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 <-- 0.775 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1rhca_) 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 d1rhca_ Coenzyme F420 dependent secondary alcohol dehydrogenaseBacterial luciferase-​likeTIM 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 <-- 0.775 --> Hit
DALI alignment (Z-score: 10.9 Raw score:1235.70) d1tx2a_ 1 kwdydlrcgeytlnlnEKTLIMGILNVTPdsfsdggsynEVDAAVRHAKEMRDEGAHIID 60 ::::::::::::: ::::::::::::::::::::: d1rhca_ 1 ----------------MKTQIGYFASLEQ---------yRPMDALEQAIRAEKVGFDSVW 35 d1tx2a_ 61 IGGESFAkvsveeeikRVVPMIQAVSKEVK-LPISI-DTYK---------AEVAKQAIEA 109 ::::::: :::::::::::::: ::::: :::: :::::::::: d1rhca_ 36 VDDHFHPwyhdnaqsaQAWAWMGAALQATKkVFISTcITCPimrynpaivAQTFATLRQM 95 d1tx2a_ 110 G--AHIINDIW---------------------gAKAEP-KIAE----------------- 128 : :::::::: ::::: :::: d1rhca_ 96 YpgRVGVAVGAgeamnevpvtgewpsvpvrqdmTVEAVkVMRMlwesdkpvtfkgdyftl 155 d1tx2a_ 129 ------vaahYDVPIILMHNrdnmnyrnlmadMIADLYDSIKIakdagvrdenIILDPGI 182 :::::::::: ::::::::::: ::::::: d1rhca_ 156 dkaflytkpdDEVPLYFSGM------------GPKGAKLAGMY---------gDHLMTVA 194 d1tx2a_ 183 GfaktpeqnleAMRNLEQ-LNVL-------------gYPVLLGTSRksfighvLDLP--- 225 : ::::::: :::: ::::::::: :::: d1rhca_ 195 A----------APSTLKNvTIPKfeegareagkdpskMEHAMLIWY--svdpdYDKAvea 242 d1tx2a_ 226 ----------------------------------------VEERLEGTGATVCLGIEKGC 245 :::::::::::::::::::: d1rhca_ 243 lrfwagclvpsmfkykvydpkevqlhanlvhcdtikenymCATDAEEMIKEIERFKEAGI 302 d1tx2a_ 246 EFVRVHD-----------VKEMSRMAKmmdamigk 269 ::::::: ::::::::: d1rhca_ 303 NHFCLGNsspdvnfgidiFKEVIPAVR-------d 330 FAST alignment (Normalized score: 7.27 Raw score:2167.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYN----EVDAAVRHAKEMRDEGA 56 :::::::::: ::::::::::::::::: d1rhca_ 1 ----------------MKTQIGYFAS-------------LEQYRPMDALEQAIRAEKVGF 31 d1tx2a_ 57 HIIDIGGESFAKVSVEEEIK--------------RVVPMIQAVSKEV-KLPISIDTY--- 98 :::::: ::::::::::::: :::::: d1rhca_ 32 DSVWVD--------------DHFHPWYHDNAQSAQAWAWMGAALQATKKVFIST---CIT 74 d1tx2a_ 99 ----------KAEVAKQAIEAGA----HIINDIWGAKA---------------------- 122 ::::::::::: ::::: d1rhca_ 75 CPIMRYNPAIVAQTFATLRQM--YPGRVGVAV------GAGEAMNEVPVTGEWPSVPVRQ 126 d1tx2a_ 123 ------EPKIAEVAAH-------------------------YDVPIILMHNRDNMNYRNL 151 :::::::: ::::::::: d1rhca_ 127 DMTVEAVKVMRMLW--ESDKPVTFKGDYFTLDKAFLYTKPDDEVPLYFSG---------- 174 d1tx2a_ 152 MAD-MIADLYDSIKIAKDAGVRDEN--IILDPGIGFAKTPEQNLE---AMRNLE-QLNV- 203 :::::::::: ::::: :::::: :::: d1rhca_ 175 ---MGPKGAKLAGM-----------YGDHLMT-------------VAAAPSTLKNVTIPK 207 d1tx2a_ 204 ------------LGYPVLLGTSRKSFIGHVLDLPVEE----------------------- 228 ::::::::: d1rhca_ 208 FEEGAREAGKDPSKMEHAMLI----------------WYSVDPDYDKAVEALRFWAGCLV 251 d1tx2a_ 229 ----------------------------------RLEGTGATVCLGIEKGCEFVRV---- 250 :::::::::::::::::::::: d1rhca_ 252 PSMFKYKVYDPKEVQLHANLVHCDTIKENYMCATDAEEMIKEIERFKEAGINHFCLGNSS 311 d1tx2a_ 251 -------HDVKEMSRMAKMMDAMIGK--- 269 ::::::::: d1rhca_ 312 PDVNFGIDIFKEVIPA----------VRD 330 TMalign alignment (TM-score: 0.52 Raw score:138.54) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTL-------------------------IMGILNVTP------ 29 : :: ::: ::::::::: d1rhca_ 1 -M------------KT-QIGYFASLEQYRPMDALEQAIRAEKVGFDSVWVDDHFHPWYHD 46 d1tx2a_ 30 -----DSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQA 84 :::::::::::: :: :::::::::: :::::::::::::::: d1rhca_ 47 NAQSA---------QAWAWMGAALQA-TK-KVFISTCITC----PIMRYNPAIVAQTFAT 91 d1tx2a_ 85 VSKEVK-LPISIDTY----------------------KAEVAKQAI-EA----------- 109 :::::: :::::::: ::::::::: :: d1rhca_ 92 LRQMYPGRVGVAVGAGEAMNEVPVTGEWPSVPVRQDMTVEAVKVMRMLWESDKPVTFKGD 151 d1tx2a_ 110 ---------------GAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMAD 154 ::::::::::::::::::::: :::::::: :::: d1rhca_ 152 YFTLDKAFLYTKPDDEVPLYFSGMGPKGAKLAGMYG-----DHLMTVAA-------APST 199 d1tx2a_ 155 MIADL-YDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTS 213 ::::: ::::::::::::::::::: ::::: d1rhca_ 200 LKNVTIPKFEEGAREAGKDPSKMEH------------------------------AMLIW 229 d1tx2a_ 214 RK-----SFIGHVLDLPVE-----------------------------------ERLEGT 233 :: :::::::::: ::: d1rhca_ 230 YSVDPDY--DKAVEALRFWAGCLVPSMFKYKVYDPKEVQLHANLVHCDTIKENY---MCA 284 d1tx2a_ 234 -GA-TVCLGIEK-G---CEFVRVHD----VKEMSRMAKMMDAMIGK 269 :: :::::::: : :::::::: ::::::::::::::::: d1rhca_ 285 TDAEEMIKEIERFKEAGINHFCLGNSSPDVNFGIDIFKEVIPAVRD 330 HHsearch alignment (Probability: 0.36 E-value:0.00) d1tx2a_ 49 KEMRDEGAHIIDIGGESF--------AKVSVEEEIKRVVPMIQAVSKEV--KLPISIDTY 98 :::::::::::::::::: ::::::::::::::::::::::: ::::::::: d1rhca_ 92 LRQMYPGRVGVAVGAGEAMNEVPVTGEWPSVPVRQDMTVEAVKVMRMLWESDKPVTFKGD 151 d1tx2a_ 99 KAEVAKQAI----EAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMAD 154 ::::::::: ::::::: :::: :::::::::::::::::::: :::::::: d1rhca_ 152 YFTLDKAFLYTKPDDEVPLY--FSGM--GPKGAKLAGMYGDHLMTVAA----APSTLKNV 203 d1tx2a_ 155 MIADLYDSIKIAKDAGVRDENI--ILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGT 212 ::: :::::::::::::::: :::::::::::::::::::::::::::::::::::: d1rhca_ 204 TIP---KFEEGAREAGKDPSKMEHAMLIWYSVDPDYDKAVEALRFWAGCLVPSMFKYKVY 260 d1tx2a_ 213 SRKSFIGHVLDLPVEERL-----EGTGA---TV-CLGIEKGCEFVRVHDV-KEMSRMAKM 262 :::::::::::::::::: ::::: :: :::::::::::::::: ::::::::: d1rhca_ 261 DPKEVQLHANLVHCDTIKENYMCATDAEEMIKEIERFKEAGINHFCLGNSSPDVNFGIDI 320 d1tx2a_ 263 MDAMI 267 ::::: d1rhca_ 321 FKEVI 325