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 <-- 1.288 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1viza_) 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 d1viza_ PcrB protein homolog YerEFMN-​linked oxidoreductasesTIM 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 <-- 1.288 --> Hit
DALI alignment (Z-score: 11.3 Raw score:1126.80) d1tx2a_ 1 kwdydlrcgeYTLNLNekTLIMGILNVTPdsfsdggsynEVDAavRHAKEMRDEGAHIID 60 :::::: ::::::::::: :::: ::::::::::::::: d1viza_ 1 ---------sLYDVTE--WKHVFKLDPNK----------DLPD--EQLEILCESGTDAVI 37 d1tx2a_ 61 IGgesfakvsveeEIKRVVPMIQAVSkEVKLPISIDTYKAEVAkqaiEAGAHIINDIWG- 119 :: ::::::::::::: :::::::::::::::: :::::::::::: d1viza_ 38 IG----------gTEDNVLRMMSKVR-RFLVPCVLEVSAIEAI----VPGFDLYFIPSVl 82 d1tx2a_ 120 -----aKAEPKIAEV-------aahydVPIILMHN-----------rDNMNYrnLMADMI 156 ::::::::: :::::::: ::::: :::::: d1viza_ 83 nsknadWIVGMHQKAmkeygelmsmeeIVAEGYCIanpdckaaalteADADL--NMDDIV 140 d1tx2a_ 157 ADLYDSIKIakdagvrdenIILDPGIGfaktpeqNLEAMRNLEQLNVLG--YPVLLGTSR 214 ::::::::: :::::::: ::::::::::::::: ::::::::: d1viza_ 141 AYARVSELL--------qlPIFYLEYS------gVLGDIEAVKKTKAVLetSTLFYGGGI 186 d1tx2a_ 215 ksfighvldlpveerlegTGATVCLGIEkGCEFVRVH--------dVKEMSRMAKMmdam 266 :::::::::: :::::::: :::::::::: d1viza_ 187 -----------------kDAETAKQYAE-HADVIVVGnavyedfdrALKTVAAVKG---- 224 d1tx2a_ 267 igk 269 d1viza_ 225 --e 225 FAST alignment (Normalized score: 8.24 Raw score:2028.00) d1tx2a_ 1 KWDYDLRCGEYT--LNLNEKTLIMGILNVTPDSFSDGGSYNEVDA-----AVRHAKEMRD 53 :::::: ::::::: :::::::::: d1viza_ 1 ------------SLYDVTEW-KHVFKLD-----------------PNKDLPDEQLEILCE 30 d1tx2a_ 54 EGAHIIDIGGESFAKVSVEE--EIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIE--A 109 :::::::: ::::::::::::: ::::::::::::::: : d1viza_ 31 SGTDAVII------------GGTEDNVLRMMSKVR-RFLVPCVLEVSAIEA------IVP 71 d1tx2a_ 110 GAHIINDIWGAKA-----------EPKIAEVAAHYD----------VPIILMHNR----- 143 ::::::: :::::::::: :::::: d1viza_ 72 GFDLYFI------PSVLNSKNADWIVGMHQKAMK--EYGELMSMEEIVAEGY---CIANP 120 d1tx2a_ 144 ---------DNMNYRNLMADMIADLYDSIKIAKDAGVRDEN---IILDPGIGFAKTPEQN 191 ::::: :::::::::::::: :::::: d1viza_ 121 DCKAAALTEADADL--NMDDIVAYARVSEL-----------LQLPIFYLE---------- 157 d1tx2a_ 192 LE------AMRNLEQLNV--LGYPVLLGTSRKSFIGHVLDLPVEERLEG----TGATVCL 239 :::::::::: :::::::: ::::::: d1viza_ 158 --YSGVLGDIEAVKKTKAVLETSTLFYG---------------------GGIKDAETAKQ 194 d1tx2a_ 240 GIEKGCEFVRVHD-----------VKEMSRMAKMMDAMIGK--- 269 ::: :::::: :::::::: d1viza_ 195 YAE-HADVIV---VGNAVYEDFDRALKTVAAV---------KGE 225 TMalign alignment (TM-score: 0.57 Raw score:153.35) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 : :::::: ::::::::::: : :::::::::::::::::: d1viza_ 1 ----S-----LYDVTE--WKHVFKLDPNK----------D--LPDEQLEILCESGTDAVI 37 d1tx2a_ 61 IGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWG- 119 :: : ::::::::::::: ::::::::::::::: :: :::::::::::: d1viza_ 38 IG-G---------TEDNVLRMMSKVR-RFLVPCVLEVSAIEA--IV-PGFDLYFIPSVLN 83 d1tx2a_ 120 A--K-AEPKIAE-VA------AH-YDVPIILMHN-------R----DNMNYRNLMADMIA 157 : : ::::::: :: :: :::::::::: : ::::: ::::::: d1viza_ 84 SKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKAAALTEADADL--NMDDIVA 141 d1tx2a_ 158 DLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLN-VLG-YPVLLGTSRK 215 ::::::: : : :::::::::: : ::: :::::::: ::: ::::::::: d1viza_ 142 YARVSEL--L-----Q-LPIFYLEYSG---V-LGD--IEAVKKTKAVLETSTLFYGGGI- 186 d1tx2a_ 216 SFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRV---H-----DVKEMSRMAKMMDAMI 267 :: :::::::::: :::::: : ::::::::::: : d1viza_ 187 -------------KD---AETAKQYAEH-ADVIVVGNAVYEDFDRALKTVAAVKG--E-- 225 d1tx2a_ 268 GK 269 d1viza_ 226 -- 226 HHsearch alignment (Probability: 0.88 E-value:0.00) d1tx2a_ 39 NEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTY 98 :::::::::::::::::::::::::: ::: :::::::::: :::::::::: d1viza_ 16 PNKDLPDEQLEILCESGTDAVIIGGT----EDN------VLRMMSKVRR-FLVPCVLEVS 64 d1tx2a_ 99 KAEVAKQAIEAGA--HIINDIWGAKAEPKIAEVAAHYDV-------------------PI 137 ::::::::::::: :::::::::::::::::::::::: :: d1viza_ 65 AIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKA 124 d1tx2a_ 138 ILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRN 197 ::: :::::: :::::::: :::::::::::: : ::: ::::::::::::: d1viza_ 125 AAL-TEADAD--LNMDDIVA----YARVSELLQLPI--F----YLE-YSGVLGDIEAVKK 170 d1tx2a_ 198 LEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCE--FVRVHDVKE 255 :::::: ::::::: ::::::::: :::::::: ::::::::: d1viza_ 171 TKAVLE-TSTLFYG----------GGIKDAETA--------KQYAEHADVIVVGNAVYED 211 d1tx2a_ 256 MSRMAKMMDAMIGK 269 :::::::::::::: d1viza_ 212 FDRALKTVAAVKGE 225