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 <-- 1.965 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1km4a_) 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 d1km4a_ Orotidine 5'​-​monophosphate decarboxylase (OMP decarboxylase)Ribulose-​phoshate binding barrelTIM 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 <-- 1.965 --> Hit
DALI alignment (Z-score: 13.6 Raw score:1293.60) d1tx2a_ 1 kwdydlrcgeytlnlnekTLIMGILNVTpdsfsdggsynEVDAAVRHAKEMRDeGAHIID 60 :::::::::: :::::::::::::: :::::: d1km4a_ 1 ----------------vmNRLILAMDLM-----------NRDDALRVTGEVRE-YIDTVK 32 d1tx2a_ 61 IGGEsfakvsveeEIKRvVPMIQAVSKEVKLPISIDTY-------KAEVAKQAIEAGAHI 113 :::: :::: :::::::::::::::::::: ::::::::::::::: d1km4a_ 33 IGYP-------lvLSEG-MDIIAEFRKRFGCRIIADFAvadipetNEKICRATFKAGADA 84 d1tx2a_ 114 INDIW-gaKAEP-KIAEVAAHYDVPIILMHN---rdNMNYrnLMADMIADLYDSIKIAKd 168 ::::: :::: :::::::::::::::::: :::: ::::::::::::::::: d1km4a_ 85 IIVHGfpgADSVrACLNVAEEMGREVFLLTEmshpgAEMF--IQGAADEIARMGVDLGV- 141 d1tx2a_ 169 agvrdenIILDPGigfaktpeqnleAMRNLEQLNVL---GYPVLLGT-SRKSfighvldl 224 :::::: ::::::::::: :::::::: :::: d1km4a_ 142 -------KNYVGP----------stRPERLSRLREIigqDSFLISPGvGAQG-------- 176 d1tx2a_ 225 pveerlegtgaTVCLGIEkGCEFVRVH-----------DVKEMSRMAkmmdamigk 269 ::::::: :::::::: ::::::::: d1km4a_ 177 ----------gDPGETLR-FADAIIVGrsiyladnpaaAAAGIIESI--------- 212 FAST alignment (Normalized score: 9.63 Raw score:2300.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKT---LIMGILNVTPDSFSDGGSYN----EVDAAVRHAKEMRD 53 ::::: :::::::::::::: d1km4a_ 1 -------------------VMNRLILA---------------MDLMNRDDALRVTGEVRE 26 d1tx2a_ 54 EGAHIIDIGGESFAKVSVEEEIKR-------VVPMIQAVSKEVKLPISIDTY-------- 98 :::::::: :::::::::::::::::::: d1km4a_ 27 -YIDTVKIG---------------YPLVLSEGMDIIAEFRKRFGCRIIADF-AVADIPET 69 d1tx2a_ 99 KAEVAKQAIEAGAHIINDIWG-AKAE----PKIAEVAAHYDVPIILMHNRDNMNYRNL-- 151 :::::::::::::::::: :::: ::::::::::::::::: d1km4a_ 70 NEKICRATFKAGADAIIV---HGFPGADSVRACLNVAEEMGREVFLL-----------TE 115 d1tx2a_ 152 ------MADMIADLYDSIKIAKDAGVRDEN-IILDPGIGFAKTPEQNLE-AMRNLEQLNV 203 ::::::::::::::::::: ::::::: :::::::::: d1km4a_ 116 MSHPGAEMFIQGAADEIARMGVDLG-----VKNYVGPS-----------TRPERLSRLRE 159 d1tx2a_ 204 ---LGYPVLLGTSRKSFIGHVLDLPVEERLEGTGA-----TVCLGIEKGCEFVRVH---- 251 :::::::::: ::::::: ::::::: d1km4a_ 160 IIGQDSFLISPGV----------------------GAQGGDPGETLR-FADAIIV-GRSI 195 d1tx2a_ 252 --------DVKEMSRMAKMMDAMIGK- 269 :::::::: d1km4a_ 196 YLADNPAAAAAGIIES----------I 212 TMalign alignment (TM-score: 0.49 Raw score:131.46) d1tx2a_ 1 -KW-----------------------DYDLRCGEYTLNLNEKTLIMGILN--VTPDSFSD 34 : :::::::::: ::: d1km4a_ 1 V-MNRLILAMDLMNRDDALRVTGEVR--------------EYIDTVKIGYPLVLS----- 40 d1tx2a_ 35 GGSYNEVDAAVRHAKEMRDEG-AHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPI 93 : :: :::::::::: ::::::::: ::: ::: :::::::::::: ::: d1km4a_ 41 -----E--GM-DIIAEFRKRFGCRIIADFAV-----ADI-PET-NEKICRATFKAG-ADA 84 d1tx2a_ 94 SIDTYK-AE-VAKQAIEAG----AHIINDIWG--------AK-AEPKIAEVAA-HYDVPI 137 :::::: :: ::::::::: ::::::::: :: :::::::::: :::::: d1km4a_ 85 IIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNY 144 d1tx2a_ 138 ILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRN 197 ::::: :::::::::: : :::::::::::::: : : :: d1km4a_ 145 VGPST------------RPERLSRLRE--I---IGQDSFLISPGVGA-Q----G--GD-- 178 d1tx2a_ 198 LEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMS 257 ::::::: :::::: ::: : ::::::::::::::::: d1km4a_ 179 PGETLRF-ADAIIV-GRS--I---------YLADNPAAAAAGIIESI------------- 212 d1tx2a_ 258 RMAKMMDAMIGK 269 d1km4a_ 213 ------------ 213 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tx2a_ 38 YNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDT 97 :::::::::::::: ::::::::::::: :::: :::::::::::::::::::: d1km4a_ 11 LMNRDDALRVTGEV-REYIDTVKIGYPL---VLSE-----GMDIIAEFRKRFGCRIIADF 61 d1tx2a_ 98 --Y-----KAEVAKQAIEAGAHIINDIWGAKAEPKIA----EVAAHYDVPIILMHNRDNM 146 : ::::::::::::::::: ::::: ::::: ::::::::::::::::::: d1km4a_ 62 AVADIPETNEKICRATFKAGADAII-VHGFP-GADSVRACLNVAEEMGREVFLLTEMSHP 119 d1tx2a_ 147 NYRNLMADMIADL 159 ::::::::::::: d1km4a_ 120 GAEMFIQGAADEI 132