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 <-- 1.783 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1ezwa_) 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 d1ezwa_ Coenzyme F420 dependent tetrahydromethanopterin reductaseBacterial luciferase-​likeTIM 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 <-- 1.783 --> Hit
DALI alignment (Z-score: 15.1 Raw score:1523.90) d1m5wa_ 1 AELLLGVNIDhiATLRnargtayPDPVQAAFIAEQAGADGITVHLRedRRHIT-DRDVRI 59 :::::::::: :::: ::::::::::::::::::::::: ::::: :::::: d1ezwa_ 1 AEVSFGIELL--PDDK------pTKIAHLIKVAEDNGFEYAWICDH--YNNYSyMGVLTL 50 d1m5wa_ 60 LRQTL-DTRMNL-EMAV----TEEMLAIAVETK-----PHFCCLV-PEKRQE-------- 99 ::::: :::::: :::: :::::::::::: ::::::: :::::: d1ezwa_ 51 AAVITsKIKLGPgITNPytrhPLITASNIATLDwisggRAIIGMGpGDKATFdkmglpfp 110 d1m5wa_ 100 ----vtteggldvaGQRDKMRDACKRLAD----------------------------AGI 127 ::::::::::::::: ::: d1ezwa_ 111 ckipiwnpeaedevGPATAIREVKEVIYQyleggpveyegkyvktgtadvkarsiqgSDI 170 d1m5wa_ 128 QVSLFIDaDEEQIKAAAEvGAPFIEIHTGcyadaktdaeqaqELARIAKAATFAASLG-- 185 ::::::: :::::::::: :::::::::: :::::::::::::::: d1ezwa_ 171 PFYMGAQ-GPIMLKTAGE-IANGVLVNAS-------------NPKDFEVAVPKIEEGAke 215 d1m5wa_ 186 -------LKVNAGHG--------------------------------------------- 193 :::::::: d1ezwa_ 216 agrsldeIDVAAYTCfsidkdedkaieatkivvafivmgspdvvlerhgidtekaeqiae 275 d1m5wa_ 194 ----------------------LTYH-------NVKAIAAIpEMHELNIGHAiIGRAvmt 224 :::: :::::::: :::::::::: :::: d1ezwa_ 276 aigkgdfgtaiglvdedmieafSIAGdpdtvvdKIEELLKA-GVTQVVVGSP-IGPD--- 330 d1m5wa_ 225 gLKDAVAEMK-RLMLEARg 242 ::::::::: ::::::: d1ezwa_ 331 -KEKAIELVGqEVIPHFK- 347 FAST alignment (Normalized score: 9.43 Raw score:2731.00) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYP--------DPVQAAFIAEQAGADGITVHLREDRRHI 52 :::::::: :::::::::::::::::::::: d1ezwa_ 1 AEVSFGIE----------------LLPDDKPTKIAHLIKVAEDNGFEYAWICDH------ 38 d1m5wa_ 53 -----TDRDVRILRQTL-DTRMNL-EMAV----TEEMLAIAVETKP--------HFCCLV 93 :::::::::::: :::::: :::: :::::::::: :::::: d1ezwa_ 39 YNNYSYMGVLTLAAVITSKIKLGPGITNPYTRHPLITASNIAT---LDWISGGRAIIGMG 95 d1m5wa_ 94 PEKRQEVTTEGGLDVA----------------------------GQRDKMRDACKRLAD- 124 : ::::::::::::::: d1ezwa_ 96 P---------------GDKATFDKMGLPFPCKIPIWNPEAEDEVGPATAIREVKEVIYQY 140 d1m5wa_ 125 ---------------------------AGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGC 157 :::::::: :::::::::::: ::::::: d1ezwa_ 141 LEGGPVEYEGKYVKTGTADVKARSIQGSDIPFYMG-AQGPIMLKTAGE-IANGVLV---- 194 d1m5wa_ 158 YADAKTDAEQAQ---ELARIAKAATFAAS---------LGLKVNAGHGL----------- 194 :::::::::::::: ::::::::::: d1ezwa_ 195 ------------NASNPKDFEVAVPKIEEGAKEAGRSLDEIDVAAYTCFSIDKDEDKAIE 242 d1m5wa_ 195 ------------------------------------------------------------ 195 d1ezwa_ 243 ATKIVVAFIVMGSPDVVLERHGIDTEKAEQIAEAIGKGDFGTAIGLVDEDMIEAFSIAGD 302 d1m5wa_ 195 ---TYHNVKAIAAIPEMHELNIGHAIIGRAVM---TGLKDAVAEMKR-LMLEARG-- 242 :::::::::: :::::::::: :::::::::::: :::: d1ezwa_ 303 PDTVVDKIEELLK-AGVTQVVVGS--------PIGPDKEKAIELVGQEVIPH---FK 347 TMalign alignment (TM-score: 0.68 Raw score:164.28) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRIL 60 :::::::::: :::: : ::::::::::::::::::::::: ::::::::::::: d1ezwa_ 1 AEVSFGIELL--PDDK-----P-TKIAHLIKVAEDNGFEYAWICDH-YNNYSYMGVLTLA 51 d1m5wa_ 61 RQTLD-TRMNLE-MAV--TE--EMLAIAVETK-----PHFCCLVPEKRQEV------TTE 103 ::::: :::::: ::: :: :::::::::: :::::::::::::: : d1ezwa_ 52 AVITSKIKLGPGITNPYTRHPLITASNIATLDWISGGRAIIGMGPGDKATFDKMGLP--F 109 d1m5wa_ 104 G--------------GLDVAGQRDKMRDACKRLAD---------------------A--G 126 : :::::::::::::::::: : : d1ezwa_ 110 PCKIPIWNPEAEDEV--GPATAIREVKEVIYQYLEGGPVEYEGKYVKTGTADVKARSIQG 167 d1m5wa_ 127 --IQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAAS- 183 :::::::::: :::::::: ::::::::: : ::::::::::::::::: d1ezwa_ 168 SDIPFYMGAQGP-IMLKTAGE-IANGVLVNA---S-------NPKDFEVAVPKIEEGAKE 215 d1m5wa_ 184 --LG--LKVNAGHGLTY------------------------------------------- 196 :: ::::::::::: d1ezwa_ 216 AGRSLDEIDVAAYTCFSIDKDEDKAIEATKIVVAFIVMGSPDVVLERHGIDTEKAEQIAE 275 d1m5wa_ 197 -------------------H--NV---------KA-IAAIPEMHELNIGHAIIGRAVMTG 225 : :: :: :::::::::::::::: : ::: d1ezwa_ 276 AIGKGDFGTAIGLVDEDMIEAFSIAGDPDTVVDKIEELLKAGVTQVVVGSPI--G--PDK 331 d1m5wa_ 226 LKDAVAEMK-RLMLEARG 242 : ::::::: ::::: :: d1ezwa_ 332 E-KAIELVGQEVIPH-FK 347 HHsearch alignment (Probability: 0.15 E-value:0.01) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITV 43 :::::::::: ::::::::::::::::::::::::: d1ezwa_ 1 AEVSFGIELL--------PDDKPTKIAHLIKVAEDNGFEYAWI 35