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 <-- 0.958 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1us3a2) 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 d1us3a2 Xylanase 10c(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 <-- 0.958 --> Hit
DALI alignment (Z-score: 10.1 Raw score:1184.10) d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGILNVTPDSfsdggsynEVDAavRHAKEMRDeGAHIID 60 :::::::::::::::: :::: :::::::: :::::: d1us3a2 1 --aysanvdhlrdlaPSDFPIGVAVSNTDSA-----tynLLTN-sREQAVVKK-HFNHLT 51 d1tx2a_ 61 I-GGESfakVSVE-----EEIKRVVPMIQAVSkEVKLPISIDTY---------------- 98 : :::: :::: :::::::::::::: ::::::::::: d1us3a2 52 AgNIMK--mSYMQptegnFNFTNADAFVDWAT-ENNMTVHGHALvwhsdyqvpnfmknwa 108 d1tx2a_ 99 -------------KAEVAKQAIEAG-AHIINDIW-------------------------- 118 :::::::::::: :::::::: d1us3a2 109 gsaedflaaldthITTIVDHYEAKGnLVSWDVVNeaiddnspanfrttdsafyvksgnss 168 d1tx2a_ 119 -gaKAEP-KIAEVAAhyDVPIILMHNrdnmnyRNLMADMIADLYDSI--KIAKdagvrde 174 :::: ::::::: ::::::::: ::::::::::::::: :::: d1us3a2 169 vyiERAFqTARAADP--AVILYYNDY-nieqnNAKTTKMVDMVKDFQarSIPI------- 218 d1tx2a_ 175 nIILDPGIGfaktpEQNLEAMRN-LEQLNVLGYPVLLGtSRKSfiGHVLD---------- 223 :::::::: ::::::::: :::::::::::::: :::: ::::: d1us3a2 219 -DGVGFQMH-vcmnYPSIANISAaMKKVVDLGLLVKITeLDVA--VNQPHcdaypankin 274 d1tx2a_ 224 ----lpveERLEGTGATVCLGIEKG----CEFVRVHDV---------------------- 253 ::::::::::::::::: ::::::::: d1us3a2 275 plteaaqlAQKKRYCDVVKAYLDTVpvnqRGGISVWGTtdantwldglyreqfedekisw 334 d1tx2a_ 254 ----------kemsRMAKMMDAM----igk 269 ::::::::: d1us3a2 335 pllfdnnyndkpalRGFADALIGtqctnth 364 FAST alignment (Normalized score: 6.05 Raw score:1893.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNE---------------KTLIMGILNVTPDSFSDG--GSYNE--- 40 ::::::::: :::: d1us3a2 1 -----------------AYSANVDHLRDLAPSDFPIGVAVS---------NTDSAT-YNL 33 d1tx2a_ 41 --VDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEE----------------EIKRVVPMI 82 ::::::::: :::::::: ::::::::: d1us3a2 34 LTNSREQAVVK----KHFNHLTA------------GNIMKMSYMQPTEGNFNFTNADAFV 77 d1tx2a_ 83 QAVSKEVKLPISIDTY-------------------------------KAEVAKQAIE-AG 110 :::: ::::::::: :::::::::: :: d1us3a2 78 DWAT-ENNMTVHGH--ALVWHSDYQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAKGN 134 d1tx2a_ 111 AHIINDIWGAKA-------------------------------EPKIAEVAAH--YDVPI 137 ::::: :::::::::: ::::: d1us3a2 135 LVSWD-------VVNEAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVIL 187 d1tx2a_ 138 ILMHNRDNMNYRN-----LMADMIADLYDSIKIAKDAGVRDEN----IILDPGIGFAKTP 188 ::: ::::::::::::::::::: :::::: d1us3a2 188 YYN----------DYNIEQNNAKTTKMVDMVKDFQAR------SIPIDGVGFQ------- 224 d1tx2a_ 189 EQNLE--------AMRNLE----QLNVLGYPVLLGTSRKSFIGHVLDLP----------- 225 :::::: ::::::::::: d1us3a2 225 -----MHVCMNYPSIANISAAMKKVVDLGLLVKI---------------TELDVAVNQPH 264 d1tx2a_ 226 ------------VEERLEGTGATVCLGIEKG----------CEFVRVHDV---------- 253 ::::::::::::::::: ::::: d1us3a2 265 CDAYPANKINPLTEAAQLAQKKRYCDVVK--AYLDTVPVNQRGGIS----VWGTTDANTW 318 d1tx2a_ 254 --------------------------KEMSRMAKMMDAMIGK--------- 269 ::::::::::: d1us3a2 319 LDGLYREQFEDEKISWPLLFDNNYNDKPALRGFADAL-----IGTQCTNTH 364 TMalign alignment (TM-score: 0.62 Raw score:166.75) d1tx2a_ 1 ----------KWDYDLRCGEYTLNLNEKTLIMGILNVTPDS-FSDGGSYNEVDAAVRHAK 49 ::::::::::::::::::: ::::::::::: d1us3a2 1 AYSANVDHLR------------DLAPSDFPIGVAVSNTDSAT-------YNLLTNSREQA 41 d1tx2a_ 50 EMRDEGAHIIDI-GGES-FAKVSV----EEEIKRVVPMIQAVSKEVKLPISIDTYK---- 99 :::: ::::::: :::: :::: :::::::::::::::: ::::::::::: d1us3a2 42 VVKK-HFNHLTAGNIMKM--SYMQPTEGNFNFTNADAFVDWATE-NNMTVHGHALVWHSD 97 d1tx2a_ 100 ------------------------A-EVAKQAIEAGAHIINDIWG--------------- 119 : ::::::::::::::::::: d1us3a2 98 YQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAKGNLVSWDVVNEAIDDNSPANFRTTD 157 d1tx2a_ 120 ------------AK-AEP-KIAEVAAHYDVPIILMHNR---DNMNYRNLMADMIADLYDS 162 :: ::: ::::::: :::::::::: ::::::::::::::: d1us3a2 158 SAFYVKSGNSSVYIERAFQTARAADP--AVILYYNDYNIEQ----NNAKTTKMVDMVKDF 211 d1tx2a_ 163 I--KIAKDAGVRDENIILDPGIGFAKTP--EQNLE--AMRNL-EQLNVLGYPVLLGTSRK 215 : :::: :::::::: :: ::: ::::: ::::::::::::::::: d1us3a2 212 QARSIPI--------DGVGFQMH---VCMN--YPSIANISAAMKKVVDLGLLVKITELDV 258 d1tx2a_ 216 SFIG-HVL-D---LP-VEE---RL-EGTGATVCLGIEK--GC----E-FVRV-H------ 251 :::: ::: : :: :: :: ::::::::::::: :: : :::: : d1us3a2 259 AVNQPHCDAYPANKIN-PLTEAAQLAQKKRYCDVVKAYLDTVPVNQRGGISVWGTTDANT 317 d1tx2a_ 252 ------------------DV------KE-MSRMAKMMDAMIG-----K 269 :: :: ::::::::::::: d1us3a2 318 WLDGLYREQFEDEKISWPLLFDNNYNDKPALRGFADALIGTQCTNTH- 364 HHsearch alignment (Probability: 0.78 E-value:0.00) d1tx2a_ 39 NEVDAAVRHAKEMRDEGAHIID---IG-GE-------SFAKVSVEEEIKRVVPMIQAVSK 87 :::::::::::::::::::::: :: :: ::::::::::::::::::::::: d1us3a2 68 FNFTNADAFVDWATENNMTVHGHALVWHSDYQVPNFMKNWAGSAEDFLAALDTHITTIVD 127 d1tx2a_ 88 EV---KLPISIDTYKAEVAKQAIE---AGAHIINDIWGAK--AEPKIAEVAAHYDVPIIL 139 :: ::::::::::::::::::: ::::::::::::: :::::::::::::::::: d1us3a2 128 HYEAKGNLVSWDVVNEAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVIL 187 d1tx2a_ 140 MHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLE 199 :::::::::::: ::::::::::::::::::::::::::::::::::::: :::::: d1us3a2 188 YYNDYNIEQNNA---KTTKMVDMVKDFQARSIPIDGVGFQMHVCMNYPSIAN--ISAAMK 242 d1tx2a_ 200 QLNVLGYPVLLG 211 :::::::::::: d1us3a2 243 KVVDLGLLVKIT 254