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 <-- 1.313 --> Intermediate <-- 1.260 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1gpja2) through the intermediate protein (d1lvla2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1lvla2 Dihydrolipoamide dehydrogenaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1gpja2 Glutamyl tRNA-​reductase middle domainNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.313 --> Intermediate
DALI alignment (Z-score: 4.5 Raw score:353.40) query 1 -----------------GMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAfw 43 ::::::::::: ::::::::::::::::::::::: d1lvla2 1 mlplggpvisstealapKALPQHLVVVG------gGYIGLELGIAYRKLGAQVSVVEA-- 52 query 44 gLLLLrdpekasqedkslyeqafssltprEAEElplskmnlggigkkmllemmkeekapK 103 :::: :::: : d1lvla2 53 -RERI-----------------------lPTYD------------------------seL 64 query 104 LSDLLSGARKKEVKFYAX------------qLSVEImgfkkeelfpevqimdvkeyLKNA 151 :::::::::::::::::: ::::: :::: d1lvla2 65 TAPVAESLKKLGIALHLGhsvegyengcllaNDGKG------------------gqLRLE 106 query 152 leSDLQLFI-- 160 ::::::: d1lvla2 107 --ADRVLVAvg 115 FAST alignment (Normalized score: 4.50 Raw score:610.50) query 1 GMEN---------------------KKMNLLLFSGDYDK---ALASLIIANAAREMEIEV 36 ::::: :::::::::::::::::: d1lvla2 1 ----MLPLGGPVISSTEALAPKALPQHLVV---------VGGGYIGLELGIAYRKLGAQV 47 query 37 TIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMM 96 ::::: d1lvla2 48 SVVEA------------------------------------------------------- 52 query 97 KEEKAP-----------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVK 145 ::::::::::::::::: ::::: d1lvla2 53 ------RERILPTYDSELTAPVAESLKKLGIALH--------------------LGHSV- 85 query 146 EYLKNA-------------------LESDLQLFI---- 160 ::::::: d1lvla2 86 ------EGYENGCLLANDGKGGQLRLEADRVL--VAVG 115 TMalign alignment (TM-score: 0.40 Raw score:63.78) query 1 ------------------GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAF 42 :: :::::::: :::::::::::::::::::::::: d1lvla2 1 MLPLGGPVISSTEALAPKAL-PQHLVVVG------GGYIGLELGIAYRKLGAQVSVVEA- 52 query 43 WGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP 102 :::::: :::::: d1lvla2 53 -RERILP--------------------TYDSEL--------------------------- 64 query 103 KLSDLLSGARKKEVKFYA-X-------------QLSVEIMGFKKEELFPEVQIMDVKEYL 148 ::::::::::::::::: : :: : ::: : d1lvla2 65 -TAPVAESLKKLGIALHLGHSVEGYENGCLLANDG--K--------------GGQ--L-- 103 query 149 KNALESDLQLFI- 160 :: ::::::::: d1lvla2 104 RL-EADRVLVAVG 115 HHsearch alignment (Probability: 0.19 E-value:0.00) query 20 LASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPL 79 :::::::::::::::::::: ::::: d1lvla2 31 YIGLELGIAYRKLGAQVSVV-----------------------------------EARER 55 query 80 SKMNLGGIGKKMLLEMMKEEKA 101 :::::::::::::::::::::: d1lvla2 56 ILPTYDSELTAPVAESLKKLGI 77
Intermediate <-- 1.260 --> Hit
DALI alignment (Z-score: 3.3 Raw score:290.00) d1lvla2 1 mlplggpvisstEALAP-----KALP-QHLVVVGGGYIGLELGIAYRKLGA-QVSVVEAR 53 ::::: :::: :::::::::::::::::::::::: :::::::: d1gpja2 1 ---segavsigsAAVELaerelGSLHdKTVLVVGAGEMGKTVAKSLVDRGVrAVLVANRT 57 d1lvla2 54 ERIlptydseltapvaeslKKLGIALHlgHSVEgyengcllandgkggqLRLE--ADRVL 111 ::: :::::::: :::: :::: ::::: d1gpja2 58 YER-----------avelaRDLGGEAV--RFDE---------------lVDHLarSDVVV 89 d1lvla2 112 VAVG-------------------------------------------------------- 115 :::: d1gpja2 90 SATAaphpvihvddvrealrkrdrrspiliidianprdveegveniedvevrtiddlrvi 149 d1lvla2 116 ---------- 116 d1gpja2 150 arenlerrrk 159 FAST alignment (Normalized score: 3.50 Raw score:473.30) d1lvla2 1 MLPLGGPVISSTEAL-----------------APKALP---QHLVVVGGGYIGLELGIAY 40 :::: ::::::::::::::::::: d1gpja2 1 ---------------SEGAVSIGSAAVELAERELGS--LHDKTVLVVGAGEMGKTVAKSL 43 d1lvla2 41 RKLG-AQVSVVEARERILPTYDSELTAPVAESLKK-LGIALHLGHSVEGYENGCLLANDG 98 :::: :::::::: :::::::::: ::::: d1gpja2 44 VDRGVRAVLVANR------------TYERAVELARDLGGEA------------------- 72 d1lvla2 99 KGGQLR----------LEADRVLVAVG--------------------------------- 115 :::::::::: d1gpja2 73 ------VRFDELVDHLARSDVVVSAT-AAPHPVIHVDDVREALRKRDRRSPILIIDIANP 125 d1lvla2 116 ---------------------------------- 116 d1gpja2 126 RDVEEGVENIEDVEVRTIDDLRVIARENLERRRK 159 TMalign alignment (TM-score: 0.48 Raw score:55.47) d1lvla2 1 -------MLPLGGPVISS-TEAL-AP-K--ALP--QHLVVVGGGYIGLELGIAYRKLGA- 45 : ::: :: : ::: :::::::::::::::::::::::: d1gpja2 1 SEGAVSI----------GS-AAVELAERELGSLHDKTVLVVGAGEMGKTVAKSLVDRGVR 49 d1lvla2 46 QVSVVEARERILPTYDSELTAPVAESLKKLGIALHLGHSVEGYENGCLLANDGKGGQLRL 105 :::::::::::: : :: :::::::::: ::: :: :: d1gpja2 50 AVLVANRTYERA--------V--EL-ARDLGGEAVR-FDE-------LV---------DH 81 d1lvla2 106 --EADRVLVAV------------------------------G------------------ 115 ::::::::: : d1gpja2 82 LARSDVVVSATAAPHPVIHVDDVREALRKRDRRSPILIIDIANPRDVEEGVENIEDVEVR 141 d1lvla2 116 ------------------ 116 d1gpja2 142 TIDDLRVIARENLERRRK 159 HHsearch alignment (Probability: 0.92 E-value:0.00) d1lvla2 21 PQHLVVVGGGYIGLELGIAYRKLGA-QVSVVEARER 55 ::::::::::::::::::::::::: :::::::::: d1gpja2 24 DKTVLVVGAGEMGKTVAKSLVDRGVRAVLVANRTYE 59