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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.687 --> Intermediate <-- 0.853 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1d8wa_) through the intermediate protein (d1tx2a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tx2a_ Dihydropteroate synthetaseDihydropteroate synthetase-​likeTIM beta/​alpha-​barrelα/β
Hit d1d8wa_ L-​rhamnose isomeraseXylose isomerase-​likeTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.687 --> Intermediate
DALI alignment (Z-score: 2.9 Raw score:483.20) query 1 ---------------SLQLRLALN----qidstvgdiagnAEAILRWTRHSAEQGAHLVA 41 ::::::::: :::::::::::::::::::: d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGIlnvtpdsfsdggsyneVDAAVRHAKEMRDEGAHIID 60 query 42 fpemALTGypvedlalrSSFVEASRTALRELAARLAeEGFGeLPVLVGYldrsesaqpky 101 :::: ::::::::::::::::::: :::: ::::::: d1tx2a_ 61 ---iGGES-------faKVSVEEEIKRVVPMIQAVS-KEVK-LPISIDT----------- 97 query 102 gqpagaprnaaavlhrGRVALT-FAKHhlpnygvfdefryfvPGDT-mpivrlhgvdiaL 159 :::::: :::: :::: : d1tx2a_ 98 -----ykaevakqaieAGAHIInDIWG--------------aKAEPkiaevaahydvpiI 138 query 160 AICE---------dlwQDGGR----vpaarsagaglllsvnaspyerdkDDTRLELVRKR 206 :::: ::::: ::::::::::: d1tx2a_ 139 LMHNrdnmnyrnlmadMIADLydsikiakdagvrdeniildpgigfaktPEQNLEAMRNL 198 query 207 aQEAG---ctTAYLAmiggqdelvFDGD------------------sivVDRDGevvara 245 :::: ::::: :::: ::::: d1tx2a_ 199 -EQLNvlgypVLLGT-------srKSFIghvldlpveerlegtgatvclGIEKG------ 244 query 246 pqfsegCVVLdldlpaaeaepptgvvddglridrlviseeplpayeaeLAGGyadrldad 305 :::: :::: d1tx2a_ 245 cefvrvHDVK-----------------------------------emsRMAK-------- 261 query 306 eevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyss 365 d1tx2a_ 262 ------------------------------------------------------------ 262 query 366 dhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqe 425 d1tx2a_ 262 ------------------------------------------------------------ 262 query 426 ghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtppip 485 d1tx2a_ 262 ------------------------------------------------------------ 262 query 486 easitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgt 545 d1tx2a_ 262 ------------------------------------------------------------ 262 query 546 kisakgfgkdrrlpitnrwregh 568 d1tx2a_ 262 ---------------mmdamigk 269 FAST alignment (Normalized score: 1.23 Raw score:478.70) query 1 ----------------SLQLRLALNQIDSTVGD---IAGNAEAILRWTRHSAEQGAHLVA 41 ::::::::::::::::: :::::::::::::::::::::::: d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 query 42 FPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGF-------------------- 81 :: d1tx2a_ 61 IG--------------------------------------GESFAKVSVEEEIKRVVPMI 82 query 82 ------GELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVF 135 ::::::: d1tx2a_ 83 QAVSKEVKLPISI----------------------------------------------- 95 query 136 DEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDK 195 d1tx2a_ 96 ------------------------------------------------------------ 96 query 196 DDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVL 255 d1tx2a_ 96 ------------------------------------------------------------ 96 query 256 DLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVG 315 d1tx2a_ 96 ------------------------------------------------------------ 96 query 316 LRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVS----------------- 358 d1tx2a_ 96 -------------------------------------------DTYKAEVAKQAIEAGAH 112 query 359 ----------------------------MPSKYSSDHSKGDAAELARRTGLNFRTVSIEP 390 :::: d1tx2a_ 113 IINDIWGAKAEPKIAEVAAHYDVPIILMHNRD---------------------------- 144 query 391 MFDAYMASLG----LTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY 446 :::::::::::::::::::: d1tx2a_ 145 ----------NMNYRNLMADMIADLYDSIKIAKD-------------------------- 168 query 447 GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVD 506 d1tx2a_ 169 ------------------------------------------------------------ 169 query 507 RDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWRE 566 d1tx2a_ 169 ------------------------------------------------------------ 169 query 567 GH---------------------------------------------------------- 568 d1tx2a_ 169 --AGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPV 226 query 569 ------------------------------------------- 569 d1tx2a_ 227 EERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 269 TMalign alignment (TM-score: 0.25 Raw score:142.24) query 1 --SLQL------RLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV 52 :::: ::: : :::: :::: ::: d1tx2a_ 1 KWDYDLRCGEYTLNL------------------------N-EKTL--IMGI--LNV---- 27 query 53 EDLALRSSFV--E-ASRTALRELAARLAEEGFGELPVLVGYLDR---SESAQPKYGQPAG 106 :: ::::: : :::::::::::::: ::: :::::::::: :: : : d1tx2a_ 28 --TP-DSFSDGGSYNEVDAAVRHAKEMR-DEG--AHIIDIGGESFAK---VS--V-E--- 72 query 107 APR-NAA-AV--LHRGRV-ALTFAKHHLPNYGVFDEFRYFVPGDTMPIV-RLHGVDIALA 160 ::: ::: :: :::::: ::::::::: :::::::: : ::::: d1tx2a_ 73 EEIKRVVPMIQAVSKEVKLPISIDTYKA-------------EVAKQAIEA-G---AHIIN 115 query 161 ICEDLWQDGGRVPAARSAGAGLLLSVNASP-YERD-K---DD-TRLELVRKRAQE--AGC 212 :::::::::::::::::: : ::::::::: :::: : :: :::::::::::: ::: d1tx2a_ 116 DIWGAKAEPKIAEVAAHY-D-VPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRD 173 query 213 T-TAYLAMIGG-QDELV-FD--GD--SIVVDRDGEVVARAPQFSE-GCVVLDLDLPAAEA 264 : ::::::::: ::: :: :: ::::: :::::::: ::: d1tx2a_ 174 ENIILDPGIGFA--KTPEQNLEAMRNLEQLN--VLGYPVLL-GTSR-------------- 214 query 265 EPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNG 324 :::::::: ::::: d1tx2a_ 215 ----------------------------------------------KSFIGHVL-DLPVE 227 query 325 FR----------------------------------------SVLIGLSGGIDSALVAAI 344 :: d1tx2a_ 228 ERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK------------------ 269 query 345 ACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGL 404 d1tx2a_ 270 ------------------------------------------------------------ 270 query 405 AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSI 464 d1tx2a_ 270 ------------------------------------------------------------ 270 query 465 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 d1tx2a_ 270 ------------------------------------------------------------ 270 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1tx2a_ 270 -------------------------------------------- 270 HHsearch alignment (Probability: 0.05 E-value:0.02) query 494 YPVLDAILELYVDRDTGADAIV---AAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 550 :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1tx2a_ 156 IADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRK 215 query 551 GF 552 :: d1tx2a_ 216 SF 217
Intermediate <-- 0.853 --> Hit
DALI alignment (Z-score: 10.3 Raw score:1235.90) d1tx2a_ 1 ------------kwdydlrcgeytlnlnEKTLIMGILN----vTPDSfsdggsyNEVDAA 44 :::::::::: :::: :::::: d1d8wa_ 1 tqleqawelakqrfaavgidveealrqlDRLPVSMHCWqgddvSGFE-nypgkaRNASEL 59 d1tx2a_ 45 VRHAKEMRDEG--aHIIDIGGE---sfAKVSV-EEEIKRvVPMIQAVSKEVKLPISIDT- 97 ::::::::::: :::::::: ::::: :::::: ::::::::::::::::::: d1d8wa_ 60 RADLEQAMRLIpgpKRLNLHAIylesdTPVSRdQIKPEH-FKNWVEWAKANQLGLDFNPs 118 d1tx2a_ 98 --------------------------yKAEVAKQAIEA-----gaHIINDIW-------- 118 ::::::::::: ::::::: d1d8wa_ 119 cfshplsadgftlshaddsirqfwidhCKASRRVSAYFgeqlgtpSVMNIWIpdgmkdit 178 d1tx2a_ 119 ---------gakAEPKIAEVaAHYD--VPIILMHNRD---NMNYrnlmaDMIADLYDSIK 164 :::::::: :::: :::::::::: :::: ::::::::::: d1d8wa_ 179 vdrlaprqrllaALDEVISE-KLNPahHIDAVESKLFgigAESY--tvgSNEFYMGYATS 235 d1tx2a_ 165 IAkdagvrdenIILDPGIGFaKTPEQNleAMRNLEQLNVLGYPVLLGTSRKSfighvldl 224 :: ::::::::: :::::: ::::::::::::::::::::::: d1d8wa_ 236 RQ---------TALCLDAGH-FHPTEV--ISDKISAAMLYVPQLLLHVSRPV----rwds 279 d1tx2a_ 225 pveeRLEG-TGATVCLGIEKGC---EFVRV--------------hDVKEMSRMAKMMDAM 266 :::: ::::::::::::: ::::: ::::::::::::::: d1d8wa_ 280 dhvvLLDDeTQAIASEIVRHDLfdrVHIGLdffdasinriaawviGTRNMKKALLRALLE 339 d1tx2a_ 267 IG---------------------------------------------------------- 268 :: d1d8wa_ 340 PTaelrkleapgdytarlalleeqkslpwqavwemycqrhdtpagsewlesvrayekeil 399 d1tx2a_ 269 --k 269 d1d8wa_ 400 srr 402 FAST alignment (Normalized score: 4.49 Raw score:1475.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNE-----------------------------KTLIMGILNVTPDS 31 ::::::: d1d8wa_ 1 -----------------TQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMH------- 36 d1tx2a_ 32 FSDGGSY-----------------NEVDAAVRHAKEMRD-EGA-HIIDIGGE------SF 66 ::::::::::::::: ::: ::::: :: d1d8wa_ 37 -------CWQGDDVSGFENYPGKARNASELRADLEQAMRLIPGPKRLNL---HAIYLESD 86 d1tx2a_ 67 AKVSVEE-----EIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAK 121 ::: ::::::::::::: :::::::: d1d8wa_ 87 TPV----SRDQIKPEHFKNWVEWAK-ANQLGLDF-------------------------- 115 d1tx2a_ 122 A------------------------------EPKIAEVAAH-----YDVPIILMHNRDNM 146 ::::::::: :::::::::::: d1d8wa_ 116 -NPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSA-YFGEQLGTPSVMNIWIP-- 171 d1tx2a_ 147 NYRNLMADM-----------------IADLYDSIKIAKDAGVRDEN-------------- 175 :::::::: :::::::: d1d8wa_ 172 ---------DGMKDITVDRLAPRQRLLAALDEVI----SEKLNPAHHIDAVESKLFGIGA 218 d1tx2a_ 176 -------------------IILDPGIGFAKTPEQNL-EAMRNLEQLNVL--GYPVLLGTS 213 :::::::: ::::: :::::::::: ::::::::: d1d8wa_ 219 ESYTVGSNEFYMGYATSRQTALCLDAG-HFHPT---EVISDKISAAM--LYVPQLLLHVS 272 d1tx2a_ 214 RKSFIGHVLDLPVEER------------LEGTGATVCLGIEKGC----EFVRVH------ 251 : ::::::::::::::: :::: d1d8wa_ 273 R---------------PVRWDSDHVVLLDDETQAIASEIVRHD-LFDRVHIG--LDFFDA 314 d1tx2a_ 252 ------DVKEMSRMAKMMDAMIGK------------------------------------ 269 ::::::::::::::: d1d8wa_ 315 SINRIAAWVIGTRNMKKALLR---ALLEPTAELRKLEAPGDYTARLALLEEQKSLPWQAV 371 d1tx2a_ 270 ------------------------------- 270 d1d8wa_ 372 WEMYCQRHDTPAGSEWLESVRAYEKEILSRR 402 TMalign alignment (TM-score: 0.61 Raw score:163.96) d1tx2a_ 1 -------------------------KWDYDLRCGEYTLNLNEK-TLIMGILNV-TPD-SF 32 ::: ::::::::: ::: :: d1d8wa_ 1 TQLEQAWELAKQRFAAVGIDVEEAL---------------RQLDRLPVSMHCWQGDDVSG 45 d1tx2a_ 33 SD------GGSYNEVDAAVRHAKEMRDEGAHIIDIGGES-----FAKVSVEEEIKRVVPM 81 :: :::::::::: :::::: ::::::::::::: :::::::::::::: d1d8wa_ 46 FENYPGKARNASELRADL-EQAMRL-IPGPKRLNLHAIYLESDT--PVSRDQIKPEHFKN 101 d1tx2a_ 82 IQAVSKEVKLPISIDTY---------------------------KAEVAKQAIEA--GA- 111 ::::::::::::::::: ::::::::::: :: d1d8wa_ 102 WVEWAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLG 161 d1tx2a_ 112 -HIINDIWG-----------------AK-AEPKIAEVAAHYDVPIILMHNR--------D 144 :::::::: :: :::::::::::::::::::::: : d1d8wa_ 162 TPSVMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESY 221 d1tx2a_ 145 NMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVL 204 :::: :: :::::::::: : :::::::: :::: ::::::::::::: d1d8wa_ 222 TVGS--NE-FYMGYATSRQ--T----------ALCLDAGH-FHPT--EVISDKISAAMLY 263 d1tx2a_ 205 GYPVLLGTSRKSFIGHVLDLPVEERLEG-TGATVCLGIEKG-C---EFVRV--------- 250 :::::::::: : ::: ::::: :::: :::::::::::: : ::::: d1d8wa_ 264 VPQLLLHVSR-P--VRW-DSDHV-VLLDDETQAIASEIVRHDLFDRVHIGLDFFDASINR 318 d1tx2a_ 251 ---H--DVKEMSRMAKMMDAM-IG------------------------------------ 268 : ::::::::::::::: :: d1d8wa_ 319 IAAWVIGTRNMKKALLRALLEPTAELRKLEAPGDYTARLALLEEQKSLPWQAVWEMYCQR 378 d1tx2a_ 269 ------------------------K 269 d1d8wa_ 379 HDTPAGSEWLESVRAYEKEILSRR- 402 HHsearch alignment (Probability: 0.04 E-value:0.03) d1tx2a_ 27 VTPDSFSDGG 36 :::::::::: d1d8wa_ 115 FNPSCFSHPL 124