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 <-- 1.233 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1psda1) 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 d1psda1 Phosphoglycerate dehydrogenaseNAD(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 <-- 1.233 --> Hit
DALI alignment (Z-score: 3.7 Raw score:334.80) d1lvla2 1 mlplggpvisSTEALA--PKAL--------------------------pQHLVVVGGGYI 32 :::::: :::: ::::::::::: d1psda1 1 -----ntrsvAELVIGelLLLLrgvpeanakahrgvwnklaagsfeargKKLGIIGYGHI 55 d1lvla2 33 GLELGIAYRKLGAQVSVVEARERIlptydseltapvaeslkkLGIALHlgHSVEgyengc 92 :::::::::::::::::::::::: :::::: :::: d1psda1 56 GTQLGILAESLGMYVYFYDIENKL----------------plGNATQV--QHLS------ 91 d1lvla2 93 llandgkggqlrLEADRVLVAVG------------------------------------- 115 ::::::::::: d1psda1 92 ---------dllNMSDVVSLHVPenpstknmmgakeislmkpgsllinasrgtvvdipal 142 d1lvla2 116 ---------------------------------------------- 116 d1psda1 143 cdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphigg 188 FAST alignment (Normalized score: 3.65 Raw score:537.00) d1lvla2 1 MLPLGGPVI-SSTEALAPKALP-------------------------------------Q 22 :::::: : d1psda1 1 ---------NTRSVAE------LVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGK 45 d1lvla2 23 HLVVVGGGYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESL---KKLGIAL 79 ::::::::::::::::::::::::::::::: ::::::: d1psda1 46 KLGIIGYGHIGTQLGILAESLGMYVYFYDIE-------------------NKLPLGNATQ 86 d1lvla2 80 HLGHSVEGYENGCLLANDGKGGQLR-------LEADRVLVAVG----------------- 115 : :::::::::: d1psda1 87 V------------------------QHLSDLLNMSDVVSLHV-PENPSTKNMMGAKEISL 121 d1lvla2 116 ------------------------------------------------------------ 116 d1psda1 122 MKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVL 181 d1lvla2 116 ------- 116 d1psda1 182 LTPHIGG 188 TMalign alignment (TM-score: 0.50 Raw score:57.87) d1lvla2 1 ----MLPLGGPVISSTEALA--PK-------------------------ALP-QHLVVVG 28 ::::::: :: ::: ::::::: d1psda1 1 NTRS---------VAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIG 51 d1lvla2 29 GGYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKLGIALHLGHSVEGY 88 :::::::::::::::::::::::::::: : : ::::::: : : d1psda1 52 YGHIGTQLGILAESLGMYVYFYDIENKL------------P--L--GNATQVQ-H-L--- 90 d1lvla2 89 ENGCLLANDGKGGQLR-LEADRVLVAVG-------------------------------- 115 : :: ::::::::::: d1psda1 91 -----S--------DLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVV 137 d1lvla2 116 --------------------------------------------------- 116 d1psda1 138 DIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGG 188 HHsearch alignment (Probability: 0.91 E-value:0.00) d1lvla2 19 ALPQHLVVVGGGYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESL------ 72 :::::::::::::::::::::::::::::::::::::::::::::: ::::::: d1psda1 42 ARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQV-QHLSDLLNMSDVV 100 d1lvla2 73 ------KKLGIALHLGHSVEGYENGCLLANDGK 99 ::::::::::::::::::::::::::: d1psda1 101 SLHVPENPSTKNMMGAKEISLMKPGSLLINASR 133