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 <-- 0.879 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1k77a_) 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 d1k77a_ Hypothetical protein YgbM (EC1530)Xylose isomerase-​likeTIM 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 <-- 0.879 --> Hit
DALI alignment (Z-score: 9.6 Raw score:1033.50) d1tx2a_ 1 kwdydlrcgeytlnlneKTLIMGILNvtpdsfsdggsynevDAAVRHAKEMRDEGAHIID 60 ::::::::: ::::::::::::::::::: d1k77a_ 1 -----------------MPRFAANLS----------mmfteVPFIERFAAARKAGFDAVE 33 d1tx2a_ 61 IGGesfakvsveeeIKRVVPMIQAVSKEVKLPI-SIDT---------------------- 97 ::: ::::::::::::::::::: :::: d1k77a_ 34 FLF----------pYNYSTLQIQKQLEQNHLTLaLFNTapgdinagewglsalpgrehea 83 d1tx2a_ 98 -yKAEVAKQAIEAGAH-IINDIW-------------gaKAEP--KIAEVAAHYDVPIILM 140 :::::::::::::: :::::: :::: :::::::::::::::: d1k77a_ 84 haDIDLALEYALALNCeQVHVMAgvvpagedaeryravFIDNirYAADRFAPHGKRILVE 143 d1tx2a_ 141 HNR---DNMNyrnlmadMIADLYDSIKIAKdagvrDENIILDPGIGFaktpeQNLEaMRN 197 ::: :::: ::::::::::::: :::::::::::: :::: ::: d1k77a_ 144 ALSpgvKPHY----lfsSQYQALAIVEEVA-----RDNVFIQLDTFH--aqkVDGN-LTH 191 d1tx2a_ 198 L-EQLNvlGYPVLLGTSRKSFIghvldlpveeRLEG-tgATVCLgIEKG-----cEFVRV 250 : :::: :::::::::::::: :::: ::::: :::: ::::: d1k77a_ 192 LiRDYA--GKYAHVQIAGLPDR---------hEPDDgeiNYPWL-FRLFdevgyqGWIGC 239 d1tx2a_ 251 H--------dvKEMSRMAKMMdamigk 269 : :::::::::: d1k77a_ 240 EykprglteegLGWFDAWRGS------ 260 FAST alignment (Normalized score: 5.89 Raw score:1557.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEK-TLIMGILNVTPDSFSDGGSYNEVD--------AAVRHAKEM 51 :::::: ::::::::: d1k77a_ 1 ------------------MPRFAAN------------------LSMMFTEVPFIERFAAA 24 d1tx2a_ 52 RDEGAHIIDIGGESFAKVSVEEEIKRVVP------MIQAVSK---EVKLPISIDTY---- 98 :::::::::: ::::::: ::::::::: d1k77a_ 25 RKAGFDAVEF-------------------LFPYNYSTLQIQKQLEQNHLTLALF--NTAP 63 d1tx2a_ 99 -------------------KAEVAKQAIE----AGAHIINDIWGAKA------------- 122 :::::::::: :::::::: d1k77a_ 64 GDINAGEWGLSALPGREHEAHADIDLALEYALALNCEQVHV------MAGVVPAGEDAER 117 d1tx2a_ 123 --------EPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIA----------DLYDSIK 164 ::::::::::::::::::::: ::::::: d1k77a_ 118 YRAVFIDNIRYAADRFAPHGKRILVEALS--------------PGVKPHYLFSSQYQALA 163 d1tx2a_ 165 IAKDAGVRDENIILDPGIGFAKTPE--------QNLEAMRNLEQLNVLGYP--------V 208 :::::: :::::::::: ::::: : d1k77a_ 164 IVEEVA--RDNVFIQLDT-------FHAQKVDGNLTHL-------------IRDYAGKYA 201 d1tx2a_ 209 LLGTSRKSFIGHVLDLPVEERLE------------GTGATVCLGIEKGC-EFVRVH---- 251 :::::: :::::::::::::: ::::: d1k77a_ 202 HVQIAG-----------------LPDRHEPDDGEINYPWLFRLFDEVGYQGWIGC-EYKP 243 d1tx2a_ 252 ---------DVKEMSRMAKMMDAMIGK-- 269 :::::: d1k77a_ 244 RGLTEEGLGWFDAWR------------GS 260 TMalign alignment (TM-score: 0.49 Raw score:132.49) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGIL--NVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHI 58 :::::::: ::::: ::: : :::::::::: : : d1k77a_ 1 -----------------MPRFAANLSMMFTEV---PFI----E-RFAAARKAGF---D-A 31 d1tx2a_ 59 IDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYK-------AEVAKQAIEAGA 111 :::::: : ::: :::::::::::::::::::::: d1k77a_ 32 VEFLFP------Y--NYS-TLQIQKQLEQNHLTLALFNTAPGDINAGE------------ 70 d1tx2a_ 112 HIINDIWG-------AK-AEPKIAEVAAHY-DVPIILMHNRDNM---NYRNLMADMIADL 159 :::: :: :::::::::::: ::::::::::::: ::::: :: ::: d1k77a_ 71 ----WGLSALPGREHEAHADIDLALEYALALNCEQVHVMAGVVPAGEDAERY--RA-VFI 123 d1tx2a_ 160 YDSIKIAKDAGVRDENIILDPGIGF--AKTPEQNLEAMRNLEQ-LN--VLGYPVLLGTSR 214 :::::::: :::::::::::::::: ::::::: ::::::: :: :::::::::::: d1k77a_ 124 DNIRYAAD-RFAPHGKRILVEALSPGVKPHYLFS--SQYQALAIVEEVARDNVFIQLDTF 180 d1tx2a_ 215 KSFIGHVLDLPVEERLEGTGATVCLGIE-KG--CEFVRVHD-----VKE----MSRMAKM 262 :::: : : :::::::: :: :::::::: ::: ::::::: d1k77a_ 181 HAQK--V----------D--GNLTHLIRDYAGKYAHVQIAGLPDRHEPDDGEINYPWLFR 226 d1tx2a_ 263 MDAMIGK--------------------------- 269 ::::::: d1k77a_ 227 LFDEVGYQGWIGCEYKPRGLTEEGLGWFDAWRGS 260 HHsearch alignment (Probability: 0.87 E-value:0.00) d1tx2a_ 39 NEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPIS-IDT 97 ::::::::::: :::::::::::::::: ::::::::: ::::::: ::: d1k77a_ 15 VPFIERFAAAR---KAGFDAVEFLFPYNYS------TLQIQKQLE----QNHLTLALFNT 61 d1tx2a_ 98 Y-------------KAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRD 144 : ::::::::::: :::::::::::::::::::::: d1k77a_ 62 APGDINAGEWGLSALPGREHEAHAD-------------IDLALEYALALNCEQVHVMAGV 108 d1tx2a_ 145 NM---NYRNLMADMIADLYDSIKIAKDAGVRDENIILDPG------IGFAKTPEQNLEAM 195 :: :::::::::::::::::::::::::: :::::: :::::::::::::: d1k77a_ 109 VPAGEDAERYRAVFIDNIRYAADRFAPHGKR---ILVEALSPGVKPHYLFSSQYQALAIV 165 d1tx2a_ 196 RNLE 199 :::: d1k77a_ 166 EEVA 169