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 <-- 1.445 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1l6wa_) 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 d1l6wa_ Fructose-​6-​phosphate aldolaseAldolaseTIM 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 <-- 1.445 --> Hit
DALI alignment (Z-score: 12.0 Raw score:1126.20) d1tx2a_ 1 kwdydlrcgeytlnlnekTLIMGILNvtpdsfsdggsynevdaAVRHAKEMRD-EGAHII 59 :::::::: :::::::::: :::::: d1l6wa_ 1 ------------------MELYLDTS-----------------DVVAVKALSRiFPLAGV 25 d1tx2a_ 60 DIGGESfakvsveeeikRVVPMIQAVSKEV--KLPISIDT------yKAEVAKQAIEAG- 110 :::::: ::::::::::::: :::::::: :::::::::::: d1l6wa_ 26 TTNPSI-----iaagkkPLDVVLPQLHEAMggQGRLFAQVmattaegMVNDALKLRSIIa 80 d1tx2a_ 111 aHIINDIWgaKAEP-KIAEVAAHYDVPIILMHNrdnmnyrnlmadMIADLYDSIKIAkda 169 ::::::: :::: :::::::::::::::::: :::::::::::: d1l6wa_ 81 dIVVKVPV--TAEGlAAIKMLKAEGIPTLGTAV-----------yGAAQGLLSALAG--- 124 d1tx2a_ 170 gvrdenIILDPGIGFAKTPEQnlEAMRNLEQL-NVLG-----YPVLLGTSRksfighvld 223 ::::::::::::::: ::::::::: :::: ::::::::: d1l6wa_ 125 -----aEYVAPYVNRIDAQGG--SGIQTVTDLhQLLKmhapqAKVLAASFK--------- 168 d1tx2a_ 224 lpveerlegTGATVCLGIEKGCEFVRVHD--VKEM-------------srmakmmdamig 268 :::::::::::::::::::: :::: d1l6wa_ 169 ---------TPRQALDCLLAGCESITLPLdvAQQMisypavdaavakfeqdwqgafgrts 219 d1tx2a_ 269 k 269 d1l6wa_ 220 i 220 FAST alignment (Normalized score: 6.29 Raw score:1529.00) d1tx2a_ 1 KWDYDLRCGEYTLN---------------------------------------------- 14 d1l6wa_ 1 --------------MELYLDTSDVVAVKALSRIFPLAGVTTNPSIIAAGKKPLDVVLPQL 46 d1tx2a_ 15 ---LNEKTLIMGILNVTPDSFSDGGSYN-EVDAAVRHAKEMRDEGA----HIIDIGGESF 66 ::::::::::::: :::::::::::::: ::::: d1l6wa_ 47 HEAMGGQGRLFAQVMA------------TTAEGMVNDALKLRS---IIADIVVKV----- 86 d1tx2a_ 67 AKVSVEEE--IKRVVPMIQAVSKEVKLPISI-DTYKAEVAKQAIEAGAHIINDIWGAKA- 122 ::::::::::::: ::::::: ::::::::::::::::::::: d1l6wa_ 87 --------PVTAEGLAAIKMLKA-EGIPTLGTAVYGAAQGLLSALAGAEYVAP------Y 131 d1tx2a_ 123 --------------EPKIAEVAAH--YDVPIILMHNRDNMNYRNLMAD----MIADLYDS 162 :::::::::: ::::::: :::::::: d1l6wa_ 132 VNRIDAQGGSGIQTVTDLHQLLKMHAPQAKVLA---------------ASFKTPRQALDC 176 d1tx2a_ 163 IKIAKDAGVRDEN---IILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIG 219 :: ::::: :::::::: d1l6wa_ 177 LL-----------AGCESITL----------PLDVAQQM--------------------- 194 d1tx2a_ 220 HVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK---------- 269 d1l6wa_ 195 --------------------------------------------------ISYPAVDAAV 204 d1tx2a_ 270 ---------------- 270 d1l6wa_ 205 AKFEQDWQGAFGRTSI 220 TMalign alignment (TM-score: 0.48 Raw score:129.68) d1tx2a_ 1 KWDY-----------------DLRCGEYTLNLNEKTLIMGILNV-T-----PDSFSDGGS 37 : : ::::::::::: : d1l6wa_ 1 -M-ELYLDTSDVVAVKALSRI------------FPLAGVTTNPSIIAAGKK--------- 37 d1tx2a_ 38 YNEVDAAVRHAKEMRDEG--AHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISI 95 ::::::::::::: ::::::::: ::::::::::::::::: ::::::: d1l6wa_ 38 -----PLDVVLPQLHEAMGGQGRLFAQVM----ATTAEGMVNDALKLRSI---IADIVVK 85 d1tx2a_ 96 DTY---KAEVAKQAIEAGAHIINDIW-GAKAEPKIAEVAAHYDVPIILM-H-NRDNMNYR 149 ::: :::::::::::::::::::: :::::::::::: :::::: : ::::::: d1l6wa_ 86 VPVTAEGLAAIKMLKAEGIPTLGTAVYGAAQGLLSALAG----AEYVAPYVNRIDAQGG- 140 d1tx2a_ 150 NLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVL 209 ::::::::::::::: ::: ::::::::: : :::::::::::::::: d1l6wa_ 141 ----SGIQTVTDLHQLLKM-HAP-QAKVLAASF--------K--TPRQALDCLLAGCESI 184 d1tx2a_ 210 LGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEK------------------------GC 245 ::: : :::::: :: d1l6wa_ 185 TLP--------------------L-DVAQQM-ISYPAVDAAVAKFEQDWQGAFGRTSI-- 220 d1tx2a_ 246 EFVRVHDVKEMSRMAKMMDAMIGK 269 d1l6wa_ 221 ------------------------ 221 HHsearch alignment (Probability: 0.19 E-value:0.01) d1tx2a_ 88 EVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIIL 139 ::::::::::::::::::::::::::: :::: :::::::::::::::::: d1l6wa_ 81 DIVVKVPVTAEGLAAIKMLKAEGIPTL--GTAV-YGAAQGLLSALAGAEYVA 129