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 <-- 1.772 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1us3a2) 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 d1us3a2 Xylanase 10c(Trans)glycosidasesTIM 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 <-- 1.772 --> Hit
DALI alignment (Z-score: 12.8 Raw score:1416.40) d1m5wa_ 1 --------------AELLLGVNIDhIATLRnargtaYPDPVQ--aaFIAEQAGADGITVH 44 :::::::::: ::::: :::::: :::::::::::::: d1us3a2 1 aysanvdhlrdlapSDFPIGVAVS-NTDSA------TYNLLTnsreQAVVKKHFNHLTAG 53 d1m5wa_ 45 --LREDR-----rhiTDRDVRILRQTL---DTRMNLEMAV-------------------- 74 ::::: :::::::::::: :::::::::: d1us3a2 54 niMKMSYmqptegnfNFTNADAFVDWAtenNMTVHGHALVwhsdyqvpnfmknwagsaed 113 d1m5wa_ 75 -----TEEMLAIAVETK----PHFCCLVPekrqevtteggLDVA---------------- 109 :::::::::::: :::::::: :::: d1us3a2 114 flaalDTHITTIVDHYEakgnLVSWDVVN-----------EAIDdnspanfrttdsafyv 162 d1m5wa_ 110 ---gqRDKMRDACKRLAD--AGIQVSLFID-------aDEEQIKAAAEV-----GAPFIE 152 ::::::::::::: :::::::::: ::::::::::: :::::: d1us3a2 163 ksgnsSVYIERAFQTARAadPAVILYYNDYnieqnnakTTKMVDMVKDFqarsiPIDGVG 222 d1m5wa_ 153 IHTGcYADAktdaeqAQELARIAKAATFAASLGLKVNAGHGLT----------------- 195 :::: :::: :::::::::::::::::::::::::::: d1us3a2 223 FQMH-VCMN------YPSIANISAAMKKVVDLGLLVKITELDVavnqphcdaypankinp 275 d1m5wa_ 196 ---------YHNVKAIAA--IPEM-----HELNIGHaIIGR------------------- 220 ::::::::: :::: ::::::: :::: d1us3a2 276 lteaaqlaqKKRYCDVVKayLDTVpvnqrGGISVWG-TTDAntwldglyreqfedekisw 334 d1m5wa_ 221 ---AVMTGlkdavaeMKRLMLEARG-------- 242 ::::: :::::::::: d1us3a2 335 pllFDNNY---ndkpALRGFADALIgtqctnth 364 FAST alignment (Normalized score: 6.96 Raw score:2066.00) d1m5wa_ 1 --------------AELLLGVNIDHIATLRNARGT------AYPDP--VQAAFIAEQAGA 38 :::::::: ::::: :::::::::::: d1us3a2 1 AYSANVDHLRDLAPSDFPIGVA-------------VSNTDSATYNLLTNSREQAVVKKHF 47 d1m5wa_ 39 DGITVHLREDRRHI----------------TDRDVRILRQT---LDTRMNLEMAV----- 74 ::::: ::::::::::: ::::::::: d1us3a2 48 NHLTA---------GNIMKMSYMQPTEGNFNFTNADAFVDWATENNMTVHGHA--LVWHS 96 d1m5wa_ 75 -------------------------TEEMLAIAVETK--PHFCCLVPEKRQEVTTEGGLD 107 ::::::::::: ::::: d1us3a2 97 DYQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAK-GNLVSWD---------------- 139 d1m5wa_ 108 VAGQ----------------------------RDKMRDACKRLAD--AGIQVSLFIDA-- 135 ::::::::::::: ::::::::: d1us3a2 140 ----VVNEAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVILYYND--YN 193 d1m5wa_ 136 -------DEEQIKAAAE-----VGAPFIEIHTGCYADAKTDAEQAQ-------ELARIAK 176 :::::::::: :::::::::: ::::::: d1us3a2 194 IEQNNAKTTKMVDMVKDFQARSIPIDGVGFQM--------------HVCMNYPSIANISA 239 d1m5wa_ 177 AATFAASLGLKVNAGHGL-----------------------------TYHNVKAIAAI-- 205 ::::::::::::::: :::::::::: d1us3a2 240 AMKKVVDLGLLVKIT---ELDVAVNQPHCDAYPANKINPLTEAAQLAQKKRYCDVVK-AY 295 d1m5wa_ 206 ------PEMHELNIGHAIIGRAVMTGLKDAV----------------------------- 230 ::::::: d1us3a2 296 LDTVPVNQRGGIS------------------VWGTTDANTWLDGLYREQFEDEKISWPLL 337 d1m5wa_ 231 -------AEMKRLMLEARG--------- 242 ::::::::::: d1us3a2 338 FDNNYNDKPALRGFADAL-IGTQCTNTH 364 TMalign alignment (TM-score: 0.71 Raw score:170.68) d1m5wa_ 1 -------------AE-LLLGVNIDHIATLRNARGTAYPDPVQA--AFIAEQAGADGITV- 43 :: :::::::: ::::: ::::::: :::::::::::::: d1us3a2 1 AYSANVDHLRDLAPSDFPIGVAVS-NTDSA------TYNLLTNSREQAVVKKHFNHLTAG 53 d1m5wa_ 44 H-LREDRR-------HITDRDVRILRQTL---DTRMNLEMAV------------------ 74 : :::::: :::::::::::: :::::::::: d1us3a2 54 NIMKMSYMQPTEGNF--NFTNADAFVDWATENNMTVHGHALVWHSDYQVPNFMKNWAGSA 111 d1m5wa_ 75 ------TEEML-AIAVETK----PHFCCLVPEKRQEVTTEGGLDV-----AG-------- 110 ::::: ::::::: :::::::: :::: :: d1us3a2 112 EDFLAALDTHITTIVDHYEAKGNLVSWDVVN----------EAIDDNSPANFRTTDSAFY 161 d1m5wa_ 111 -----QRDKMRDACKRLAD-A-GIQVSLFI--DA-----DEEQIKAAA-E----VGAPFI 151 :::::::::::::: : :::::::: :: ::::::::: : :::::: d1us3a2 162 VKSGNSSVYIERAFQTARAADPAVILYYNDYNIEQNNAKTTKMVDMVKDFQARSIPIDGV 221 d1m5wa_ 152 EIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLT---------------- 195 ::::: :: : : ::: ::::::::::::::::::::::::: d1us3a2 222 GFQMH-VC-M--N--YPS-IANISAAMKKVVDLGLLVKITELDVAVNQPHCDAYPANKIN 274 d1m5wa_ 196 ------Y--H--NVKAIAAI--PEM----H-ELNIGHAIIG------------------- 219 : : :::::::: ::: : :::::: ::: d1us3a2 275 PLTEAAQLAQKKRYCDVVKAYLDTVPVNQRGGISVWG-TTDANTWLDGLYREQFEDEKIS 333 d1m5wa_ 220 ----RAVMTGLKDAVAEMKRLMLEAR-G------- 242 :::::: :: ::: ::::::: : d1us3a2 334 WPLLFDNNYN--DK-PAL-RGFADALIGTQCTNTH 364 HHsearch alignment (Probability: 0.05 E-value:0.08) d1m5wa_ 76 EEMLAIAVETKPHFC--CLV 93 ::::::::::::::: ::: d1us3a2 74 DAFVDWATENNMTVHGHALV 93