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 <-- 0.850 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1itua_) 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 d1itua_ Renal dipeptidaseMetallo-​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 <-- 0.850 --> Hit
DALI alignment (Z-score: 8.2 Raw score:1005.70) d1tx2a_ 1 kwdydlrcgeytlnlnEKTLIMGILN--VTPDsfsdggsyNEVDA-------avrhakEM 51 :::::::::: :::: ::::: :: d1itua_ 1 ---dffrdeaerimrdSPVIDGHNDLpwQLLD-------mFNNRLqderanlttlagtHT 50 d1tx2a_ 52 RD-------EGAHIIDIGGESfaKVSVEEEIKRVVPMIQAVSKEV--------------- 89 :: :::::::::::: :::::::::::::::::::::: d1itua_ 51 NIpklragfVGGQFWSVYTPC--DTQNKDAVRRTLEQMDVVHRMCrmypetflyvtssag 108 d1tx2a_ 90 ----------KLPISIDTYK-----AEVAKQAIEAGAHIINDI----------------- 117 :::::::::: :::::::::::::::::: d1itua_ 109 irqafregkvASLIGVEGGHsidssLGVLRALYQLGMRYLTLThscntpwadnwlvdtgd 168 d1tx2a_ 118 ------wgakAEPKIAEVAAHYDVPIILMHNrdnmnyrnlmadMIADLYDSIKIAKdagv 171 ::::::::::::::::::::: ::::::::::::: d1itua_ 169 sepqsqglspFGQRVVKELNRLGVLIDLAHV------------SVATMKATLQLSR---- 212 d1tx2a_ 172 rdENIILdpgigfaktpeqNLEA-mrnLEQLNVLG----YPVLLGtSRKSF-IGHVLdlp 225 ::::: :::: :::::::: :::::: ::::: ::::: d1itua_ 213 --APVIF-----shssaysVCASrrnvPDDVLRLVkqtdSLVMVN-FYNNYiSCTNK--- 261 d1tx2a_ 226 veERLEGTGATVCLGIE---KGCEFVRVH------------DVKEmSRMAKMMDA---MI 267 ::::::::::::::: ::::::::: :::: ::::::::: :: d1itua_ 262 --ANLSQVADHLDHIKEvagARAVGFGGDfdgvprvpegleDVSK-YPDLIAELLrrnWT 318 d1tx2a_ 268 GK------------------------------------------------- 269 :: d1itua_ 319 EAevkgaladnllrvfeaveqasnltqapeeepipldqlggscrthygyss 369 FAST alignment (Normalized score: 4.28 Raw score:1348.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNE--------------KTLIMGILNVTPDSFSDG----------- 35 :::: d1itua_ 1 -----------------DFFRDEAERIMRDSPVID--------------GHNDLPWQLLD 29 d1tx2a_ 36 ------GSYNEVDA-----------AVRHAKEMRDEGAHIIDIGGESFAKV--------- 69 :::: ::::::: ::::::::: d1itua_ 30 MFNNRLQDER----ANLTTLAGTHTNIPKLRA---GFVGGQFWS-------VYTPCDTQN 75 d1tx2a_ 70 --SVEEEIKRVVPMIQAVSKEVK------------------------LPISIDT-----Y 98 ::::::: ::::::::::: ::::::: : d1itua_ 76 KDAVRRTLE-QMDVVHRMCRM--YPETFLYVTSSAGIRQAFREGKVASLIGVEGGHSIDS 132 d1tx2a_ 99 KAEVAKQAIEAGAHIINDIWGAKA------------------------------EPKIAE 128 ::::::::::::::::: :::::: d1itua_ 133 SLGVLRALYQLGMRYLT-------LTHSCNTPWADNWLVDTGDSEPQSQGLSPFGQRVVK 185 d1tx2a_ 129 VAAHYDVPIILMHNRDNMNYRNLMAD---MIADLYDSIKIAKDAGVRDENIILDPGIGFA 185 ::::::::::: ::::::::::: d1itua_ 186 ELNRLGVLIDL---------------AHVSVATMKATLQL-------------------- 210 d1tx2a_ 186 KTPEQNLEAMRN--------------------------LEQLNVLGYPVLLGTSR---KS 216 ::::::::::::: :: d1itua_ 211 ------------SRAPVIFSHSSAYSVCASRRNVPDDVLRLVKQTDSLVMV----NFYNN 254 d1tx2a_ 217 FIGHVLDLPVEE------RLEGTGATVCLGIEKGC------EFVRV-------------- 250 :: :::::::::::::: ::::: d1itua_ 255 YI----------SCTNKANLSQVADHLDHIKE---VAGARAVGFGGDFDGVPRVPEGLED 301 d1tx2a_ 251 -HDVKEMSRMAKMMDAMIGK---------------------------------------- 269 :::::::::::: d1itua_ 302 VSKYPDLIAELLR-------RNWTEAEVKGALADNLLRVFEAVEQASNLTQAPEEEPIPL 354 d1tx2a_ 270 --------------- 270 d1itua_ 355 DQLGGSCRTHYGYSS 369 TMalign alignment (TM-score: 0.53 Raw score:143.08) d1tx2a_ 1 ------------KWD-YD------------------------------------------ 5 ::: : d1itua_ 1 DFFRDEAERIMRDSPV-IDGHNDLPWQLLDMFNNRLQDERANLTTLAGTHTNIPKLRAGF 59 d1tx2a_ 6 ---------------------------------------------LRCGEYTLN-LNEK- 18 ::: :::: d1itua_ 60 VGGQFWSVYTPCDTQNKDAVRRTLEQMDVVHRMCRMYPETFLYVT------SSAGIRQAF 113 d1tx2a_ 19 -----TLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFA------ 67 ::::::::::: :::: :::::::::::: :::::::::: d1itua_ 114 REGKVASLIGVEGGHS---------IDSS--LGVLRALYQLGM-RYLTLTHSCNTPWADN 161 d1tx2a_ 68 -------KVSVEEEIK-RVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAG-AHIINDIW 118 ::::::::: ::::::::::: :::::::::::::::::::::: :::::::: d1itua_ 162 WLVDTGDSEPQSQGLSPFGQRVVKELNR-LGVLIDLAHVSVATMKATLQLSRAPVIFSHS 220 d1tx2a_ 119 GAK-------A-EPKIAEVAAHYDVPIILMHN-R---DNMNYRNLMADMIADLYDSIKIA 166 ::: : :::::::::::::::::::: : ::::: : ::::::::::: d1itua_ 221 SAYSVCASRRNVPDDVLRLVKQTDSLVMVNFYNNYISCTNKA-----N-LSQVADHLDHI 274 d1tx2a_ 167 KDAGVRDENIILDPGI-GFAKTPEQNLEAMRNLEQLNV-L---------G--YPV--LLG 211 ::::: :::::::::: ::::: ::::::::::::::: : : ::: d1itua_ 275 KEVAG-ARAVGFGGDFDGVPRV-PEGLEDVSKYPDLIAELLRRNWTEAEVKGALADN--- 329 d1tx2a_ 212 TSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCE------------------------- 246 :: d1itua_ 330 ---------------------------------LLRVFEAVEQASNLTQAPEEEPIPLDQ 356 d1tx2a_ 247 -------------FVRVHDVKEMSRMAKMMDAMIGK 269 d1itua_ 357 LGGSCRTHYGYSS----------------------- 369 HHsearch alignment (Probability: 0.67 E-value:0.00) d1tx2a_ 101 EVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNR---DNMNYRNLMADMIA 157 :::::::::: ::::::::: ::::::::::::::::::::: :::::::::::::: d1itua_ 182 RVVKELNRLG--VLIDLAHVS-VATMKATLQLSRAPVIFSHSSAYSVCASRRNVPDDVLR 238 d1tx2a_ 158 DLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNL-EAMRNLEQLNVLG 205 :: ::::::: ::::::::::: :::::: ::::::::::::: d1itua_ 239 LV------KQTDSLV--MVNFYNNYISC-TNKANLSQVADHLDHIKEVA 278