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 <-- 1.828 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1b5ta_) 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 d1b5ta_ Methylenetetrahydrofolate reductaseFAD-​linked oxidoreductaseTIM 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 <-- 1.828 --> Hit
DALI alignment (Z-score: 12.9 Raw score:1305.80) d1m5wa_ 1 aELLLGVNIDhiATLRnargtAYPD--PVQAAFIAEQAGADGITVHLREDRRH--ITDRD 56 ::::::::: :::: :::: :::::::::::::::::::::::::: ::::: d1b5ta_ 1 gQINVSFEFF--PPRT-----SEMEqtLWNSIDRLSSLKPKFVSVTYGANSGErdRTHSI 53 d1m5wa_ 57 VRILRQTLDTRMNLEMAVT----EEMLAIAVETK---PHFCCLVPEKRQevtteggldva 109 ::::::::::::::::::: ::::::::::: :::::::::::: d1b5ta_ 54 IKGIKDRTGLEAAPHLTCIdatpDELRTIARDYWnngIRHIVALRGDLP-------pgsg 106 d1m5wa_ 110 gqrDKMRDACKRLAD-AGIQVSLFIDA-----------DEEQIKAAAEVGAPFIEIHTGC 157 :::::::::::: ::::::::::: :::::::::::::::::::::: d1b5ta_ 107 kpeMYASDLVTLLKEvADFDISVAAYPevhpeaksaqaDLLNLKRKVDAGANRAITQFFF 166 d1m5wa_ 158 yadaktdaeqaqELARIAKAATFAA--SLGLKVNAGHGL--------------------- 194 ::::::::::::: :::::::::::: d1b5ta_ 167 ------------DVESYLRFRDRCVsaGIDVEIIPGILPvsnfkqakkfadmtnvripaw 214 d1m5wa_ 195 ----------------------TYHNVKAIAAIPeMHELNIGHaiigravmtgLKDAVAE 232 :::::::::::: :::::::: ::::::: d1b5ta_ 215 maqmfdgldddaetrklvganiAMDMVKILSREG-VKDFHFYT--------lnRAEMSYA 265 d1m5wa_ 233 MKRLMLearg 242 :::::: d1b5ta_ 266 ICHTLGvrpa 275 FAST alignment (Normalized score: 9.42 Raw score:2431.00) d1m5wa_ 1 AELLLGVNIDHIATLR---NARGTAYP----DPVQAAFIAEQAGADGITVHLREDRRHI- 52 :::::::: :::: ::::::::::::::::::::::::::: d1b5ta_ 1 GQINVSFE--------FFPPRTS----EMEQTLWNSIDRLSSLKPKFVSVTYGANSGE-R 47 d1m5wa_ 53 --TDRDVRILRQTLDTRMNLEMAV----TEEMLAIAVE---TKPHFCCLVPEKRQEVTTE 103 :::::::::::::::::::::: :::::::::: :::::::::: d1b5ta_ 48 DRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALR--------- 98 d1m5wa_ 104 GGLDVAGQRD------------KMRDACKRLAD-AGIQVSLFIDA-----------DEEQ 139 ::::::::::: ::::::::::: :::: d1b5ta_ 99 ----------GDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLN 148 d1m5wa_ 140 IKAAAEVGAPFIEIHTGCYADAKTDAEQAQ----ELARIAKAATFAAS--LGLKVNAGHG 193 :::::::::::::: :::::::::::::: ::::::: d1b5ta_ 149 LKRKVDAGANRAIT----------------QFFFDVESYLRFRDRCVSAGIDVEIIP--- 189 d1m5wa_ 194 L-----------------------------------------------TYHNVKAIAAIP 206 ::::::::::: d1b5ta_ 190 -GILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSRE- 247 d1m5wa_ 207 EMHELNIGHAIIGRAVMTG----LKDAVAEMKRLMLEARG------ 242 ::::::: ::::::::::: d1b5ta_ 248 GVKDFHF------------YTLNRAEMSYAICHT------LGVRPA 275 TMalign alignment (TM-score: 0.66 Raw score:159.42) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLRED--RRHITDRDVR 58 :::::::::: :: ::: :::::::::::::::::::::::::::: :::::::::: d1b5ta_ 1 GQINVSFEFF--PP--RTS-EMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIK 55 d1m5wa_ 59 ILRQTLDTRMNLEMAV--T-E-EMLAIAVETK---PHFCCLVPEKRQE----VTTEGGLD 107 :::::::::::::::: : : :::::::::: ::::::::::::: : d1b5ta_ 56 GIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGK-------P 108 d1m5wa_ 108 VAGQRDKMRDACKRLADAGIQVSLFIDA-----------DEEQIKAAAEVGAPFIEIHTG 156 : ::::::::::::: : :::::::::: :::::::::::::::::::: d1b5ta_ 109 E-MYASDLVTLLKEV-A-DFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQF- 164 d1m5wa_ 157 CYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLT--------------------- 195 :: ::::::::::::::: ::::::::::::: d1b5ta_ 165 -FF-------DVESYLRFRDRCVSA-GIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWM 215 d1m5wa_ 196 ------------------Y-HN--VK-AIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEM 233 : :: :: :::::: ::::::::::: : :::::: d1b5ta_ 216 AQMFDGLDDDAETRKLVGANIAMDMVKILSREG-VKDFHFYTLNR-------A-EMSYAI 266 d1m5wa_ 234 KRLMLE---ARG 242 :::::: d1b5ta_ 267 CHTLGVRPA--- 275 HHsearch alignment (Probability: 0.06 E-value:0.04) d1m5wa_ 26 PVQAAFIAEQAGADGI--TVHLREDRRHITDRDVRILRQTLDTRM--NLEM--AVTEEML 79 :::::::::::::::: ::::::::::::::::::::::::::: :::: ::::::: d1b5ta_ 21 LWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELR 80 d1m5wa_ 80 AIAVETK---PHFCCLV-PEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFID- 134 ::::::: ::::::: :::: ::::::: ::::::::::::::::::::::::: d1b5ta_ 81 TIARDYWNNGIRHIVALRGDLP----PGSGKPE-MYASDLVTLLKEVADFDISVAAYPEV 135 d1m5wa_ 135 -ADE---E-QIK---AAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGL 186 ::: : ::: :::::::::: ::::: : ::::::::::::::::: d1b5ta_ 136 HPEAKSAQADLLNLKRKVDAGANRA--ITQFF---F-------DVESYLRFRDRCVSAGI 183 d1m5wa_ 187 K--VNAGHG--LTYHNVKAIAAIPEMHELNIGHAIIGR---------A-VMTGLKDAVAE 232 : :::::: ::::::::::::::: ::::::::: : ::::::::::: d1b5ta_ 184 DVEIIPGILPVSNFKQAKKFADMTNV---RIPAWMAQMFDGLDDDAETRKLVGANIAMDM 240 d1m5wa_ 233 MKRLMLE 239 ::::::: d1b5ta_ 241 VKILSRE 247