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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.883 --> Intermediate <-- 1.196 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1o5za1) through the intermediate protein (d1vi2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vi2a1 Putative shikimate dehydrogenase YdiBNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1o5za1 Folylpolyglutamate synthetase,​ C-​terminal domainMurD-​like peptide ligases,​ peptide-​binding domainMurD-​like peptide ligases,​ peptide-​binding domainα/β

Supporting Alignments

Query <-- 0.883 --> Intermediate
DALI alignment (Z-score: 4.6 Raw score:365.80) query 1 --------------GMENKKMNLLLfsgdydkALASLIIANAAREMEI-EVTIFCAFWgl 45 ::::::::::: :::::::::::::::: ::::::::: d1vi2a1 1 dgtghiraikesgfDIKGKTMVLLG------aGGASTAIGAQGAIEGLkEIKLFNRRD-- 52 query 46 LLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllemmkeekapkls 105 :::: d1vi2a1 53 EFFD-------------------------------------------------------- 56 query 106 dlLSGARKKE------VKFYAXQlsveimgfkkeelfpevqimDVKEYLKNALESDLQLF 159 :::::::: ::::::: ::::::::::::::::: d1vi2a1 57 kaLAFAQRVNentdcvVTVTDLA--------------------DQQAFAEALASADILTN 96 query 160 ------------------------------------------------------------ 160 d1vi2a1 97 gtkvgmkpleneslvndisllhpgllvtecvynphmtkllqqaqqagcktidgygmllwq 156 query 160 -------------------------i 160 d1vi2a1 157 gaeqftlwtgkdfpleyvkqvmgfga 182 FAST alignment (Normalized score: 4.17 Raw score:711.70) query 1 --------------GMENKKMNLLLFSGDYDK---ALASLIIANAAREME-IEVTIFCA- 41 ::::::::: ::::::::::::::: :::::::: d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVL---------LGAGGASTAIGAQGAIEGLKEIKLFNRR 51 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKA 101 ::::: d1vi2a1 52 DEFFD------------------------------------------------------- 56 query 102 PK-LSDLLSGARK---KEVKFYAXQLSVEIMGFKKEELFPEVQIM--DVKEYLKNALESD 155 :::::::::: ::::::: ::::::::::::: d1vi2a1 57 --KALAFAQRVNENTDCVVTVTD----------------------LADQQAFAEALASAD 92 query 156 LQLFI------------------------------------------------------- 160 ::: d1vi2a1 93 ILT--NGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGY 150 query 161 -------------------------------- 161 d1vi2a1 151 GMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 182 TMalign alignment (TM-score: 0.31 Raw score:49.46) query 1 ------GMENKKMNL------------LLFSGDYD-KALASLIIAN-AAR--EMEIEVTI 38 :::: ::::: :::::::::: ::: d1vi2a1 1 DGTGHI-----RAIKESGFDIKGKTMV---LLGAGGASTAIGAQGAIEGLKE-------- 44 query 39 FCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKE 98 ::::::::: : ::::::::::::: d1vi2a1 45 ----------------------------------IKLFNRRDE-F--FDKALAFAQRVNE 67 query 99 EK-APKLS------------DLLSGARKKEVKFYA----XQLS----VEIMG--FKKEEL 135 :: ::::: ::::: : ::: : :::: :::::: d1vi2a1 68 NTDCVVTVTDLADQQAFAEA--LASAD---I-LTNGTKV---GMKPL-ENESLVNDISLL 117 query 136 FPEV-Q---------------IMD-----VKEYLKNALESDLQL---------------- 158 :::: : ::: ::: ::: ::::: d1vi2a1 118 HPGLLVTECVYNPHMTKLLQQAQQAGCKT--IDG-YGM-LLWQGAEQFTLWTGKDFPLEY 173 query 159 ---------FI 160 d1vi2a1 174 VKQVMGFGA-- 182 HHsearch alignment (Probability: 0.01 E-value:0.14) query 102 PKLSDLLSGARKKEVKFY 119 :::::::::::::::::: d1vi2a1 130 PHMTKLLQQAQQAGCKTI 147
Intermediate <-- 1.196 --> Hit
DALI alignment (Z-score: 4.9 Raw score:386.00) d1vi2a1 1 ----------------------DGTGHIRAIKESgFDIKGKTMVLlGAGG--asTAIGAQ 36 :::::::::::: :::::::::: :::: :::::: d1o5za1 1 grfeilekngkmyildgahnphGAESLVRSLKLY-FNGEPLSLVI-GILDdknrEDILRK 58 d1vi2a1 37 GAIeGLKEIKLFNR---rDEFFDKALAFAQRVNentdcVVTVTDLadqqAFAEALaSADI 93 ::: :::::::::: ::::::::::::::: ::::::: :::::: :::: d1o5za1 59 YTG-IFERVIVTRVpsprMKDMNSLVDMAKKFF----kNVEVIED--plEAIEST-ERAT 110 d1vi2a1 94 LTNGTKVgmkplenESLV-NDISllhpgllvtecvynphmtkllqqaqqagcktidgygm 152 ::::::: :::: :::: d1o5za1 111 VVTGSLF-----lvGYVReFLTT------------------------------------- 128 d1vi2a1 153 llwqgaeqftlwtgkdfpleyvkqvmgfga 182 d1o5za1 129 ---------------------gkineewkl 137 FAST alignment (Normalized score: 3.72 Raw score:587.80) d1vi2a1 1 D-----------------------GTGHIRAIKESGFDI----KGKTMVLLGAGG----- 28 :::::::::: ::::::: d1o5za1 1 -GRFEILEKNGKMYILDGAHNPHGAESLVRSLKL-----YFNGEPLSLVI-----GILDD 49 d1vi2a1 29 -ASTAIGAQGAIEGLKEIKLFNRR-------DEFFDKALAFAQRVNENTD--CVVTVTDL 78 ::::::::::: ::::::: ::::::::::::: :::::: d1o5za1 50 KNREDILRKYTG-IFERVIV----TRVPSPRMKDMNSLVDMAKK------FFKNVEVI-- 96 d1vi2a1 79 ADQQ-AFAEALASADIL-----TNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHM 132 ::::::::: :::: d1o5za1 97 ----EDPLEAIEST---ERATVVTGS---------------------------------- 115 d1vi2a1 133 ----TKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA------ 182 :::::::: d1o5za1 116 LFLVGYVREFLT------------------------------------------TGKINE 133 d1vi2a1 183 ---- 183 d1o5za1 134 EWKL 137 TMalign alignment (TM-score: 0.42 Raw score:76.14) d1vi2a1 1 ---------------------D-GTGHIRAIKESGFDIKGKTMVLLGAG--GASTAIGAQ 36 : ::::::::::: :::::::::: ::: ::::::::: d1o5za1 1 GRFEILEKNGKMYILDGAHNPHGAESLVRSLKLY-FNGEPLSLVI-GILDDKNREDILRK 58 d1vi2a1 37 GAIEGLKEIKLFN-RRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILT 95 : ::::::::::: ::::::: ::::::::: ::::::::::: :: ::::: ::::::: d1o5za1 59 Y-TGIFERVIVTRVPSPRMKD-MNSLVDMAK-KFFKNVEVIED-PL-EAIES-TERATVV 112 d1vi2a1 96 NGTKVGMKPLENESLV-NDISL--------LHPGLLVTECVYNPHMTKLLQQAQQAGCKT 146 ::::::: :::: ::::: d1o5za1 113 TGSLFLV-----GYVREFLTTGKINEEWKL------------------------------ 137 d1vi2a1 147 IDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 182 d1o5za1 138 ------------------------------------ 138 HHsearch alignment (Probability: 0.04 E-value:0.52) d1vi2a1 131 HMTKLLQQAQQAGCKTIDGYGMLLWQGAEQF 161 ::::::::::::::::::::::::::::::: d1o5za1 96 IEDPLEAIESTERATVVTGSLFLVGYVREFL 126