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 <-- 1.485 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1xeaa1) 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 d1xeaa1 Putative oxidoreductase VCA1048NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/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 <-- 1.485 --> Hit
DALI alignment (Z-score: 8.0 Raw score:582.30) d1vi2a1 1 dgtghiraikesgfdikGKTMVLLGAGGAST-AIGAQGAIEGlKEIKLFNRrdeFFDKAL 59 :::::::::::::: :::::::::: :::::::: :::::: d1xeaa1 1 -----------------SLKIAMIGLGDIAQkAYLPVLAQWPdIELVLCTR---NPKVLG 40 d1vi2a1 60 AFAQRVNentdcVVTVTDLadqqAFAEAlaSADILTNGTKVGmkplenESLVND-ISLLh 118 ::::::: ::::::: ::::: :::::::::::: :::::: :::: d1xeaa1 41 TLATRYR-----VSATCTD--yrDVLQY--GVDAVMIHAATD----vhSTLAAFfLHLG- 86 d1vi2a1 119 pgLLVTECVYNP----hmtkllQQAQQAGCKTIDGygmLLWQ---gaeqftlwtgkdfpl 171 :::::::::: ::::::::::::: :::: d1xeaa1 87 --IPTFVDKPLAasaqecenlyELAEKHHQPLYVG---FNGFdamvqdwlqvaaagklpt 141 d1vi2a1 172 eyvkqvmGFGA--------------- 182 :::: d1xeaa1 142 hiiernlASHQlaeaicqqitqqvtk 167 FAST alignment (Normalized score: 5.60 Raw score:976.30) d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVLLGAGGAST-AIGAQGAIEGL--KEIKLFNRRDE-FFD 56 :::::::::::::: ::::::::: ::::::: ::: d1xeaa1 1 -----------------SLKIAMIGLGDIAQKAYLPVLAQW--PDIELVLCT----RNPK 37 d1vi2a1 57 KALAFAQRVNENTDCV---VTVTDLADQQAFAEALA-SADILTNGTKVGMKPLENESLVN 112 :::::::: :::: :::::::: ::::::::: d1xeaa1 38 VLGTLATR--------YRVSATC--TDYRDVLQ---YGVDAVMIHA-------------- 70 d1vi2a1 113 DISLLH--------------PGLLVTECV---YNPHM---TKLLQQAQQAGCKTIDGYGM 152 :::::::: :::: ::::::::::::::::: d1xeaa1 71 ------ATDVHSTLAAFFLHLGIPTFVD-KPLAASA-QECENLYELAEKHHQPLYVG--- 119 d1vi2a1 153 LLWQGAEQFTLWTGKDFPLEYVKQVMGFGA------------------------------ 182 d1xeaa1 120 ------------------------------FNGFDAMVQDWLQVAAAGKLPTHIIERNLA 149 d1vi2a1 183 ------------------ 183 d1xeaa1 150 SHQLAEAICQQITQQVTK 167 TMalign alignment (TM-score: 0.54 Raw score:97.42) d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVLLGAGGAST-AIGAQGAIEGLKEIKLFNRRDEFFDKAL 59 :::::::::::::: ::::::::::::::::::: : ::::: d1xeaa1 1 -----------------SLKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTR-N--PKVLG 40 d1vi2a1 60 AFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHP 119 ::::::: :::::::: : ::::: :::::::::: : :::::::::::::: d1xeaa1 41 TLATRYR-----VSATCTDY-R-DVLQY--GVDAVMIHAA--T--DVHSTLAAFFLHLG- 86 d1vi2a1 120 GLLVTECVY--NPH--MTKLLQQAQQAGCKTIDGYGMLLWQ-GAE--------------- 159 :::::::: ::: ::::::::::::::::: ::::: :: d1xeaa1 87 -IPTFVDKPLAASAQECENLYELAEKHHQPLYV---GFNGFD-AMVQDWLQVAAAGKLPT 141 d1vi2a1 160 ----QFTLWTGKDFPLEYVKQ--VMGFG-A-------------- 182 : ::: : d1xeaa1 142 HIIE----------------RNL--ASHQLAEAICQQITQQVTK 167 HHsearch alignment (Probability: 0.96 E-value:0.00) d1vi2a1 19 KTMVLLGAGGASTA-IGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTD 77 :::::::::::::: ::::::::::::::::::::::::::::: :: ::::::: d1xeaa1 2 LKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATR---YR----VSATCTD 54 d1vi2a1 78 LADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHM----- 132 : ::: :::::::::::::::::: :::::::::::::: :::::: d1xeaa1 55 Y---RDV--LQYGVDAVMIHAATDVHS------TLAAFFLHLGIPTF--VDKPLAASAQE 101 d1vi2a1 133 -TKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKD 168 :::::::::::::::::::::::::::::::::::: d1xeaa1 102 CENLYELAEKHHQPLYVGFNGFDAMVQDWLQVAAAGK 138