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 <-- 0.929 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1h3ga3) 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 d1h3ga3 Cyclomaltodextrinase,​ central domain(Trans)glycosidasesTIM 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 <-- 0.929 --> Hit
DALI alignment (Z-score: 10.0 Raw score:1217.00) d1tx2a_ 1 kwdyDLRCgeytlnlnekTLIMGILNVT-------pDSFS------------dggsyNEV 41 :::: :::::::::: :::: ::: d1h3ga3 1 -gsaQRQG-------fgpGDAIYQIMPDrfangdpsNDNVagmreqadrrhgggrhgGDI 52 d1tx2a_ 42 DAAVRHAKEMRDEGAHIIDI-GGESFAK----------VSVEEE------IKRVVPMIQA 84 :::::::::::::::::::: ::::::: :::::: :::::::::: d1h3ga3 53 RGTIDHLDYIAGLGFTQLWPtPLVENDAaaysyhgyaaTDHYRIdprygsNEDFVRLSTE 112 d1tx2a_ 85 VSkEVKLPISIDTYK--------------------------------------------- 99 :: :::::::::::: d1h3ga3 113 AR-KRGMGLIQDVVLshigkhhwwmkdlptpdwinyggkfvptqhhrvavqdpyaaqads 171 d1tx2a_ 100 --------------------------AEVAKQAIE-AGAHIINDIWgAKAE-----PKIA 127 ::::::::: :::::::::: :::: :::: d1h3ga3 172 enftkgwfvegmpdlnqtnplvanylIQNNIWWIEyAGLSGLRIDT-YGYSdgaflTEYT 230 d1tx2a_ 128 EVAAHYD--VPIILMHNRdnmnyrnlmaDMIADLYDSI---------KIAKdagvrdenI 176 ::::::: ::::::::: :::::::::: :::: : d1h3ga3 231 RRLMAEYprLNMVGEEWS----------TRVPVVARWQrgkanfdgyTSHL--------P 272 d1tx2a_ 177 ILDPG-IGFA-----------kTPEQNLEAMRNleqLNVLGY--PVLLGTS-----RKSF 217 ::::: :::: ::::::::::: :::::: ::::::: :::: d1h3ga3 273 SLMDFpLVDAmrnalsktgeenGLNEVYETLSL---DYLYPEpqNLVLFGGnhdmaRMFS 329 d1tx2a_ 218 IGhvLDLPveERLEGTGATVCLGiekgCEFVRVHD------------------------- 252 :: :::: ::::::::::::: :::::::: d1h3ga3 330 AA--GEDF--DRWRMNLVFLMTM----PRIPQFYSgdeilmtstvkgrddasyrrdfpgg 381 d1tx2a_ 253 ---------------------vkEMSRMAKMMDaMIGK---- 269 :::::::::: :::: d1h3ga3 382 wagdkanafsgagltsqqraaqdLVRKLANWRK-NQPVihng 422 FAST alignment (Normalized score: 4.16 Raw score:1402.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEK----------TLIMGILNVTPDSFSDGGSYN----------- 39 :::::::: d1h3ga3 1 ------------------GSAQRQGFGPGDAIYQIM-------------PDRFANGDPSN 29 d1tx2a_ 40 ---------------------EVDAAVRHAKEMRDEGAHIIDIGGESFAK---------- 68 :::::::::::::::::::::: d1h3ga3 30 DNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWP-------TPLVENDAAA 82 d1tx2a_ 69 --------VSVEE-------EIKRVVPMIQAVSKEVKLPISIDTY--------------- 98 :::: ::::::::::::: :::::::::: d1h3ga3 83 YSYHGYAATDHY-RIDPRYGSNEDFVRLSTEAR-KRGMGLIQDV-VLSHIGKHHWWMKDL 139 d1tx2a_ 99 ---------------------------------------------------------KAE 101 ::: d1h3ga3 140 PTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQ 199 d1tx2a_ 102 VAKQAI-EAGAHIINDIWGAKAE---PKIAEVAAH-----YDVPIILMHNRDNMNYRNLM 152 :::::: :::::::::: :::: ::::::::: ::::::: d1h3ga3 200 NNIWWIEYAGLSGLRID-TYGY-SDGAFLTEYTRRLMAEYPRLNMVG------------- 244 d1tx2a_ 153 AD-----MIADLYDSIKIAK----------DAGV-------------------------- 171 :::::::: :::: d1h3ga3 245 --EEWSTRVPVVARW-----QRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLN 297 d1tx2a_ 172 -------------RDENIILDPGIGFAKT----------------PEQNLEAMRNLEQLN 202 :::::::: :::::::::: d1h3ga3 298 EVYETLSLDYLYPEPQNLVLF--------GGNHDMARMFSAAGEDFDRWRMNLVF----- 344 d1tx2a_ 203 V---LGYPVLLGTSRKSFIGHVLD--------------LPVEER---------------- 229 ::::::: :::: d1h3ga3 345 -LMTMPRIPQF-------------YSGDEILMTSTVKGRDDA--SYRRDFPGGWAGDKAN 388 d1tx2a_ 230 -------LEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK------------- 269 ::::::::::::: d1h3ga3 389 AFSGAGLTSQQRAAQDLVRK---------------------------LANWRKNQPVIHN 421 d1tx2a_ 270 - 270 d1h3ga3 422 G 422 TMalign alignment (TM-score: 0.60 Raw score:160.72) d1tx2a_ 1 --KWDYDLRCGEYTLN-LNE---------------------------------------- 17 ::::::: ::: d1h3ga3 1 GS-------AQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIR 53 d1tx2a_ 18 ------------KTLIMGI-LNVTPDSF-------SDGGSYNEVD--AAVRHAKEMRDEG 55 ::::::: :::::::: :::::::::: ::::::::::::: d1h3ga3 54 GTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEA 113 d1tx2a_ 56 ----AHIIDIGG--ESFA------------------------------------------ 67 :::::::: :::: d1h3ga3 114 RKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSEN 173 d1tx2a_ 68 --------KVSVEEE----IK-RVVPMIQAVSKEVKLPISIDTYKAEV-A--K-QAIEAG 110 ::::::: :: :::::::::::::::::::::::::: : : :::::: d1h3ga3 174 FTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRL 233 d1tx2a_ 111 ------AHIINDIWGAKAEPKIAEVAAH---------YDVPIILM--HNR-DNMN-YRNL 151 :::::::: ::::::::::::: :::::::: ::: ::: :::: d1h3ga3 234 MAEYPRLNMVGEEW-STRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAM-RNALSKTG 291 d1tx2a_ 152 M-ADMIADLYDSIKIAKDAGVRDENIILDPGIG-FAKTPEQN-LE--AMRN-LEQLNVLG 205 : :::::::::::: ::: :::::::::::::: :::::::: :: :::: :::::::: d1h3ga3 292 EENGLNEVYETLSL-DYL-YPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMP 349 d1tx2a_ 206 YPVLLGTSRKSFIGH----------VLDLPVEERL------EGT-G-------A-TVCLG 240 ::::::::::::::: ::::::: ::: : : ::::: d1h3ga3 350 RIPQFYSGDEILMTSTVKGRDDASY---RRDFPGGWAGDKANAFSGAGLTSQQRAAQDLV 406 d1tx2a_ 241 IEKGCEFVRVHDVKEMSRMAKMMDAMIGK------- 269 :::: : :::: d1h3ga3 407 RKLA-------------------N-WRKNQPVIHNG 422 HHsearch alignment (Probability: 0.26 E-value:0.01) d1tx2a_ 24 ILNVTPDSFSDGGSY---------------------NEVDAAVRHAKEMRDEGAHIIDIG 62 ::::::::::::::: :::::::::::::::::::::::: d1h3ga3 14 IYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPT 73 d1tx2a_ 63 G 63 : d1h3ga3 74 P 74