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 <-- 0.989 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1nowa1) 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 d1nowa1 beta-​hexosaminidase 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 <-- 0.989 --> Hit
DALI alignment (Z-score: 10.3 Raw score:1202.60) d1tx2a_ 1 kwdydlrcgeytlnlneKTLIMGILNVtpdsfsdggsynEVDAAVRHAKEMRDEGAHIID 60 :::::::::: ::::::::::::::::::::: d1nowa1 1 -----------------FSHRGILIDT-------srhylPVKIILKTLDAMAFNKFNVLH 36 d1tx2a_ 61 IGGESFAKVsveEEIK-----------------RVVPMIQAVSKEVK---LPISIDTYK- 99 ::::::::: :::: :::::::::::::: ::::::::: d1nowa1 37 WHIVDDQSF---PYQSitfpelsnkgsyslshvYTPNDVRMVIEYARlrgIRVLPEFDTp 93 d1tx2a_ 100 -------------------------------------aEVAKQAIEAGAH-IINDIW--- 118 :::::::::::: :::::: d1nowa1 94 ghtlswgkgqkdlltpcysldsfgpinptlnttysfltTFFKEISEVFPDqFIHLGGdev 153 d1tx2a_ 119 ---------------------------gakAEPKIAEVAAHYDVPIILMHNrdnmnyrnl 151 ::::::::::::::::::::: d1nowa1 154 efkcwesnpkiqdfmrqkgfgtdfkklesfYIQKVLDIIATINKGSIVWQE--------- 204 d1tx2a_ 152 madmiadLYDSiKIAKdagvrdENIILDPGIgfaktpeqNLEAMrNLEQ-LNVLGYPVLL 210 :::: :::: ::::::::: ::::: :::: :::::::::: d1nowa1 205 ------vFDDK-AKLA------PGTIVEVWK--------DSAYP-EELSrVTASGFPVIL 242 d1tx2a_ 211 G-TSRKSFighvLDLPveERLEGTGAtvCLGIEK--------gCEFVRVH---------- 251 : :::::: :::: :::::::: :::::: ::::::: d1nowa1 243 SaPWYLDL----ISYG--QDWRKYYK--VEPLDFggtqkqkqlFIGGEAClwgeyvdatn 294 d1tx2a_ 252 -------DVKEMSRMAKMMDAM------------------------------igk 269 ::::::::::::::: d1nowa1 295 ltprlwpRASAVGERLWSSKDVrdmddaydrltrhrcrmvergiaaqplyagycn 349 FAST alignment (Normalized score: 6.21 Raw score:1904.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYN------EVDAAVRHAKEMRDE 54 ::::::::: ::::::::::::::: d1nowa1 1 -----------------FSHRGILID-------------TSRHYLPVKIILKTLDAMAFN 30 d1tx2a_ 55 GAHIIDIGGESFAKVSVEE---------------------------EIKRVVPMIQAVSK 87 :::::::::: ::::::::::::: d1nowa1 31 KFNVLHWHIV---------DDQSFPYQSITFPELSNKGSYSLSHVYTPNDVRMVIEYAR- 80 d1tx2a_ 88 EVKLPISIDTY---------------------------------------KAEVAKQAIE 108 :::::::::: :::::::::: d1nowa1 81 LRGIRVLPEF-DTPGHTLSWGKGQKDLLTPCYSLDSFGPINPTLNTTYSFLTTFFKEISE 139 d1tx2a_ 109 -AGAHIINDIWGAKA------------------------------------EPKIAEVAA 131 :::::::: ::::::::: d1nowa1 140 VFPDQFIHL------GGDEVEFKCWESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDIIA 193 d1tx2a_ 132 HYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKD-------AGVRDENIILDPGIGF 184 ::::::::: ::::: :::::: d1nowa1 194 TINKGSIVW----------------------------QEVFDDKAKLAP-GTIVEV---- 220 d1tx2a_ 185 AK-TPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVE-----------ERLEG 232 :::::::: :::::::::::::: ::::: d1nowa1 221 --WKDSAYPEE---LSRVTASGFPVILS----------------APWYLDLISYGQDWRK 259 d1tx2a_ 233 TGATVCLGIEK----------GCEFVRVH-------------------DVKEMSRMAKMM 263 ::: :::: :::::: :::::::::: d1nowa1 260 YYK--VEPL--DFGGTQKQKQLFIGGE--ACLWGEYVDATNLTPRLWPRASAVGERLW-- 311 d1tx2a_ 264 DAMIGK-------------------------------------- 269 d1nowa1 312 ------SSKDVRDMDDAYDRLTRHRCRMVERGIAAQPLYAGYCN 349 TMalign alignment (TM-score: 0.60 Raw score:162.61) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNV--TPDSFSDGGSYNEVDAAVRHAKEMRDEGAHI 58 :::::::::: ::: ::::::::::::::::::: d1nowa1 1 -----------------FSHRGILIDTSRHYL---------PVKIILKTLDAMAFNKFNV 34 d1tx2a_ 59 IDIGGESFAKVS-------VEE--EI-----KRVVPMIQAVSKEVK---LPISIDTYK-- 99 :::::::::::: ::: :: ::::::::::::::: ::::::::: d1nowa1 35 LHWHIVDDQSFPYQSITFPELSNKGSYSLSHVYTPNDVRMVIEYARLRGIRVLPEFDTPG 94 d1tx2a_ 100 -----------------------------------A-EVAKQAIEAGAH-IINDIWG--- 119 : :::::::::::: ::::::: d1nowa1 95 HTLSWGKGQKDLLTPCYSLDSFGPINPTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVE 154 d1tx2a_ 120 --------------------------AK-AEPKIAEVAAHYDVPIILMHNRDNMNYRNLM 152 :: :::::::::::::::::::::: d1nowa1 155 FKCWESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDIIATINKGSIVWQEV--------- 205 d1tx2a_ 153 ADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGT 212 :: : :::: : :: :::::::: : :::::::::::::::::::: d1nowa1 206 -FD--D-KAKL---A-----PG-TIVEVWKD-------S-AYPEELSRVTASGFPVILSA 244 d1tx2a_ 213 -SRKSFIGHVLDLPVEERLEGTGATVCLGIEK------G--CEFVRVH------------ 251 :::: : ::::::::::::: : :::: : ::::::: d1nowa1 245 PWYLD--L----ISYGQDWRKYYKV-E-PLDFGGTQKQKQLFIGGEACLWGEYVDATNLT 296 d1tx2a_ 252 -----DVKEMSRMAKMMDAM---------------------------------IGK 269 ::::::::::::::: d1nowa1 297 PRLWPRASAVGERLWSSKDVRDMDDAYDRLTRHRCRMVERGIAAQPLYAGYCN--- 349 HHsearch alignment (Probability: 0.04 E-value:0.17) d1tx2a_ 30 DSFSDGGSYNEVDAAVRHAKEMRDEGAHII---DIGGESFA------------------- 67 ::::::: :::::::::::::::::::::: :::::::: d1nowa1 59 GSYSLSH-VYTPNDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSLDSFG 117 d1tx2a_ 68 KVSV--EEEIKRVVPMIQAVSKEVK---LPISIDT-------YKAEVAKQAIEAGAH-II 114 :::: ::::::::::::::::::: ::::::: ::::::::::::::: :: d1nowa1 118 PINPTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMRQKGFGTDF 177 d1tx2a_ 115 NDIWGAKAEPKIAEVAAHYDVPIILMHNR---DNMNYRNLMADMIADL----YDSIKIAK 167 :::::: :::::::::::::::::::::: ::::::::: ::::: :::::::: d1nowa1 178 KKLESF-YIQKVLDIIATINKGSIVWQEVFDDKAKLAPGTI--VEVWKDSAYPEELSRVT 234 d1tx2a_ 168 DAGVRDENIILDPGIGFA-KTPEQNLEAMRNLEQLN----VLGYPVLLGTSRKSFIGHVL 222 ::::: :::::::::: ::::::::::::::::: :::::::::::::::::::: d1nowa1 235 ASGFP---VILSAPWYLDLISYGQDWRKYYKVEPLDFGGTQKQKQLFIGGEACLWGEYVD 291 d1tx2a_ 223 DLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMA 260 ::::::::::::::::::::::::: :::::::::: d1nowa1 292 ATNLTPRLWPRASAVGERLWSSKDV---RDMDDAYDRL 326