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 <-- 0.692 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1kfwa1) 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 d1kfwa1 Psychrophilic chitinase B(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 <-- 0.692 --> Hit
DALI alignment (Z-score: 10.3 Raw score:1216.10) d1tx2a_ 1 kwdydlrcgeYTLNlnEKTLIMGILNV-TPDSfsdggsynevdAAVRHA-KEMRDeGAHI 58 :::: ::::::::::: :::: :::::: ::::: :::: d1kfwa1 1 ---------pLTST-vNGYRNVGYFAQwGVYG--------rafQAKQLDvSGTAK-NLTH 41 d1tx2a_ 59 IDIGGE---------------------sfaKVSVEEEIK--------------------- 76 :::::: ::::::::: d1kfwa1 42 INYSFGninnqtltcfmankaqgtgpngsdGAGDAWADFgmgyaadksvsgkadtwdqpl 101 d1tx2a_ 77 -RVVPMIQAVSKEVK-LPISIDTY---------------------kaevaKQAI------ 107 :::::::::::::: :::::::: :::: d1kfwa1 102 aGSFNQLKQLKAKNPkLKVMISLGgwtwsknfskaaateasrqklvssciDLYIkgnlpn 161 d1tx2a_ 108 ----------EAGAHIINDIW-------------------gakaePKIAEVAAHYD---- 134 ::::::::::: ::::::::::: d1kfwa1 162 fegrggagaaAGIFDGIDIDWewpgtnsglagngvdtvndranfkALLAEFRKQLDaygs 221 d1tx2a_ 135 -----VPIILMHNrdnmnyrnLMADMI-ADLYD-sIKIAkdagvrdenIILDPGIgFAKT 187 :::::::: :::::: ::::: :::: ::::::: :::: d1kfwa1 222 tnnkkYVLSAFLP-------aNPADIDaGGWDDpaNFKS--------lDFGSIQG-YDLH 265 d1tx2a_ 188 -------------------------PEQNleAMRNLEQLN-VLGY--PVLLGTSRKsfig 219 :::: ::::::::: :::: ::::::::: d1kfwa1 266 gawnptltghqanlyddpadprapsKKFS--ADKAVKKYLaAGIDpkQLGLGLAAD---- 319 d1tx2a_ 220 hvldlpveeRLEGTGATVCLGIEKGCEFVRVH---------DVKEMSRMAKMMDA----- 265 ::::::::::::::::::::::: :::::::::::::: d1kfwa1 320 ---------NIATTKQKTDYIVSKGLGGGMWWelsgdrngeLVGAMSDKFRAAAPgpvte 370 d1tx2a_ 266 migk 269 d1kfwa1 371 aapp 374 FAST alignment (Normalized score: 3.20 Raw score:1016.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNE-------KTLIMGILNVTPDSFSDGGSYN---------EVDAA 44 ::::::::: ::::: d1kfwa1 1 -----------------PLTSTVNGYRNVGYFA-------------QWGVYGRAFQAKQL 30 d1tx2a_ 45 VRHAKEMRD----EGAHIIDIGGESFAKVS------------------------------ 70 :: :::::::: d1kfwa1 31 DV-------SGTAKNLTHINY---------SFGNINNQTLTCFMANKAQGTGPNGSDGAG 74 d1tx2a_ 71 VEEE----------------------IKRVVPMIQAVSKEV-KLPISIDTYKAEVAKQAI 107 :::: ::::::::::::::: ::::::: d1kfwa1 75 DAWADFGMGYAADKSVSGKADTWDQPLAGSFNQLKQLKAKNPKLKVMIS----------- 123 d1tx2a_ 108 EA--------------------------------------------------GAHIINDI 117 ::::::: d1kfwa1 124 --LGGWTWSKNFSKAAATEASRQKLVSSCIDLYIKGNLPNFEGRGGAGAAAGIFDGIDI- 180 d1tx2a_ 118 WGAKAEPKIAEVAAHYD------------------------------------------- 134 d1kfwa1 181 -----------------DWEWPGTNSGLAGNGVDTVNDRANFKALLAEFRKQLDAYGSTN 223 d1tx2a_ 135 -------------------------------VPIILMHNRDNMNYRNLMADMIA------ 157 ::::::: d1kfwa1 224 NKKYVLSAFLPANPADIDAGGWDDPANFKSLDFGSIQG----------------YDLHGA 267 d1tx2a_ 158 --------------------------DLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQN 191 ::::::::::::::::::: d1kfwa1 268 WNPTLTGHQANLYDDPADPRAPSKKFSADKAVKKYLAAGIDPKQL--------------- 312 d1tx2a_ 192 LEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEE---RLEGTGATVCLGIEKGCEFV 248 :::: :::::::::::::::::::: d1kfwa1 313 ---------------GLGL------------------AADNIATTKQKTDYIVSKGLGGG 339 d1tx2a_ 249 RVHDV---------KEMSRMAKMMDAMIGK----------- 269 : :::::::::::::: d1kfwa1 340 M----WWELSGDRNGELVGAMSDKFRAA--APGPVTEAAPP 374 TMalign alignment (TM-score: 0.61 Raw score:165.18) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNV-TPDSFSDGGSYNEVDAAVRHAK--EMRDEGAH 57 : ::::: ::::::::::: :::: :: ::::::: :::: ::: d1kfwa1 1 ----P-----LTSTV-NGYRNVGYFAQWGVYG-------RA--FQAKQLDVSGTAK-NLT 40 d1tx2a_ 58 IIDIGGES-------------FAK------VSVEEEIKRVV------------------- 79 :::::::: :: ::::::::::: d1kfwa1 41 HINYSFGNINNQTLTCFMANK-AQGTGPNGSDGAGDAWADFGMGYAADKSVSGKADTWDQ 99 d1tx2a_ 80 ---PMIQAVSKEV--K--LPISIDTY-------K------------A--EVAKQAI-E-- 108 :::::::::: : :::::::: : : ::::::: : d1kfwa1 100 PLAGSFNQLKQLKAKNPKLKVMISLGGWTWSKNFSKAAATEASRQKLVSSCIDLYIKGNL 159 d1tx2a_ 109 -----------A--GAHIINDIWGAK---------------A--EP--KIAEVAAHYD-- 134 : :::::::::::: : :: :::::::::: d1kfwa1 160 PNFEGRGGAGAAAGIFDGIDIDWEWPGTNSGLAGNGVDTVNDRANFKALLAEFRKQLDAY 219 d1tx2a_ 135 -------VPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFA-- 185 ::::::::: :::: : ::::::::::: : : ::::::::::: d1kfwa1 220 GSTNNKKYVLSAFLPA-NPAD--I--DAGGWDDPANF--K---S---LDFGSIQGYDLHG 266 d1tx2a_ 186 -----------------------KTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVL 222 :::::::::: :::::::::::::::::: d1kfwa1 267 AWNPTLTGHQANLYDDPADPRAPSKKFSADKAV-KKYLAAGIDPKQLGLGLA-------- 317 d1tx2a_ 223 DLPVEERLEGTGATVCLGIEKGCEFVRV--H-------DVKEMSRMAKMMDAMIGK---- 269 : ::::::::::::::::::::::: : :::::::::::::: ::: d1kfwa1 318 ---A-DNIATTKQKTDYIVSKGLGGGMWWELSGDRNGELVGAMSDKFRAAAP-GPVTEAA 372 d1tx2a_ 270 -- 270 d1kfwa1 373 PP 374 HHsearch alignment (Probability: 0.05 E-value:0.01) d1tx2a_ 158 DLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLG 211 ::::::::::::::::::::: :::: ::::::::::::::::::::::::: d1kfwa1 294 SADKAVKKYLAAGIDPKQLGL--GLAA--DNIATTKQKTDYIVSKGLGGGMWWE 343