HorA Server Transitive Detail

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


Query <-- 2.121 --> Intermediate <-- 1.922 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1u1ja1) through the intermediate protein (d1rcqa2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1rcqa2 Alanine racemasePLP-​binding barrelTIM beta/​alpha-​barrelα/β
Hit d1u1ja1 5-​methyltetrahydropteroyltriglutamate-​-​homocysteine methyltransferase MetEUROD/​MetE-​likeTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 2.121 --> Intermediate
DALI 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 <-- 1.922 --> Hit
DALI alignment (Z-score: 7.2 Raw score:876.40) d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja1 1 ashivgyprmgpkrelkfalesfwdgkstaedlqkvsadlrssiwkqmsaagtkfipsnt 60 d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja1 61 fahydqvldttamlgavpprygytggeigldvyfsmargnasvpamemtkwfdtnyhyiv 120 d1rcqa2 1 ----------IDLQALRHNYRLAREAtGARALAVIKA----------------------- 27 :::::::::::::::: :::::::::: d1u1ja1 121 pelgpevnfsYASHKAVNEYKEAKAL-GVDTVPVLVGpvsylllskaakgvdksfellsl 179 d1rcqa2 28 -dayGHGAVRCAEALAA-EADGFAVAC---------------ieeGLELReAGIR-QPIL 69 ::::::::::::: ::::::::: ::::: :::: :::: d1u1ja1 180 lpkiLPIYKEVITELKAaGATWIQLDEpvlvmdlegqklqaftgaYAELE-STLSgLNVL 238 d1rcqa2 70 LLE--gfFEASELELIVAH--DFWCVVHC---AWQLEAIERAsLARPLNVWLXMDSGMHr 122 ::: :::::::::::: :::::::: :::::::::: :::::::::::::::: d1u1ja1 239 VETyfadIPAEAYKTLTSLkgVTAFGFDLvrgTKTLDLVKAG-FPEGKYLFAGVVDGRNi 297 d1rcqa2 123 vgfFPEDFRAAHERLRASGkvAKIVMMS--HFSR-ADELDC------------pRTEEQL 167 :::::::::::::::: ::::::: :::: :::::: :::::: d1u1ja1 298 wanDFAASLSTLQALEGIVgkDKLVVSTscSLLHtAVDLINetklddeikswmaFAAQKV 357 d1rcqa2 168 AAFSAASQGLEgeislrnspavlgwpkvpsdwvrpgillygatpferahpladrlrpvm 226 ::::::::::: d1u1ja1 358 VEVNALAKALA----------------------gqkdealfsanaaalasrrssprvtn 394 FAST alignment (Normalized score: 4.71 Raw score:1405.00) d1rcqa2 1 IDL--------------------------------------------------------- 3 d1u1ja1 1 ---ASHIVGYPRMGPKRELKFALESFWDGKSTAEDLQKVSADLRSSIWKQMSAAGTKFIP 57 d1rcqa2 4 ------------------------------------------------------------ 4 d1u1ja1 58 SNTFAHYDQVLDTTAMLGAVPPRYGYTGGEIGLDVYFSMARGNASVPAMEMTKWFDTNYH 117 d1rcqa2 4 ----------------QALRHNYRLAREATGARALAVIKADAYGH--------------- 32 :::::::::::: :::::::: d1u1ja1 118 YIVPELGPEVNFSYASHKAVNEYKEAKA-LGVDTVPV--------LVGPVSYLLLSKAAK 168 d1rcqa2 33 -----------------GAVRCAEALAA-EADGFAVA----------------CIEEGLE 58 ::::::::::: ::::::: ::::::: d1u1ja1 169 GVDKSFELLSLLPKILPIYKEVITELKAAGATWIQL-DEPVLVMDLEGQKLQAFTGAYAE 227 d1rcqa2 59 LREAG--IRQPILLLEGF------FEASELELIVAHD-----FWCVVH----CAWQLEAI 101 ::: ::::::: :::::::::: ::::: :::::::: d1u1ja1 228 LES--TLSGLNVLV----ETYFADIPAEAYKTLT---SLKGVTAFGF-DLVRGTKTLDLV 277 d1rcqa2 102 ERASLA----RPLNVWLAMDSGMHRVGF----------FPEDFRAAHERLRASGKVA--- 144 : :::::::: :::::::::::::: d1u1ja1 278 K-----AGFPEGKYLFAG----------VVDGRNIWANDFAASLSTLQALEG-----IVG 317 d1rcqa2 145 --KIVMMSHFSRADELDCP----------------------------RTEEQLAAFSAAS 174 :::: ::::::::::::: d1u1ja1 318 KDKLVV-------------STSCSLLHTAVDLINETKLDDEIKSWMAFAAQKVVEVNALA 364 d1rcqa2 175 QGLEGEISLRNSPAVLGWPKVPSDWVRPGILLYGATPFERAHPLADRLRPVM-------- 226 :: d1u1ja1 365 KA--------------------------------------------------LAGQKDEA 374 d1rcqa2 227 -------------------- 227 d1u1ja1 375 LFSANAAALASRRSSPRVTN 394 TMalign alignment (TM-score: 0.58 Raw score:131.45) d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja1 1 ASHIVGYPRMGPKRELKFALESFWDGKSTAEDLQKVSADLRSSIWKQMSAAGTKFIPSNT 60 d1rcqa2 1 ------------------------------------------------------------ 1 d1u1ja1 61 FAHYDQVLDTTAMLGAVPPRYGYTGGEIGLDVYFSMARGNASVPAMEMTKWFDTNYHYIV 120 d1rcqa2 1 -----------IDLQALRHNYRLAREATGARALAVIKAD-AYG----------------- 31 ::: ::::::::::::::: :::::::: ::: d1u1ja1 121 PELGPEVNFSYASH-KAVNEYKEAKALGVD-TVPVLVGPVSYLLLSKAAKGVDKSFELLS 178 d1rcqa2 32 ----H--GAVRCAEALAA-EADGFAVAC--I----------EEGLELREA-GI-R-QPIL 69 : ::::::::::: ::::::::: : ::::::::: :: : :::: d1u1ja1 179 LLPKILPIYKEVITELKAAGATWIQLDEPVLVMDLEGQKLQAFTGAYAELESTLSGLNVL 238 d1rcqa2 70 LLEG--FF---EASELELIVAHDFWCVVHC---AWQLEAIERASLARPLNVWLAMDSGMH 121 :::: :: :::::::: :::::::::: :::::::::::: :::::::::::::: d1u1ja1 239 VETYFADIPAEAYKTLTSL-KGVTAFGFDLVRGTKTLDLVKAGFP-EGKYLFAGVVDGRN 296 d1rcqa2 122 R--VGFFPEDFRAAHERLRASGKVAKIVMMS--HF--SRADELDCP------------RT 163 : :::::::::::::::::::::::::: :: ::: ::::: :: d1u1ja1 297 IWA--NDFAASLSTLQALEGIVGKDKLVVSTSCSLLHTAV-DLINETKLDDEIKSWMAFA 353 d1rcqa2 164 EEQLAAFSAASQGLEG-------------------------EISLRNSPAVLGWPKVPSD 198 :::::::::::::::: d1u1ja1 354 AQKVVEVNALAKALAGQKDEALFSANAAALASRRSSPRVTN------------------- 394 d1rcqa2 199 WVRPGILLYGATPFERAHPLADRLRPVM 226 d1u1ja1 395 ---------------------------- 395 HHsearch alignment (Probability: 0.04 E-value:0.08) d1rcqa2 165 EQLAAFSAASQGLE-GEISLRNSPAVLGWP 193 :::::::::::::: ::::::::::::::: d1u1ja1 304 ASLSTLQALEGIVGKDKLVVSTSCSLLHTA 333