARPLNVWLXMDSGMHRVG-FFPEDFRAAHERLRASGKVAKIVMMS-H 151 query 148 NCENKDF--GLFDRMLGEIEERFGALIAR-VDWVSLGGGIHFTGDDYPVDAFSARLRAFS 204 ::::::: :::::::::::::::: ::::: d1rcqa2 152 FSRADELDCPRTEEQLAAFSAASQG----LEGEIS------------------------- 182 query 205 DRYGVQ---------------IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAH 249 ::::::::: d1rcqa2 183 ------LRNSPAVLGWPKVPSDWVRPGILL------------------------------ 206 query 250 MLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTM 309 d1rcqa2 207 ------------------------------------------------------------ 207 query 310 VKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-------------------- 348 d1rcqa2 207 ---------------------------------------YGATPFERAHPLADRLRPVM 226 TMalign alignment (TM-score: 0.48 Raw score:167.26) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-F---ATWSVFDLMRDYMDGTT 56 ::::::::::::::::: : ::::::::: : ::::::::::::::::: d1rcqa2 1 --------IDLQALRHNYRLAREAT--G-ARALAVIKADAYGHGAVRCAEALAAEADGFA 49 query 57 SSSLFEVRLGRE-RFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFA-DKA-AG 113 :::::::::::: :::::::::::::::::::::::::::::::::::::::: ::: :: d1rcqa2 50 VACIEEGLELREAGIRQPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERASLARP 109 query 114 IARGLRLNPQ--RLGEWDVPKVERVMD-RI-------NGFMIHNNCENKDFGLFDRMLGE 163 :::::::::: ::::::: ::::::: :: ::::::::::::: :: ::: :: d1rcqa2 110 LNVWLXMDSGMHRVGFFPE-DFRAAHERLRASGKVAKIVMMSHFSRADEL-DC-PRT-EE 165 query 164 IEERFGA-LIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITK 222 ::::::: :::::::::::::::: :: :: :: :: :::::::::::: d1rcqa2 166 QLAAFSAASQGLEGEISLRNSPAV----LG--WP--KV--PS------DWVRPGILLYGA 209 query 223 S------------TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHS 270 : d1rcqa2 210 TPFERAHPLADRL----------------------------------------------- 222 query 271 YMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDG 330 :::: d1rcqa2 223 -------------------------------RPVM------------------------- 226 query 331 SVRTVREFTYADYEQSLS 348 d1rcqa2 227 ------------------ 227 HHsearch alignment (Probability: 0.98 E-value:0.00) query 9 IDKAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFDLMRDYMDGTTSSSLFEVR 64 :::::::::::::::: ::::::::::::: :::::::::::::::::::::::: d1rcqa2 1 IDLQALRHNYRLAREA---TGARALAVIKADAYGHGAVRCAEALAAEADGFAVACIEEGL 57 query 65 LGRERFGKETHAYSVAY-GDNEIDEVVSHADKIIFNSISQLERFADKA--AGIARGLRLN 121 ::::::::::::::::: :::::::::::::::::::::::::::::: :::::::::: d1rcqa2 58 ELREAGIRQPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERASLARPLNVWLXMD 117 query 122 P--QRLGEWDVPKVERV-------MDRINGFMIHNNCEN-KDFGLFDRMLGEIEERFGAL 171 : :::::::::::::: ::::::::::::::: :::::::::::::::::::: d1rcqa2 118 SGMHRVGFFPEDFRAAHERLRASGKVAKIVMMSHFSRADELDCPRTEEQLAAFSAASQGL 177 query 172 IARVDWVSLGGGIHFTGDDYPVDAFSARL 200 ::::::::::::::::::::::::::::: d1rcqa2 178 EGEISLRNSPAVLGWPKVPSDWVRPGILL 206
Intermediate <-- 1.360 --> HitDALI alignment (Z-score: 7.3 Raw score:851.70) d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja2 1 egvqkaaaalkgsdhrratnvsarldaqqkklnlpilptttigsfpqtvelredyvkaik 60 d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja2 61 eeikkvvdlqeeldidvlvhgeperndmveyfgeqlsgfaftangwvqsygsrcvkppvi 120 d1rcqa2 1 ------IDLQaLRHNYRLAREATGARALAVIKAD--------------------ayghGA 34 :::: ::::::::::::::::::::::: :: d1u1ja2 121 ygdvsrPKAM-TVFWSAMAQSMTSRPMKGMLTGPvtilnwsfvrndqprhetcyqialAI 179 d1rcqa2 35 VRCAEALAA-EADGFAVAC---------------------iEEGLELReAGIR--QPILL 70 ::::::::: ::::::::: ::::::: :::: ::::: d1u1ja2 180 KDEVEDLEKgGIGVIQIDEaalreglplrksehafyldwavHSFRITN-CGVQdsTQIHT 238 d1rcqa2 71 LE-gfFEASELELIVAHDF-WCVVHC-AWQLEAIERAS--LARPLNVWLX-MDSGMhrvg 124 :: :::::::::::::: :::::: ::::::::::: :::::::::: ::::: d1u1ja2 239 HMcysHFNDIIHSIIDMDAdVITIENsRSDEKLLSVFRegVKYGAGIGPGvYDIHS-pri 297 d1rcqa2 125 ffPEDFRAAHERLRASGKVAKIVMMS--HFSRAdeldcpRTEEQLAAFSAASQGLEgeis 182 :::::::::::::::::::::::: ::::: ::::::::::::::::: d1u1ja2 298 psSEEIADRVNKMLAVLEQNILWVNPdcGLKTR------KYTEVKPALKNMVDAAK---- 347 d1rcqa2 183 lrnspavlgwpkvpsdwvrpgillygatpferahpladrlrpvm 226 d1u1ja2 348 ---------------------------------------lirsq 352 FAST alignment (Normalized score: 2.97 Raw score:837.70) d1rcqa2 1 IDLQALRHNYRLAREATGARALAVIKADAYGHGAVRCAEALAAEADGFAVACIEEGLELR 60 d1u1ja2 1 ------------------------------------------------------------ 1 d1rcqa2 61 EAGI-----------------------------------RQPILLLEGFF---------- 75 :::::: d1u1ja2 1 ----EGVQKAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTT-----IGSFPQTVEL 51 d1rcqa2 76 ------EASELELIVAHDFWCVVHCA---------------------------------- 95 :::::::::: d1u1ja2 52 REDYVKAIKEEIKKVV----------DLQEELDIDVLVHGEPERNDMVEYFGEQLSGFAF 101 d1rcqa2 96 ----------------------------WQLEAIER--ASLARPLNVWLAMDSGMHRVGF 125 :::::::: ::::::::::::: d1u1ja2 102 TANGWVQSYGSRCVKPPVIYGDVSRPKAMTVFWSAMAQSMTSRPMKGMLTG--------- 152 d1rcqa2 126 ----------------------FPEDFRAAHERLRASGKVAKIVMMSHFSRA-------- 155 ::::::::::::::: ::::::::: d1u1ja2 153 PVTILNWSFVRNDQPRHETCYQIALAIKDEVEDLEKG-GIGVIQIDE-----AALREGLP 206 d1rcqa2 156 DELD--CPRTEEQLAAFSAASQGL----EGEISLRNSPA-----VLGWPK----VPSDWV 200 :::: :::::::::::::::::: ::::: :::::: :::::: d1u1ja2 207 LRKSEHAFYLDWAVHSFRITNCGVQDSTQIHTH------MCYSHFNDIIHSIIDMDADVI 260 d1rcqa2 201 RPGILLYGATPFERAHPLADRLRPVM---------------------------------- 226 :: d1u1ja2 261 TI------------------------ENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPR 296 d1rcqa2 227 -------------------------------------------------------- 227 d1u1ja2 297 IPSSEEIADRVNKMLAVLEQNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLIRSQ 352 TMalign alignment (TM-score: 0.57 Raw score:129.59) d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja2 1 EGVQKAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTTIGSFPQTVELREDYVKAIK 60 d1rcqa2 1 ----------------------------------I------------------------- 1 : d1u1ja2 61 EEIKKVVDLQEELDIDVLVHGEPERNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPVI 120 d1rcqa2 2 ------DLQALRHNYRLAREATG-ARALAVIK--ADA-YG-------------HGAVRCA 38 ::::::::::::::::: :::::::: ::: :: ::::::: d1u1ja2 121 YGDVSRPKAMTVFWSAMAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRHETCYQIALAIK 180 d1rcqa2 39 EALAA-E---A-DGFAV-A-CI-------------E--EGLELREAGI-R----QPILLL 71 ::::: : : ::::: : :: : :::::::::: : :::::: d1u1ja2 181 DEVEDLEKGGIGVIQIDEAALREGLPLRKSEHAFYLDWAVHSFRITNCGVQDSTQIHTHM 240 d1rcqa2 72 EGFFEASELELIVAHDF-WCVVHC-AWQLEAIER-AS-LARPLNVWLAMDSGMHR-VGFF 126 ::::::::::::::::: :::::: ::::::::: :: ::::::::::::::::: :: d1u1ja2 241 CYSHFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPR--IP 298 d1rcqa2 127 P-EDFRAAHERLRASGKVAKIVMMS--HFSRADELDCPRTEEQLAAFSAASQGLEG---- 179 : ::::::::::::::::::::::: ::::: :::::::::::::::::: d1u1ja2 299 SSEEIADRVNKMLAVLEQNILWVNPDCGLKTR------KYTEVKPALKNMVDAAKLIRSQ 352 d1rcqa2 180 EISLRNSPAVLGWPKVPSDWVRPGILLYGATPFERAHPLADRLRPVM 226 d1u1ja2 353 ----------------------------------------------- 353 HHsearch alignment (Probability: 0.02 E-value:0.65) d1rcqa2 141 GKVAKIVMMS-HFSRADELDCPRTEEQLAAFSAASQGLEGEISLRN 185 :::::::::: ::::: :: ::::::::::::::::::::::: d1u1ja2 282 GAGIGPGVYDIHSPRI---PS--SEEIADRVNKMLAVLEQNILWVN 322