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 <-- 0.892 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1k87a2) 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 d1k87a2 Proline dehydrohenase domain of bifunctional PutA proteinFAD-​linked oxidoreductaseTIM 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 <-- 0.892 --> Hit
DALI alignment (Z-score: 9.2 Raw score:1089.80) d1tx2a_ 1 kwdydlrcgeytlnlnektlimgilnvtpdsfsdggsyNEVDAAVRHAKEMRDEGAHIID 60 :::::::::::::::::::::: d1k87a2 1 -------------------------------------gETIAEALANARKLEEKGFRYSY 23 d1tx2a_ 61 IGGES-FAKV-SVEEEIKRVVPMIQAVSKEVK------LPISIDTY-------------- 98 ::::: :::: ::::::::::::::::::::: :::::::: d1k87a2 24 DMLGEaALTAaDAQAYMVSYQQAIHAIGKASNgrgiyeGPGISIKLsalhprysraqydr 83 d1tx2a_ 99 ----KAEVAKQAIEAG----AHIINDIW---gaKAEP-KIAEVAAH----yDVPIILMHN 142 :::::::::::: :::::::: :::: :::::::: ::::::::: d1k87a2 84 vmeeLYPRLKSLTLLArqydIGINIDAEeadrlEISLdLLEKLCFEpelagWNGIGFVIQ 143 d1tx2a_ 143 rdnmnyrnlMADMIADLYDSIKIAKDagVRDEnIILDPGIGFAK---------------- 186 ::::::::::::::::: :::: ::::::::::: d1k87a2 144 -------ayQKRCPLVIDYLIDLATR--SRRR-LMIRLVKGAYWdseikraqmdglegyp 193 d1tx2a_ 187 ---TPEQNLEAMRN-LEQLNVLG--YPVLLGTSrksfighvldlpveerlegTGATVCLG 240 ::::::::::: :::::::: :::::::: :::::::: d1k87a2 194 vytRKVYTDVSYLAcAKKLLAVPnlIYPQFATH-------------------NAHTLAAI 234 d1tx2a_ 241 IEKG-------cEFVRVH---DVKEMSRMA------KMMD-------------------- 264 :::: :::::: ::::::::: :::: d1k87a2 235 YQLAgqnyypgqYEFQCLhgmGEPLYEQVTgkvadgKLNRpcriyapvgthetllaylvr 294 d1tx2a_ 265 ----------------------------------------------------amigk 269 d1k87a2 295 rllengantsfvnriadtslpldelvadpvtaveklaqqegqtglphpkiplprdly 351 FAST alignment (Normalized score: 5.97 Raw score:1834.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNE-----------------KTLIMGILNV--TPDSFSDGG----S 37 :::::::: :::: : d1k87a2 1 -----------------GETIAEALANARKLEEKGFRYSYDM--LGEAAL-----TAADA 36 d1tx2a_ 38 YNEVDAAVRHAKEMRDEGA----------HIIDIGGESF-------AKVSVEEEIKRVVP 80 :::::::::::::::: ::::::: :::::::::::::: d1k87a2 37 QAYMVSYQQAIHAIGK---ASNGRGIYEGPGISIKL---SALHPRYSRAQYDRVMEELYP 90 d1tx2a_ 81 MIQAVSKE---VKLPISIDTY----------KAEVAKQAIEAGA----------HIINDI 117 :::::::: ::::::: ::::::::: ::::: d1k87a2 91 RLKSLTLLARQYDIGINI---DAEEADRLEISLDLLEKLC----FEPELAGWNGIGFVI- 142 d1tx2a_ 118 WGAKA----------EPKIAEVAAHYDVPIILMHNRDNMNYR------------------ 149 :::::::::::::::::::: d1k87a2 143 -----QAYQKRCPLVIDYLIDLATRSRRRLMIRLV-------KGAYWDSEIKRAQMDGLE 190 d1tx2a_ 150 ---------NLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQ---NLEAMRN 197 ::::::::::::::: ::::::::: :::: d1k87a2 191 GYPVYTRKVYTDVSYLACAKKLLA-------VPNLIYPQF----------ATHNAHT--- 230 d1tx2a_ 198 LEQLNVL---------GYPVLLGTSRKSFIGHVLDLPVEERLEG----TGATVCLGI--- 241 :::::: :::::: :::::::: d1k87a2 231 LAAIYQ-LAGQNYYPGQYEFQC----------------------LHGMGEPLYEQV-TGK 266 d1tx2a_ 242 ----EKGC-EFVRVHDVKEMSRMAKMMDAMIGK--------------------------- 269 :::: ::::: d1k87a2 267 VADGKLNRPCRIYA-------------------PVGTHETLLAYLVRRLLENGANTSFVN 307 d1tx2a_ 270 -------------------------------------------- 270 d1k87a2 308 RIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRDLY 351 TMalign alignment (TM-score: 0.58 Raw score:155.46) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 : : :::::::::::::::::: :: d1k87a2 1 -------------------------G-E-----------TIAEALANARKLEEKGFR-YS 22 d1tx2a_ 61 IGGESFAKV---SVEEEIKRVVPMIQAVSKEVK-L----PISIDTYK------------- 99 ::::::::: ::::::::::::::::::::: : :::::::: d1k87a2 23 YDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYD 82 d1tx2a_ 100 ------A-EVAKQAIEA--GAHIINDIW-----G--AKAEP-KIAEV-AAHYDVPIILMH 141 : ::::::::: ::::::::: : ::::: ::::: :::::::::::: d1k87a2 83 RVMEELYPRLKSLTLLARQYDIGINIDAEEADRLEISLDLLEKLCFEPELAGWNGIGFVI 142 d1tx2a_ 142 NRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGF----------------- 184 :: :: : ::::::::::::::: ::: :::::::::: d1k87a2 143 QA-YQ-K-----RCPLVIDYLIDLATR-SRR--RLMIRLVKGAYWDSEIKRAQMDGLEGY 192 d1tx2a_ 185 -AKT-PEQNLEAMRN-LEQLNVLG--YPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCL 239 ::: :::::::::: :::::::: :::::::: ::::::: d1k87a2 193 PVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATH-------------------NAHTLAA 233 d1tx2a_ 240 GIEKG-------CEFVRV-H--DVKEMSRMAK-----MMDA------------------- 265 ::::: :::::: : :::::::::: :::: d1k87a2 234 IYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLV 293 d1tx2a_ 266 ----------------------------------------------------------MI 267 d1k87a2 294 RRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRDLY-- 351 d1tx2a_ 268 GK 269 d1k87a2 352 -- 352 HHsearch alignment (Probability: 0.58 E-value:0.04) d1tx2a_ 40 EVDAAVRHAKEMRDEGAH-IIDIGGESFAKVSVEE-EIKRVVPMIQAVSK 87 :::::::::::::::::: :::::::::::::::: :::::::::::::: d1k87a2 3 TIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGK 52