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 <-- 2.033 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1thfd_) 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 d1thfd_ Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisFRibulose-​phoshate binding barrelTIM 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 <-- 2.033 --> Hit
DALI alignment (Z-score: 15.4 Raw score:1536.60) d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGILNVTP---dsfsdggsynevDAAVRHAKEMRDEGAH 57 :::::::::::::: :::::::::::::::: d1thfd_ 1 ---------------MLAKRIIACLDVKDgrvvkgsnfenlrdsGDPVELGKFYSEIGID 45 d1tx2a_ 58 IIDIGGESfakvsVEEEIKRVVPMIQAVSKEVKLPISID--TYKAEVAKQAIEAGAHIIN 115 :::::::: :::::::::::::::::::::::::: ::::::::::::::::::: d1thfd_ 46 ELVFLDIT----aSVEKRKTMLELVEKVAEQIDIPFTVGggIHDFETASELILRGADKVS 101 d1tx2a_ 116 DIWGAKAEPKIA-EVAAHYD-VPIILMHN--------------RDNMNYrnlmaDMIADL 159 :::::::::::: ::::::: :::::::: :::::: :::::: d1thfd_ 102 INTAAVENPSLItQIAQTFGsQAVVVAIDakrvdgefmvftysGKKNTG----iLLRDWV 157 d1tx2a_ 160 YDSIKIAkdagvrdeNIILDPGIGfaktpeqnleAMRNLEQLNV-LGYPVLLGTSRksfi 218 ::::::: ::::::::: :::::::::: ::::::::::: d1thfd_ 158 VEVEKRG--------AGEILLTSI-drdgtksgyDTEMIRFVRPlTTLPIIASGGA---- 204 d1tx2a_ 219 ghvldlpveerleGTGATVCLGIEKGCEFVRVHD-----vKEMSRMAKMMDAMIGK---- 269 ::::::::::::::::::::: :::::::::::::::: d1thfd_ 205 -------------GKMEHFLEAFLAGADAALAASvfhfreIDVRELKEYLKKHGVNvrle 251 d1tx2a_ 270 -- 270 d1thfd_ 252 gl 253 FAST alignment (Normalized score: 10.88 Raw score:2838.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVD------------------ 42 :::::::::::: d1thfd_ 1 ---------------MLAKRIIACLDV---------------KDGRVVKGSNFENLRDSG 30 d1tx2a_ 43 AAVRHAKEMRDEGAHIIDIGGESFAKVS----VEEEIKRVVPMIQAVSKEVKLPISID-- 96 :::::::::::::::::::: :::::::::::::::::::::::::: d1thfd_ 31 DPVELGKFYSEIGIDELVFL--------DITASVEKRKTMLELVEKVAEQIDIPFTVGGG 82 d1tx2a_ 97 TYKAEVAKQAIEAGAHIINDIWG--AKAEPKI-AEVAAHYDV---PIILMHNRD------ 144 ::::::::::::::::::::: ::::::: ::::::: ::::::: d1thfd_ 83 IHDFETASELILRGADKVSIN--TAAVENPSLITQIAQTF--GSQAVVVAID--AKRVDG 136 d1tx2a_ 145 ---------NMNYRNLMA--DMIADLYDSIKIAKDAGVRDEN---IILDPGIGFAKTPEQ 190 :::: ::::::::::: :::::: d1thfd_ 137 EFMVFTYSGKKNT-----GILLRDWVVEVEK-----------RGAGEILLT--------- 171 d1tx2a_ 191 NLE-----------AMRNLEQLN-VLGYPVLLGTSRKSFIGHVLDLPVEERLEG----TG 234 ::::::::: ::::::::: :: d1thfd_ 172 ---SIDRDGTKSGYDTEMIRFVRPLTTLPIIAS---------------------GGAGKM 207 d1tx2a_ 235 ATVCLGIEKGCEFVRV--------HDVKEMSRMAKMMDAMIGK---------- 269 :::::::::::::::: :::::::::::: d1thfd_ 208 EHFLEAFLAGADAALAASVFHFREIDVRELKEYLKK-------HGVNVRLEGL 253 TMalign alignment (TM-score: 0.65 Raw score:175.93) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDS----------FSDGGSYNEVDAAVRHAKE 50 : :: ::::::::::::: :::::::::::: d1thfd_ 1 M--------------LA-KRIIACLDVKDGRVVKGSNFENL-------RDSGDPVELGKF 38 d1tx2a_ 51 MRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDT-YKA-EVAKQAIE 108 :::::::::::: :::::: ::::::::::::::::::::::::: ::: :::::::: d1thfd_ 39 YSEIGIDELVFL-DITASV---EKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELIL 94 d1tx2a_ 109 AGAHIINDIWGAKAEPKIA-EVAAHYDVP-IILMHNRDNMNYRNLM-----------ADM 155 ::::::::::::::::::: ::::::::: ::::::: :::::::: ::: d1thfd_ 95 RGADKVSINTAAVENPSLITQIAQTFGSQAVVVAIDA-KRVDGEFMVFTYSGKKNTGILL 153 d1tx2a_ 156 IADLYDSIKIAKDAGVRDENIILDPGIGFAKTP--EQNLEAMRNLEQLNV-LGYPVLLGT 212 ::::::::: : : :::::::::: ::: ::::::::::::: ::::::::: d1thfd_ 154 RDWVVEVEK-R----G---AGEILLTSID-RDGTK--SGYDTEMIRFVRPLTTLPIIASG 202 d1tx2a_ 213 SRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVH--D--V-KEMSRMAKMMDAMI 267 :: :: :::::::::::::::::: : : :::::::::::::: d1thfd_ 203 GA---------------GK--MEHFLEAFLAGADAALAASVFHFREIDVRELKEYLKKHG 245 d1tx2a_ 268 GK------ 269 :: d1thfd_ 246 VNVRLEGL 253 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tx2a_ 41 VDAAVRHAKEMRDEGAH---IIDIGG-ESFAKVSVEEEIKRVVPMIQAVSKEVKLPISID 96 ::::::::::::::::: :::::: :::::: ::::::::::::::::::: d1thfd_ 29 SGDPVELGKFYSEIGIDELVFLDITASVEKRKT--------MLELVEKVAEQIDIPFTVG 80 d1tx2a_ 97 --TYKAEVAKQAIEAGAHIINDIWGAKAEPK-IAEVAAHYDVP-IILMH--NRDNMNYR- 149 ::::::::::::::::::::::::::::: ::::::::::: ::::: :::::::: d1thfd_ 81 GGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGSQAVVVAIDAKRVDGEFMV 140 d1tx2a_ 150 --NL-MADMIADLYDSIKIAKDAGVRDENIIL-DPGIGFAKTPEQNLEAMRNLEQLNVLG 205 :: :::::::::::::::::::::: ::: ::: :::::::::::::::::::: : d1thfd_ 141 FTYSGKKNTGILLRDWVVEVEKRGAGE--ILLTSID-RDGTKSGYDTEMIRFVRPLT--T 195 d1tx2a_ 206 YPVLL--GTSRKSFIGHVLDLPVEERLEG 232 ::::: :::::::::::::::::::::: d1thfd_ 196 LPIIASGGAGKMEHFLEAFLAGADAALAA 224