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 <-- 1.616 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1piia1) 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 d1piia1 Indole-​3-​glycerophosphate synthase,​ IPGSRibulose-​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 <-- 1.616 --> Hit
DALI alignment (Z-score: 14.0 Raw score:1408.70) d1tx2a_ 1 ---------------------------kwdydlrCGEY--TLNLNEKTLIMGILNVTpds 31 :::: ::::::::::::::::: d1piia1 1 mqtvlakivadkaiwvearkqqqplasfqnevqpSTRHfyDALQGARTAFILECKKA-sp 59 d1tx2a_ 32 fsdggSYNEvdAAVRHAKEMRDeGAHIIDIGGESFakvsveeeikRVVPMIQAVSKEVKL 91 :::: ::::::::::: :::::::::::: ::::::::::::::: d1piia1 60 skgviRDDF--DPARIAAIYKH-YASAISVLTDEK-------yfqGSFNFLPIVSQIAPQ 109 d1tx2a_ 92 PISIDT-YKAE-VAKQAIEAGAHIINDIW--gaKAEP-KIAEVAAHYDVPIILMHNrdnm 146 :::::: :::: ::::::::::::::::: :::: :::::::::::::::::: d1piia1 110 PILCKDfIIDPyQIYLARYYQADACLLMLsvldDDQYrQLAAVAHSLEMGVLTEVS---- 165 d1tx2a_ 147 nyrnlmadMIADLYDSIKIAkdagvrdenIILDPGIGFAKtPEQNleAMRNLEQL-NVLG 205 :::::::::::: ::::::::::: :::: :::::::: :::: d1piia1 166 --------NEEEQERAIALG--------aKVVGINNRDLR-DLSI--DLNRTRELaPKLG 206 d1tx2a_ 206 --YPVLLGTSRksfighvldlpveerleGTGATVCLGIEkGCEFVRVH-----------D 252 ::::::::: ::::::::::: :::::::: : d1piia1 207 hnVTVISESGI-----------------NTYAQVRELSH-FANGFLIGsalmahddlhaA 248 d1tx2a_ 253 VKEMSRmakmmdamigk 269 :::::: d1piia1 249 VRRVLL----------- 254 FAST alignment (Normalized score: 9.30 Raw score:2431.00) d1tx2a_ 1 KWDYDLRC----------------------------------GEYTLN-----LNEKTLI 21 :::: ::::::: d1piia1 1 --------MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRH--FYDALQGARTAF 50 d1tx2a_ 22 MGILNVTPDSFSDGGSYNEVD--------------AAVRHAKEMRDEGAHIIDIGGESFA 67 :::: :::::::::: ::::::::: d1piia1 51 ILEC-----------------KKASPSKGVIRDDFDPARIAAIYK-HYASAISVL----- 87 d1tx2a_ 68 KVSVEEEIKR--------VVPMIQAVSKEVKLPISID--TYKAEVAKQAIEAGAHIINDI 117 ::::::::::::::::::: :::::::::::::::::::: d1piia1 88 ----------TDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLL- 136 d1tx2a_ 118 WGAKA---------EPKIAEVAAHYDVPIILMHNRDNMNYRNL-MADMIADLYDSIKIAK 167 ::::::::::::::::::: :::::::::: d1piia1 137 -----MLSVLDDDQYRQLAAVAHSLEMGVLTEV----------SNEEEQERAIA------ 175 d1tx2a_ 168 DAGVRDEN---IILDPGIGFAKTPEQ--------NLEAMR-NLEQLNV--LGYPVLLGTS 213 ::::::: :::::: :::: ::::::: d1piia1 176 --------LGAKVVGINN--------RDLRDLSIDLNRTRELAPK---LGHNVTVIS--- 213 d1tx2a_ 214 RKSFIGHVLDLPVEERLEG-----TGATVCLGIEKGCEFVRVH------------DVKEM 256 :::::::::: ::::::: ::::: d1piia1 214 -------------------ESGINTYAQVRELSH-FANGFLI-GSALMAHDDLHAAVRRV 252 d1tx2a_ 257 SRMAKMMDAMIGK- 269 : d1piia1 253 L------------L 254 TMalign alignment (TM-score: 0.60 Raw score:160.33) d1tx2a_ 1 ----------------------------------KWDYDLRCGEY--TLNLNEKTLIMGI 24 :::: ::::::::::::: d1piia1 1 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQP-------STRHFYDALQGARTAFILE 53 d1tx2a_ 25 LNVT--------PDSFSDGGSYNE-VDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEI 75 :::: : :::::::::::: ::::::::::::::: : d1piia1 54 CKKASPSKGVIR-----------DD-FDPARIAAIYKH-YASAISVLTDEKYFQ----G- 95 d1tx2a_ 76 KRVVPMIQAVSKEVKLPISIDTYK--AEVAKQAIEAGAHIINDIWGAKA--EP-KIAEVA 130 :: :::::::::::::::::::: ::::::::::::::::::::::: :: :::::: d1piia1 96 -SF-NFLPIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVA 153 d1tx2a_ 131 AHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGF-AKTPE 189 :::::::::::: :: ::::::::: : : ::::::::: :::: d1piia1 154 HSLEMGVLTEVS-----------NE-EEQERAIAL-G-----A--KVVGINNRDLRDLS- 192 d1tx2a_ 190 QNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVR 249 ::::::::::::::::::::::::: :: :::::::::: ::::: d1piia1 193 IDLNRTRELAPKLGHNVTVISESGI---------------NT--YAQVRELSHF-ANGFL 234 d1tx2a_ 250 VH--D---------VKEMSRMAKMMDAMIGK 269 :: : :::::: d1piia1 235 IGSALMAHDDLHAAVRRVLL----------- 254 HHsearch alignment (Probability: 0.28 E-value:0.00) d1tx2a_ 26 NVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPM--IQ 83 ::::::::::::::: :::::::: ::::::::::::::::::::::::::::::: :: d1piia1 53 ECKKASPSKGVIRDD-FDPARIAA-IYKHYASAISVLTDEKYFQGSFNFLPIVSQIAPQP 110 d1tx2a_ 84 AVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAE---PKIAEVAAHYDVPIIL 139 ::::: :::: :::::::::::::::::::::::: :::::::::::::::: d1piia1 111 ILCKD----FIID---PYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLT 162