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 <-- 1.197 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1tyga_) 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 d1tyga_ Thiazole biosynthesis protein ThiGThiG-​like (Pfam 05690)TIM 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 <-- 1.197 --> Hit
DALI alignment (Z-score: 12.1 Raw score:1221.40) d1tx2a_ 1 kwdyDLRCgeyTLNLnektLIMGILNVtpdsfsdggsynevDAAVRHAKEMRDEGAHIID 60 :::: :::: :::::::: ::::::::::::::::::: d1tyga_ 1 --mlTIGG---KSFQ---sRLLLGTGK-------------yPSFDIQKEAVAVSESDILT 39 d1tx2a_ 61 IGGesfakvsveeEIKR-vvpmiqAVSKEV---KLPISIDTY-------KAEVAKQAIEA 109 ::: :::: :::::: ::::::::: ::::::::::: d1tyga_ 40 FAV----------RRMNifeasqpNFLEQLdlsKYTLLPNTAgastaeeAVRIARLAKAS 89 d1tx2a_ 110 -GAHIINDIW------------gAKAEpkIAEVAAHyDVPIILMHNrdnmnyrnlmadMI 156 ::::::::: :::: ::::::: ::::::::: :: d1tyga_ 90 gLCDMIKVEVigcsrsllpdpveTLKA--SEQLLEE-GFIVLPYTS-----------dDV 135 d1tx2a_ 157 ADLYDSIKIAkdagvrdenIILDPGIGFaktpeqNLEAmRNLEQLN-VLGYPVLL-GTSR 214 :::::::::: ::::::::: :::: ::::::: :::::::: :::: d1tyga_ 136 VLARKLEELG--------vHAIMPGASPigsgqgILNP-LNLSFIIeQAKVPVIVdAGIG 186 d1tx2a_ 215 ksfighvldlpveerlegTGATVCLGIEKGCEFVRVH-----------DVKEMSRMAKMM 263 ::::::::::::::::::: :::::::::::: d1tyga_ 187 ------------------SPKDAAYAMELGADGVLLNtavsgaddpvkMARAMKLAVEAG 228 d1tx2a_ 264 DAMIGK-------- 269 :::::: d1tyga_ 229 RLSYEAgriplkqy 242 FAST alignment (Normalized score: 7.89 Raw score:2012.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKT-----------LIMGILNVTPDSFSDGGSYN-----EVDAA 44 ::::: ::::: d1tyga_ 1 -------------------MLTIGGKSFQSRLLLG---------------TGKYPSFDIQ 26 d1tx2a_ 45 VRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQ------------AVSKEV--- 89 :::::: ::::::::: :::::: d1tyga_ 27 KEAVAV---SESDILTFA---------------------VRRMNIFEASQPNFLEQLDLS 62 d1tx2a_ 90 KLPISIDTY----------KAEVAKQAIE-AGAHIINDIWGAKA---------------E 123 :::::: :::::::::: :::::::: : d1tyga_ 63 KYTLLP---NTAGASTAEEAVRIARLAKASGLCDMIKV------EVIGCSRSLLPDPVET 113 d1tx2a_ 124 PKIAEVAAHYDVPIILMHNRDNMNYRNLMAD---MIADLYDSIKIAKDAGVRDEN---II 177 ::::::::::::::::: :::::::::: :: d1tyga_ 114 LKASEQLLEEGFIVLPY--------------TSDDVVLARKLEE-----------LGVHA 148 d1tx2a_ 178 LDPGIGFAKTPEQNLE----------AMRNLEQLN-VLGYPVLLGTSRKSFIGHVLDLPV 226 ::::: ::::::::: ::::::: d1tyga_ 149 IMPGA-----------SPIGSGQGILNPLNLSFIIEQAKVPVI----------------- 180 d1tx2a_ 227 EERLEG------TGATVCLGIEKGCEFVRVH------------DVKEMSRMAKMMDAMIG 268 :::::::::::::::::: ::::::::::::::: d1tyga_ 181 ------VDAGIGSPKDAAYAMELGADGVLL-NTAVSGADDPVKMARAMKLAVEAGRLS-- 231 d1tx2a_ 269 K----------- 269 d1tyga_ 232 -YEAGRIPLKQY 242 TMalign alignment (TM-score: 0.53 Raw score:143.58) d1tx2a_ 1 KWDYDLRCGEYTLNLN--------------------EKTLIMGILNVTPDSFSDGGSYN- 39 :::::: :::::: :::::::::::::: : d1tyga_ 1 ---MLTIGG-KSFQSRLLLGTGKYPSFDIQKEAVAV-SESDILTFAVRRMN-------IF 48 d1tx2a_ 40 -----EVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPIS 94 ::::::::::::::::::: ::::::::::::::::: :: :::: d1tyga_ 49 EASQP------NFLEQLDLSKYTLLPNTAG----ASTAEEAVRIARLAKAS--GL-CDMI 95 d1tx2a_ 95 IDT---------Y----KAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMH 141 ::: : :::::::::::::::::: :::: ::::::::::::::::::: d1tyga_ 96 KVEVIGCSRSLLPDPVETLKASEQLLEEGFIVLPY-TSDD-VVLARKLEELGVHAIMPGA 153 d1tx2a_ 142 NRD-NMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQ 200 ::: : : :: : :::::::::::: :: ::::::::: : ::::::: d1tyga_ 154 SPIG-S-G--QG--I-LNPLNLSFIIEQ--AK-VPVIVDAGI--------G--SPKDAAY 193 d1tx2a_ 201 LNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCE-------------- 246 :::::::::::::::::: : ::::::::::::::: d1tyga_ 194 AMELGADGVLLNTAVSGA---D---------DPVKMARAMKLAVEAGRLSYEAGRIPLKQ 241 d1tx2a_ 247 -FVRVHDVKEMSRMAKMMDAMIGK 269 d1tyga_ 242 Y----------------------- 242 HHsearch alignment (Probability: 0.91 E-value:0.00) d1tx2a_ 6 LRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGES 65 :::::::::: ::::: :::::::::::: :::::::::::::::: d1tyga_ 2 LTIGGKSFQS---RLLLG-----------TGKYPSFDIQKE---AVAVSESDILTFAVRR 44 d1tx2a_ 66 FAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAI 107 ::::::: :::: ::::: :::::::::::::::::::: d1tyga_ 45 MNIFEAS--QPNF---LEQLD-LSKYTLLPNTAGASTAEEAV 80