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 <-- 0.953 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1pbga_) 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 d1pbga_ 6-​phospho-​beta-​D-​galactosidase,​ PGAL(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 <-- 0.953 --> Hit
DALI alignment (Z-score: 10.6 Raw score:1292.70) d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGIL---nVTPDSFSD-------------------ggsy 38 :::::::::: :::::::: d1pbga_ 1 ----------mtktlPKDFIFGGATaayqAEGATHTDgkgpvawdkylednywytaepas 50 d1tx2a_ 39 NEVDAAVRHAKEMRDEGAHIIDIGGEsfakVSVE---------EEIKRVVPMIQAVSkEV 89 :::::::::::::::::::::::::: :::: :::::::::::::: :: d1pbga_ 51 DFYHKYPVDLELAEEYGVNGIRISIA---wSRIFptgygevneKGVEFYHKLFAECH-KR 106 d1tx2a_ 90 KLPISIDTY--------------------------KAEVAKQAIeaGAHIINDIW----- 118 ::::::::: ::::::::: ::::::::: d1pbga_ 107 HVEPFVTLHhfdtpealhsngdflnreniehfidyAAFCFEEFP--EVNYWTTFNeigpi 164 d1tx2a_ 119 --------------------------gaKAEP-KIAEVAA--HYDVPIILMHN------- 142 :::: ::::::: ::::::::::: d1pbga_ 165 gdgqylvgkfppgikydlakvfqshhnmMVSHaRAVKLYKdkGYKGEIGVVHAlptkypy 224 d1tx2a_ 143 ------rdnmNYRNLmADMIADLYDSIK-----------------------------iaK 167 ::::: :::::::::::: : d1pbga_ 225 dpenpadvraAELEDiIHNKFILDATYLghysdktmegvnhilaenggeldlrdedfqaL 284 d1tx2a_ 168 DAGVRDeNIILDPGIGfaKTPE-----------------------------qNLEAMRN- 197 :::::: ::::::::: :::: ::::::: d1pbga_ 285 DAAKDL-NDFLGINYY--MSDWmqafdgeteikyqikgvgrrvapdyvpwiiYPEGLYDq 341 d1tx2a_ 198 LEQLNVL---GYPVLL-GTSRksfighvLDLP--------VEERLEGTGATVCLGIEKG- 244 ::::::: :::::: :::: :::: ::::::::::::::::::: d1pbga_ 342 IMRVKNDypnYKKIYItENGL-------GYKDefvdntvyDDGRIDYVKQHLEVLSDAIa 394 d1tx2a_ 245 ----CEFVRVH--------------------------------dvKEMSRM--AKMMdam 266 ::::::: :::::: :::: d1pbga_ 395 dganVKGYFIWslmdvfswsngyekryglfyvdfdtqerypkksaHWYKKLaeTQVI--- 451 d1tx2a_ 267 igk 269 d1pbga_ 452 --e 452 FAST alignment (Normalized score: 5.67 Raw score:1975.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNE-------KTLIMGILNV----TPDSFSDGGSYNE--------- 40 ::::::::: ::::: d1pbga_ 1 -----------------MTKTLPKDFIFGGATA-AYQAEGATH--------TDGKGPVAW 34 d1tx2a_ 41 ------------------VDAAVRHAKEMRDEGAHIIDIGGESFAKVS------------ 70 :::::::::::::::::::::: d1pbga_ 35 DKYLEDNYWYTAEPASDFYHKYPVDLELAEEYGVNGIRIS--------IAWSRIFPTGYG 86 d1tx2a_ 71 --VEEEIKRVVPMIQAVSKEVKLPISIDTY------------------------KAEVAK 104 :::::::::::::::: ::::::::: :::::: d1pbga_ 87 EVNEKGVEFYHKLFAECH-KRHVEPFVT--LHHFDTPEALHSNGDFLNRENIEHFIDYAA 143 d1tx2a_ 105 QAIE--AGAHIINDIWGAKA--------------------------------EPKIAEVA 130 :::: ::::::: :::::::: d1pbga_ 144 FCFEEFPEVNYWT-------TFNEIGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVSH 196 d1tx2a_ 131 AH---------YDVPIILMHNRDNMNYR------------------NLMADMIADLYDSI 163 :: :::::::: :::::::::::::: d1pbga_ 197 ARAVKLYKDKGYKGEIGVV---------HALPTKYPYDPENPADVRAAELEDIIHNKFIL 247 d1tx2a_ 164 KIAKDAGV-----------------------------------RDEN-IILDPGIGFAK- 186 :::: :::: :::::: d1pbga_ 248 DATY----LGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLNDFLGIN-----Y 298 d1tx2a_ 187 -----------------------------------TPEQNLEAMRNLEQLN-VLG--YPV 208 ::::::: :::::: ::: ::: d1pbga_ 299 YMSDWMQAFDGETEIKYQIKGVGRRVAPDYVPWIIYPEGLYD---QIMRVKNDYPNYKKI 355 d1tx2a_ 209 LLGTSRKSFIGHVLDLPV------------------EERLEGTGATVCLGIE-----KGC 245 :: :::::::::::::::: ::: d1pbga_ 356 YI----------------TENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANV 399 d1tx2a_ 246 EFVRVH----------------------------------DVKEMSRMAKMMDAMIGK-- 269 :::: :::::::::: d1pbga_ 400 KGYF--IWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAE--------TQ 449 d1tx2a_ 270 --- 270 d1pbga_ 450 VIE 452 TMalign alignment (TM-score: 0.65 Raw score:174.63) d1tx2a_ 1 ----KWDYDLRCGEYTLNLNEKTLIMGILN---VTPDSFSDGG----------------- 36 :::::::::::: :::::::::: d1pbga_ 1 MTKT--------------LPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWYTA 46 d1tx2a_ 37 ----SYNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEE-E---IK-RVVPMIQAVSK 87 :::::::::::::::::::::::::: :::::: : :: ::::::::::: d1pbga_ 47 EPAS--DFYHKYPVDLELAEEYGVNGIRISIA---WSRIFPTGYGEVNEKGVEFYHKLFA 101 d1tx2a_ 88 EVK---LPISIDTY----------------------KAEVAKQAI-EA-GAHIIN-DI-W 118 ::: :::::::: ::::::::: :: :::::: :: : d1pbga_ 102 ECHKRHVEPFVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWTTFNEI 161 d1tx2a_ 119 G-----------------------------AKAEP-KIAEVAA-H-YDVPIILMHNR--D 144 : ::::: ::::::: : ::::::::::: d1pbga_ 162 GPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPT- 220 d1tx2a_ 145 NM------------NYRNLMA-DMIADLYDSIKI-------------------------- 165 : ::::::: :::::::::::: d1pbga_ 221 -KYPYDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELDLRDE 279 d1tx2a_ 166 ----AKDAGVRDENIILDPGIGFAK--------------------T-------PEQNLEA 194 ::::::: :::::::::::: : ::::::: d1pbga_ 280 DFQALDAAKDL--NDFLGINYYMSDWMQAFDGETEIKYQIKGVGRRVAPDYVPWIIYPEG 337 d1tx2a_ 195 MRNLEQ-LNV--L-GYPVLLGTSRKSFIGHVLDLPVE-------E-RLE-GTGATVCLGI 241 :::::: ::: : :::::::::: :: :::: : ::: :::::::::: d1pbga_ 338 LYDQIMRVKNDYPNYKKIYITENG---LG----YKDEFVDNTVYDDGRIDYVKQHLEVLS 390 d1tx2a_ 242 EKG-----CEFVRV--H---------------D---------------VKEMSRMAKMMD 264 ::: :::::: : : :::::::::: : d1pbga_ 391 DAIADGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAET-Q 449 d1tx2a_ 265 AMIGK 269 ::: d1pbga_ 450 VIE-- 452 HHsearch alignment (Probability: 0.02 E-value:0.07) d1tx2a_ 234 GATVCLGIEKGCEF 247 :::::::::::::: d1pbga_ 386 LEVLSDAIADGANV 399