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 <-- 1.875 --> Intermediate <-- 1.717 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1to3a_) through the intermediate protein (d1m5wa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1m5wa_ Pyridoxine 5'​-​phosphate synthasePyridoxine 5'​-​phosphate synthaseTIM beta/​alpha-​barrelα/β
Hit d1to3a_ Putative aldolase YihTAldolaseTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.875 --> Intermediate
DALI alignment (Z-score: 11.1 Raw score:1066.10) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCFA------------TWSVFDLM 48 :::::::::::: :::::::: d1m5wa_ 1 ---------------------------aELLLGVNIDHIAtlrnargtaypdPVQAAFIA 33 query 49 RD-YMDGTTSSS--------LFEVRLGRERFGKETHAYSVaYGDNEIDEVVSH-ADKIIF 98 :: ::::::::: :::::::::::::::::::: :::::::::::: :::::: d1m5wa_ 34 EQaGADGITVHLredrrhitDRDVRILRQTLDTRMNLEMA-VTEEMLAIAVETkPHFCCL 92 query 99 N-----------------sISQLERFADKAA--GIARGLRLNPqrlgewDVPKVERVMD- 138 : :::::::::::: :::::::::: :::::::::: d1m5wa_ 93 VpekrqevtteggldvagqRDKMRDACKRLAdaGIQVSLFIDA------DEEQIKAAAEv 146 query 139 RINGFMIHNNceNKDFG--LFDRMLGEIEERFGALIARVDWVSLGGGIHFtgddypvdaF 196 :::::::::: ::::: ::::::::::::::::::::::::::::::: : d1m5wa_ 147 GAPFIEIHTGcyADAKTdaEQAQELARIAKAATFAASLGLKVNAGHGLTY--------hN 198 query 197 SARLRAFSdrygVQIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldlliy 256 :::::::: :::::::::::::::: d1m5wa_ 199 VKAIAAIP----EMHELNIGHAIIGRAV-------------------------------- 222 query 257 retakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfQDAAgytmvkknwfn 316 :::: d1m5wa_ 223 ---------------------------------------------MTGL----------- 226 query 317 gvkmpaiaireldgsvrtvreftyadyeqsls 348 d1m5wa_ 227 ----------------kdavaemkrlmlearg 242 FAST alignment (Normalized score: 6.41 Raw score:1859.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALKCFA--------------TWSVF 45 :::::::::: ::::: d1m5wa_ 1 ----------------------------AELLLGVNIDH--IATLRNARGTAYPDPVQAA 30 query 46 DLMR-DYMDGTTS--------SSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVS-HADK 95 :::: :::::::: ::::::::::::::::::::: :::::::::::: :::: d1m5wa_ 31 FIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEM-AVTEEMLAIAVETKPHF 89 query 96 IIFN------------------SISQLERFADKA---AGIARGLRLNPQRLGEW----DV 130 ::: ::::::::::: :::::::::: :: d1m5wa_ 90 CCL-VPEKRQEVTTEGGLDVAGQRDKMRDACKR-LADAGIQVSLFID-------ADEEQI 140 query 131 PKVERVMD-RINGFMI--HNNCENKDFGLFDRMLGEIEERFGALIARV--DWVSLGGGIH 185 ::::: ::::::: :::::::::::::::::::::::::::: ::::::::: d1m5wa_ 141 KAAAE---VGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAAS--LGLKVNAGHGL- 194 query 186 FTGDDYPVDA---FSARLRAFSDRYGVQ----IYLEPGEASITKSTTLEVTVLDTLYNKN 238 ::::::: ::::::::: d1m5wa_ 195 ----------TYHNVKAIAA--------IPEMHELNIGHAI------------------- 217 query 239 LAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDR 298 d1m5wa_ 218 ------------------------------------------------------------ 218 query 299 ISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS---------- 348 d1m5wa_ 218 --------------------------------------------------IGRAVMTGLK 227 query 349 --------------- 349 d1m5wa_ 228 DAVAEMKRLMLEARG 242 TMalign alignment (TM-score: 0.43 Raw score:150.40) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFA------------TWSVFDLM 48 ::::::::::::: :::::::: d1m5wa_ 1 ---------------------------AELLLGVNIDHIATLRNARGTAYPDPVQAAFIA 33 query 49 RD-YMDGTTSSS-------LF-EVRLGRERFGKETHAYSVAYGDNEIDEVV-SHADKIIF 98 :: ::::::::: :: :::::::::::::::::::: :::::::: :::::::: d1m5wa_ 34 EQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVT-EEMLAIAVETKPHFCCL 92 query 99 -------------NSI--S--QLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDR 139 ::: : :::::::::: :::::::::: :::::::::::: d1m5wa_ 93 VPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDA-----DEEQIKAAAEVG 147 query 140 INGFMIHNNCENKD--FG-LFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAF 196 :::::::::::::: : ::::::::::::::::::::::::::::::: ::: : d1m5wa_ 148 APFIEIHTGCYADAKT-DAEQAQELARIAKAATFAASLGLKVNAGHGLTY----HNV--K 200 query 197 SARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIY 256 : ::: :: : ::::::::::::::: d1m5wa_ 201 A-IAA-IP--E--MHELNIGHAIIGRAV-------------------------------- 222 query 257 RETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAG---------- 306 :::: d1m5wa_ 223 ----------------------------------------------MTGLKDAVAEMKRL 236 query 307 ------YTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1m5wa_ 237 MLEARG------------------------------------------ 242 HHsearch alignment (Probability: 0.05 E-value:0.11) query 110 KAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLF-----DRMLGEI 164 :::::::::::::: ::::::::::::::::::::::::::::: ::::::: d1m5wa_ 123 ADAGIQVSLFIDAD-----EEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKA 177 query 165 EERFGALIARVDWVSLGGGI 184 ::::::::::: :::::: d1m5wa_ 178 ATFAASLGLKV---NAGHGL 194
Intermediate <-- 1.717 --> Hit
DALI alignment (Z-score: 15.7 Raw score:1577.40) d1m5wa_ 1 ------------AELLLGVNIDH-iaTLRNA--------RGTAY--PDPVQAAFIAEQaG 37 ::::::::::: ::::: ::::: :::::::::::: : d1to3a_ 1 lnnytikditraSGGFAMLAVDQreaMRLMFaaagaktpVADSVltDFKVNAAKILSP-Y 59 d1m5wa_ 38 ADGITVHLredrrhitDRDVRILR--QTLD--TRMNLEMA--------------VTEEMl 79 :::::::: :::::::: :::: :::::::: ::::: d1to3a_ 60 ASAVLLDQ--------QFCYRQAVeqNAVAksCAMIVAADdfipgngipvdnvvLDKKI- 110 d1m5wa_ 80 aIAVETK---PHFCCLVPekrqevtteggldvAGQRDKMRDACKRLADAGIQVSLFID-- 134 :::::: :::::::: :::::::::::::::::::::::::: d1to3a_ 111 -NAQAVKrdgAKALKLLV------lwrsdedaQQRLNMVKEFNELCHSNGLLSIIEPVvr 163 d1m5wa_ 135 ------------aDEEQI-KAAAeVGAPFIEIHTGCYADAktdaEQAQELARIAKAATFA 181 ::::: :::: :::::::::::::::: :::::::::::::::: d1to3a_ 164 pprcgdkfdreqaIIDAAkELGD-SGADLYKVEMPLYGKG----ARSDLLTASQRLNGHI 218 d1m5wa_ 182 AslgLKVNAGHG-----lTYHNVKAIAAIpEMHELNIGHAIIGRAV---------mTGLK 227 : :::::::: ::::::::::: :::::::::::::::: :::: d1to3a_ 219 N---MPWVILSSgvdeklFPRAVRVAMEA-GASGFLAGRAVWSSVIglpdtelmlrDVSA 274 d1m5wa_ 228 DAVAEMKRLMLEARG-- 242 ::::::::::::::: d1to3a_ 275 PKLQRLGEIVDEMMGkr 291 FAST alignment (Normalized score: 10.11 Raw score:2682.00) d1m5wa_ 1 A-------------ELLLGVNIDHIA-------TLRNARGTAYP---------------D 25 :::::::: :::: : d1to3a_ 1 -LNNYTIKDITRASGGFAMLAV----DQREAMRLMFA-------AAGAKTPVADSVLTDF 48 d1m5wa_ 26 PVQAAFIAEQAGADGITVHLREDRRHIT-DRDVRILRQT-----LDTRMNLEMA------ 73 :::::::::: :::::::: ::::::::: :::::::: d1to3a_ 49 KVNAAKILSP-YASAVLLD---------QQFCYRQAVE-QNAVAKSCAMIVA--ADDFIP 95 d1m5wa_ 74 ----------VTEE-MLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAG-----------Q 111 :::: :::::::::::::::: : d1to3a_ 96 GNGIPVDNVVLDKKINAQAVKRDGAKALKLL-----------------VLWRSDEDAQQR 138 d1m5wa_ 112 RDKMRDACKRLADAGIQVSLFIDA----------------DEEQIKAAAEVGAPFIEIHT 155 :::::::::::::::::::::: :::::::::::::::::: d1to3a_ 139 LNMVKEFNELCHSNGLLSIIEP--VVRPPRCGDKFDREQAIIDAAKELGDSGADLYKV-- 194 d1m5wa_ 156 GCYADAKTDA--------EQAQELARIAKAATFAASLGLKVNAGHGL---------TYHN 198 ::::::::::::::: ::::::: :::: d1to3a_ 195 ----------EMPLYGKGARSDLLTASQRLNGH---INMPWVI----LSSGVDEKLFPRA 237 d1m5wa_ 199 VKAIAAIPEMHELNIGHAIIGRAVMT-------------GLKDAVAEMKRLMLEARG--- 242 :::::: ::::::::::::::: ::::::::::::::::: d1to3a_ 238 VRVAME-AGASGFLAGRAVWSS----VIGLPDTELMLRDVSAPKLQRLGEIVDEMM-GKR 291 TMalign alignment (TM-score: 0.70 Raw score:169.88) d1m5wa_ 1 ------------AELLLGVNIDHI--AT--L----R--NARGTA-YPDPVQAAFIAEQAG 37 :::::::::::: :: : : :::::: ::::::::::::: : d1to3a_ 1 LNNYTIKDITRASGGFAMLAVDQREAMRLMFAAAGAKTPVADSVLTDFKVNAAKILSP-Y 59 d1m5wa_ 38 ADGITVHLREDRRHITDRDVRILRQ-T-LD--TRMNLEMA------------VTEEMLAI 81 :::::::: :: ::::::: : :: :::::::: ::: :::: d1to3a_ 60 ASAVLLDQ------QF--CYRQAVEQNAVAKSCAMIVAADDFIPGNGIPVDNVVL-DKKI 110 d1m5wa_ 82 AV-ETK---PHFCCLVPEKRQEVTTEGG-LDVAG-QRDKMRDACKRLADAGIQVSLFID- 134 :: ::: ::::::::: ::: :::: :::::::::::::::::::::::: d1to3a_ 111 NAQAVKRDGAKALKLLVL-------WRSD-EDAQQRLNMVKEFNELCHSNGLLSIIEPVV 162 d1m5wa_ 135 --------------ADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATF 180 ::::::::::: ::::::::: ::::: :: :::::::::::::: d1to3a_ 163 RPPRCGDKFDREQAIIDAAKELGDS-GADLYKVEM-PLYGK--GA-RSDLLTASQRLNGH 217 d1m5wa_ 181 AASLGLKVNAG-HGLTYHNVKAIAA--IP-EMHELNIGHAIIGRAV-M----TGLKD-AV 230 : : :::::: ::::::::::::: :: :::::::::::::::: : ::::: :: d1to3a_ 218 I--N-MPWVILSSGVDEKLFPRAVRVAMEAGASGFLAGRAVWSSVIGLPDTELMLRDVSA 274 d1m5wa_ 231 AEMKRLMLEA-RG---- 242 :::::::::: :: d1to3a_ 275 PKLQRLGEIVDEMMGKR 291 HHsearch alignment (Probability: 0.74 E-value:0.07) d1m5wa_ 7 VNIDHIATLRNAR-------GTAYPDPVQAAFI---AEQAGADGITVHLREDRRHITDRD 56 ::::::::::::: ::::::::::::: :::::::::::::::::::::::: d1to3a_ 19 LAVDQREAMRLMFAAAGAKTPVADSVLTDFKVNAAKILSPYASAVLLDQQFCYRQAVEQN 78 d1m5wa_ 57 VRILR--QTLD--TRMNLEMAVTEEM-------LAIAVETKPHFC-CLVPEKRQEVTTEG 104 ::::: :::: ::::::::::::: :::::::::::: :::::::::: d1to3a_ 79 AVAKSCAMIVAADDFIPGNGIPVDNVVLDKKINAQAVKRDGAKALKLLVLWRSDED---- 134 d1m5wa_ 105 GLDVAGQRDKMRDACKRLADAGIQVSLFID----------ADEE----QIKAAAEVGAPF 150 ::::::::::::::::::::::::::: :::: :::::::::::: d1to3a_ 135 ---AQQRLNMVKEFNELCHSNGLLSIIEPVVRPPRCGDKFDREQAIIDAAKELGDSGADL 191 d1m5wa_ 151 IEIH-TGCYADAKTDAEQAQELARIAKAATFAASLGLK-VNAGHGLTYHNVK---AIAAI 205 :::: ::: :::::: :::::::::::::::: ::::::::::::: ::::: d1to3a_ 192 YKVEMPLY-GKGARS-------DLLTASQRLNGHINMPWVILSSGVDEKLFPRAVRVAME 243 d1m5wa_ 206 PEMHELNIGHAIIGRAVMT-GLKDA--------VAEMKRLMLEAR 241 ::::::::::::::::::: ::::: :::::::::::: d1to3a_ 244 AGASGFLAGRAVWSSVIGLPDTELMLRDVSAPKLQRLGEIVDEMM 288