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 <-- 1.437 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1lt8a_) 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 d1lt8a_ Betaine-​homocysteine S-​methyltransferaseHomocysteine S-​methyltransferaseTIM 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 <-- 1.437 --> Hit
DALI alignment (Z-score: 14.9 Raw score:1635.60) d1tx2a_ 1 kwdYDLRcgeytLNLN-EKTLIMGILNV-------TPDS---fsDGGSYNeVDAAVRHAK 49 :::: :::: ::::::::::: :::: :::::: ::::::::: d1lt8a_ 1 ---KGIL-----ERLNaGEIVIGDGGFVfalekrgYVKAgpwtpEAAVEH-PEAVRQLHR 51 d1tx2a_ 50 EMRDEGAHIIDI-GGESfakVSVEeeIKRVVPMIQAVSKEVK---LPISIDTY------- 98 :::::::::::: :::: :::: :::::::::::::::: :::::::: d1lt8a_ 52 EFLRAGSNVMQTfTFYA--sEDKG--QEVNEAAADIARQVADegdALVAGGVSqtpsyls 107 d1tx2a_ 99 ----------KAEVAKQAIEAGAHIINDI------WGAKaepkIAEVAAHYDVPIILMHN 142 ::::::::::::::::::: :::: ::::::::::::::::: d1lt8a_ 108 aksetevkkvFLQQLEVFMKKNVDFLIAEyfehveEAVW----AVETLIASGKPVAATMA 163 d1tx2a_ 143 -----RDNMnyrnlmADMIADLYDSIKIAkdagvrdenIILDPGIGfaktpeqnLEAMRN 197 :::: :::::::::::::: :::::::: :::::: d1lt8a_ 164 igpegDLHG------VPPGEAAVRLVKAG--------aSIIGVNCH-----fdpTISLKT 204 d1tx2a_ 198 LEQ-LNVL-----GYPVLLGTSRKsfIGHV--------------ldLPVEERLEGTGATV 237 ::: :::: ::::::::::: :::: :::::::::::::: d1lt8a_ 205 VKLmKEGLeaaqlKAHLMSQPLAY--HTPDankqgfidlpefpfglEPRVATRWDIQKYA 262 d1tx2a_ 238 CLGIEKGCEFVRV------hDVKEMSRMAKMMDA-------------------------- 265 ::::::::::::: :::::::::::::: d1lt8a_ 263 REAYNLGVRYIGGccgfepyHIRAIAEELAPERGflppasekhgswgsgldmhtkpwvra 322 d1tx2a_ 266 ----------------------migk 269 d1lt8a_ 323 rarkeywenlriasgrpynpsmskpd 348 FAST alignment (Normalized score: 7.96 Raw score:2436.00) d1tx2a_ 1 KWDYDLRCGEYTLNLN---------EKTLIMGILNVTPDSFSDGGSYN------------ 39 ::::::: d1lt8a_ 1 ----------------KGILERLNAGEIVIGD----------------GGFVFALEKRGY 28 d1tx2a_ 40 -------------EVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEE----------EIK 76 ::::::::::::::::::::: ::: d1lt8a_ 29 VKAGPWTPEAAVEHPEAVRQLHREFLRAGSNVMQ-------------TFTFYASEDKGQE 75 d1tx2a_ 77 RVVPMIQAVS---KEVKLPISIDTY-------------------KAEVAKQAIEAGAHII 114 :::::::::: :::::::::: :::::::::::::::: d1lt8a_ 76 VNEAAADIARQVADEGDALVAGG--VSQTPSYLSAKSETEVKKVFLQQLEVFMKKNVDFL 133 d1tx2a_ 115 NDIWGAKA--------EPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIA--------- 157 :: ::::::::::::::::::: d1lt8a_ 134 IA------EYFEHVEEAVWAVETLIASGKPVAATM----------------AIGPEGDLH 171 d1tx2a_ 158 --DLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQ----NLEAMRNLEQLNV------LG 205 :::::::::::::: :::::: ::::::::::::: :: d1lt8a_ 172 GVPPGEAAVRLVKAGA----SIIGVN---------CHFDPTISLKTVKLMKEGLEAAQLK 218 d1tx2a_ 206 YPVLLG-TSRKSFIGHVLDL-----------------PVEE---RLEGTGATVCLGIEKG 244 :::::: :::: :::: :::::::::::::::: d1lt8a_ 219 AHLMSQPLAYH---------TPDANKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLG 269 d1tx2a_ 245 CEFVRVH--------DVKEMSRMAKMMDAMIGK--------------------------- 269 ::::: :::::::::::: d1lt8a_ 270 VRYIG--GCCGFEPYHIRAIAEELAPE------RGFLPPASEKHGSWGSGLDMHTKPWVR 321 d1tx2a_ 270 --------------------------- 270 d1lt8a_ 322 ARARKEYWENLRIASGRPYNPSMSKPD 348 TMalign alignment (TM-score: 0.69 Raw score:186.60) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNV--T----PDS-----FSDGGSYNEVDAAVRHAK 49 :::: :::::::::::::::: : ::: ::::::: ::::::::: d1lt8a_ 1 ---KGIL----ERLNAGEIVIGDGGFVFALEKRGYVKAGPWT-PEAAVEH-PEAVRQLHR 51 d1tx2a_ 50 EMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVK---LPISIDTY-------- 98 :::::::::::::::: :::::::::::::::::::::: :::::::: d1lt8a_ 52 EFLRAGSNVMQTFTFY---ASEDKGQEVNEAAADIARQVADEGDALVAGGVSQTPSYLSA 108 d1tx2a_ 99 --------KA-EVAKQAIEAGAHIINDI-W-GAKAEPKIAEVAAHYDVPIILMH-N---- 142 :: ::::::::::::::::: : ::::::::::::::::::::::: : d1lt8a_ 109 KSETEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVETLIASGKPVAATMAIGPEG 168 d1tx2a_ 143 RDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLN 202 ::: :: ::::::::::: : : ::::: :::: ::::::::::::::::: d1lt8a_ 169 DLH-GV-----PPGEAAVRLVK-A----G---ASIIG-VNCH-FDPTISLKTVKLMKEGL 212 d1tx2a_ 203 V---LGYPVLLGTSRKSFIGH--------------VLDLPVEERLEGTGATVCLGIEKGC 245 : ::::::::::::::::: ::::::::::::::::::::::: d1lt8a_ 213 EAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFG--LEPRVATRWDIQKYAREAYNLGV 270 d1tx2a_ 246 EFVRV---H---DVKEMSRMAKMMDA---------------------------------- 265 ::::: : :::::::::::::: d1lt8a_ 271 RYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWVRARARKEYWE 330 d1tx2a_ 266 ------------------MIGK 269 d1lt8a_ 331 NLRIASGRPYNPSMSKPD---- 348 HHsearch alignment (Probability: 0.94 E-value:0.00) d1tx2a_ 17 EKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIK 76 ::::::::::::::::::::::::::::::::::::::::::::::: ::::::: d1lt8a_ 91 GDALVAGGVSQTPSYLSAKSETEVKKVFLQQLEVFMKKNVDFLIAEY-----FEHVEEA- 144 d1tx2a_ 77 RVVPMIQAVSKEVKLP----ISIDT-------YKAEVAKQAIEAGAHIINDIWGAKAEPK 125 ::::::::: :::: ::::: :::::::::::::::::: ::::::::: d1lt8a_ 145 --VWAVETLIA-SGKPVAATMAIGPEGDLHGVPPGEAAVRLVKAGASIIG-VNCHFDPTI 200 d1tx2a_ 126 IAEVA---AHY------DVPIILMHNRDNMNY------------RNLMAD---MIADLYD 161 ::::: ::: ::::::::::::::: :::::: ::::::: d1lt8a_ 201 SLKTVKLMKEGLEAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFGLEPRVATRWDIQK 260 d1tx2a_ 162 SIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSF 217 ::::::::::: :: :::::::::::::::::::::: ::::::::::: d1lt8a_ 261 YAREAYNLGVR---YI---GGCCGFEPYHIRAIAEELAPER----GFLPPASEKHG 306