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 <-- 0.922 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1j6oa_) 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 d1j6oa_ Hypothetical protein TM0667Metallo-​dependent hydrolasesTIM 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 <-- 0.922 --> Hit
DALI alignment (Z-score: 7.5 Raw score:845.70) d1tx2a_ 1 kwdydlrcgeytlnlnektLIMGILNVTPdsfsdggsynevdAAVRHAKEMR-DEGAHII 59 :::::::::: :::::::::: ::::::: d1j6oa_ 1 --------------hhhhmVDTHAHLHFH---------qfddDRNAVISSFEeNNIEFVV 37 d1tx2a_ 60 DIGGEsfakvsveeeikrVVPMIQaVSKEVK-LPISIDTY----------KAEVAKQAIE 108 ::::: :::::: :::::: :::::::: :::::::::: d1j6oa_ 38 NVGVN----------ledSKKSLD-LSKTSDrIFCSVGVHphdakevpedFIEHLEKFAK 86 d1tx2a_ 109 A-GAHIINDIW-----------gaKAEP-KIAEVAAHYDVPIILMHNRdnmnyrnlmadM 155 : ::::::::: :::: ::::::::::::::::::: : d1j6oa_ 87 DeKVVAIGETGldffrnispaevqKRVFvEQIELAGKLNLPLVVHIRD-----------A 135 d1tx2a_ 156 IADLYDSIKIakdAGVRDENIILDPGIgfaktpeqnleamrNLEQ-LNVLG---YPVLLG 211 :::::::::: :::::::::::::: :::: ::::: :::::: d1j6oa_ 136 YSEAYEILRT---ESLPEKRGVIHAFS--------------SDYEwAKKFIdlgFLLGIG 178 d1tx2a_ 212 TsrksfighvldlpveerlegtgaTVCL-----GIEKG------cEFVRV---------- 250 : :::: ::::: ::::: d1j6oa_ 179 G-----------------------PVTYpkneaLREVVkrvgleyIVLETdcpflppqpf 215 d1tx2a_ 251 ----HDVKEMSRMAKMMDAMIGK---------------------- 269 ::::::::::::::::::: d1j6oa_ 216 rgkrNEPKYLKYVVETISQVLGVpeakvdeattenarriflevke 260 FAST alignment (Normalized score: 4.52 Raw score:1196.00) d1tx2a_ 1 KWDYDLRCGEYTLNLN-------------------------------------------- 16 d1j6oa_ 1 ----------------HHHHMVDTHAHLHFHQFDDDRNAVISSFEENNIEFVVNVGVNLE 44 d1tx2a_ 17 ------------EKTLIMGILNVTPDSFS--------DGGSYNEVDAAVRHAKEMRDEGA 56 :::::: :::::::::::::::: :::: d1j6oa_ 45 DSKKSLDLSKTSDRIFCS-----------VGVHPHDAKEVPEDFIEHLEKFAK---DEKV 90 d1tx2a_ 57 HI-IDIGGESFA------KVSVEEEIKRVVPMIQAVSKEVKLPISIDT-YKAEVAKQA-I 107 :: :::: ::::::::::::::::::: :::::::::: ::::::::: : d1j6oa_ 91 VAIGETG-----LDFFRNISPAEVQKRVFVEQIELAG-KLNLPLVVHIRDAYSEAYEILR 144 d1tx2a_ 108 EAG----AHIINDIWGAKA-----EPKIAEVAAHYDVPIILMHNRDNMNYRNLMADM--- 155 ::: :::: :::::::::::::::::: d1j6oa_ 145 TESLPEKRGVI--------HAFSSDYEWAKKFIDLGFLLGIG---------------GPV 181 d1tx2a_ 156 ----IADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLE-----------AMRNLEQ 200 :::::::::: :::::::::::::: ::::::: d1j6oa_ 182 TYPKNEALREVVKR-----VGLEYIVLETDCPF---------LPPQPFRGKRNEPKYLKY 227 d1tx2a_ 201 LNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMA 260 ::: d1j6oa_ 228 VVE--------------------------------------------------------- 230 d1tx2a_ 261 KMMDAMIGK------------------------------ 269 d1j6oa_ 231 ---------TISQVLGVPEAKVDEATTENARRIFLEVKE 260 TMalign alignment (TM-score: 0.49 Raw score:130.70) d1tx2a_ 1 KW-----------------------------DYDLRCGEYTLNLN-EKTLIM-------- 22 :: : ::::: d1j6oa_ 1 HHHHMVDTHAHLHFHQFDDDRNAVISSFEEN-------------NI-EFVVNVGVNLEDS 46 d1tx2a_ 23 --------------GILNV---TPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGES 65 ::::: :::: : :::::::::::::: : ::::::::::: d1j6oa_ 47 KKSLDLSKTSDRIFCSVGVHPHDAKE-V---PEDFIEHLEKFAKD--E-KVVAIGETGLD 99 d1tx2a_ 66 ---FAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTY-KA-EVAKQAIEA-GA--HIINDI 117 ::::: :::::::::::::::: :::::::::: :: ::::::::: :: :::::: d1j6oa_ 100 FFRNISPA-EVQKRVFVEQIELAGK-LNLPLVVHIRDAYSEAYEILRTESLPEKRGVIHA 157 d1tx2a_ 118 WGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENII 177 ::: :::::::::::::::::::: ::::::::::::::: ::::::: d1j6oa_ 158 -FSS-DYEWAKKFIDLGFLLGIGGP-----------VTYPKNEALREVVKR--VGLEYIV 202 d1tx2a_ 178 LDPGIGFAK---TPEQNLEAMRNLEQLNV-LG---------YPV--LLGTSRKSFIGHVL 222 ::::::::: :::::: :::::::::: :: ::: d1j6oa_ 203 LETDCPFLPPQPFRGKRN-EPKYLKYVVETISQVLGVPEAKVDEAT-------------- 247 d1tx2a_ 223 DLPVEERLEGTGATVCLGIEKGCEFV---RVHDVKEMS----RMAKMMDAMIGK 269 ::::: : d1j6oa_ 248 ---------------------TENARRIF--------LEVKE------------ 260 HHsearch alignment (Probability: 0.72 E-value:0.00) d1tx2a_ 125 KIAEVAAHYDVPIILM 140 :::::::::::::::: d1j6oa_ 116 EQIELAGKLNLPLVVH 131