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 <-- 2.161 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1vlwa_) 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 d1vlwa_ KDPG aldolaseAldolaseTIM 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 <-- 2.161 --> Hit
DALI alignment (Z-score: 17.1 Raw score:1562.20) d1tx2a_ 1 kwdYDLRcgeyTLNLneKTLIMGILNVTpdsfsdggsynEVDAAVRHAKEMRDEGAHIID 60 :::: :::: ::::::::::: ::::::::::::::::::::: d1vlwa_ 1 -hhMKME----ELFK--KHKIVAVLRAN-----------SVEEAKEKALAVFEGGVHLIE 42 d1tx2a_ 61 IGGEsfakvsveeeiKRVVPMIQAVsKEVK---LPISID-TYKAEVAKQAIEAGAHIIND 116 :::: :::::::::: :::: :::::: :::::::::::::::::::: d1vlwa_ 43 ITFT----------vPDADTVIKEL-SFLKekgAIIGAGtVTSVEQCRKAVESGAEFIVS 91 d1tx2a_ 117 IWGAkaePKIAEVAAHYDVPIILMHNrdnmnyrnlmadMIADLYDSIKIAkdagvrdenI 176 :::: ::::::::::::::::::: :::::::::::: : d1vlwa_ 92 PHLD---EEISQFCKEKGVFYMPGVM------------TPTELVKAMKLG--------hT 128 d1tx2a_ 177 ILDP-GIGFaktpeqnleAMRNLEQLN--VLGYPVLLGTSrksfighvldlpveerlegT 233 :::: :::: ::::::::: ::::::::::: : d1vlwa_ 129 ILKLfPGEV--------vGPQFVKAMKgpFPNVKFVPTGG------------------vN 162 d1tx2a_ 234 GATVCLGIEKGCEFVRVH-------------DVKEMSRMAKMMdamigk 269 :::::::::::::::::: :::::::::::: d1vlwa_ 163 LDNVCEWFKAGVLAVGVGsalvkgtpdevreKAKAFVEKIRGC------ 205 FAST alignment (Normalized score: 11.57 Raw score:2718.00) d1tx2a_ 1 KWDYDLRCGEYTL-------NLNEKTLIMGILNVTPDSFSDGGSYN-EVDAAVRHAKEMR 52 ::::: :::::::: ::::::::::::: d1vlwa_ 1 -------------HHMKMEELFKKH-KIVAVLRA------------NSVEEAKEKALAVF 34 d1tx2a_ 53 DEGAHIIDIGGESFAKVSVEEEIK----RVVPMIQAVSK---EVKLPISI-DTYKAEVAK 104 :::::::::: :::::::::: :::::::: ::::::::: d1vlwa_ 35 EGGVHLIEIT--------------FTVPDADTVIKELS-FLKEKGAIIGAGTVTSVEQCR 79 d1tx2a_ 105 QAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMAD-MIADLYDSI 163 :::::::::::::: :::::::::::::::::::: ::::::::: d1vlwa_ 80 KAVESGAEFIVSPH---LDEEISQFCKEKGVFYMPGV-------------MTPTELVKAM 123 d1tx2a_ 164 KIAKDAGVRDEN---IILDPGIGFAKTPEQNLE------AMRNLEQLNV--LGYPVLLGT 212 : ::::: :::::::::: ::::::: d1vlwa_ 124 K-----------LGHTILKL-------------FPGEVVGPQFVKAMKGPFPNVKFVP-- 157 d1tx2a_ 213 SRKSFIGHVLDLPVEERLEG----TGATVCLGIEKGCEFVRVH--------------DVK 254 :::::::::::::::::: ::: d1vlwa_ 158 --------------------TGGVNLDNVCEWFKAGVLAVGV-GSALVKGTPDEVREKAK 196 d1tx2a_ 255 EMSRMAKMMDAMIGK- 269 :::::::: d1vlwa_ 197 AFVEKIRG-------C 205 TMalign alignment (TM-score: 0.62 Raw score:165.62) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 ::::: ::::: :::::::::::: :::::::::::::::::::: d1vlwa_ 1 ---HHMKM--EELFK--KHKIVAVLRANS-----------VEEAKEKALAVFEGGVHLIE 42 d1tx2a_ 61 IGGESFAKVSVEEEIKRVVPMIQAVSKEVK---LPISID-TYKAEVAKQAIEAGAHIIND 116 ::::: : ::::::::: :::: :::::: :::::::::::::::::::: d1vlwa_ 43 ITFTV--------P--DADTVIKEL-SFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVS 91 d1tx2a_ 117 IWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENI 176 :::: ::::::::::::::::::: :::::::::: :: : : d1vlwa_ 92 PHLD---EEISQFCKEKGVFYMPGVM------------TPTELVKAMK-LG-----H--T 128 d1tx2a_ 177 ILDPGIGFAKTPEQNLEAMRNLEQLN--VLGYPVLLGTSRKSFIGHVLDLPVEERLEGTG 234 ::::::: : : :::::::::: :::::::::::: :: d1vlwa_ 129 ILKLFPG----E--V-VGPQFVKAMKGPFPNVKFVPTGGV------------------NL 163 d1tx2a_ 235 ATVCLGIEKGCEFVRVH--D-----------VKEMSRMAKMMDAMIGK 269 ::::::::::::::::: : ::::::::::: d1vlwa_ 164 DNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGC------ 205 HHsearch alignment (Probability: 0.92 E-value:0.00) d1tx2a_ 18 KTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKR 77 ::::::::: ::::::::::::::::::::::::::: :: ::::: d1vlwa_ 11 KHKIVAVLR-----------ANSVEEAKEKALAVFEGGVHLIEITFT--VP----DADTV 53 d1tx2a_ 78 VVPMIQAVSKEVKLPISID-TYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVP 136 :::::: :: ::::::::: ::::::::::::::::::: ::: ::::::::::::::: d1vlwa_ 54 IKELSF-LK-EKGAIIGAGTVTSVEQCRKAVESGAEFIV--SPH-LDEEISQFCKEKGVF 108 d1tx2a_ 137 IILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMR 196 :::::: : :::::::::::::: :::::::::::::: : d1vlwa_ 109 YMPGVM----T------------PTELVKAMKLGHTI--LKLFPGEVVGPQFV------K 144 d1tx2a_ 197 NLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRV--HDVK 254 ::::: ::::::::: : :::::: ::::::::::::::::::::: :::: d1vlwa_ 145 AMKGP-FPNVKFVPT-------G---GVNLDN-VCEWFKAGVLAVGVGSALVKGTPDEVR 192 d1tx2a_ 255 EMSRMAKMMDAMI 267 : :::::::::: d1vlwa_ 193 E--KAKAFVEKIR 203