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 <-- 1.673 --> Intermediate <-- 1.799 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1h7wa4) through the intermediate protein (d1onfa2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1onfa2 Glutathione reductaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1h7wa4 Dihydropyrimidine dehydrogenase,​ domain 2Nucleotide-​binding domainNucleotide-​binding domainα/β

Supporting Alignments

Query <-- 1.673 --> Intermediate
DALI alignment (Z-score: 4.3 Raw score:336.20) query 1 ------------------GMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAf 42 ::::::::::: ::::::::::::::::::::::: d1onfa2 1 fppvkgientissdeffnIKESKKIGIVG------sGYIAVELINVIKRLGIDSYIFAR- 53 query 43 wgLLLLrdpekasqedkslyeqafssltprEAEELplskmnlggigkkmllemmkeekap 102 :::: ::::: d1onfa2 54 --GNRI-----------------------lRKFDE------------------------s 64 query 103 KLSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKEYLknaLESDLQLF- 159 ::::::::::::::::: :::: ::::::: :::::::: d1onfa2 65 VINVLENDMKKNNINIVtfADVV-----eikkvsdknlsihLSDGRIY---EHFDHVIYc 116 query 160 i 160 d1onfa2 117 v 117 FAST alignment (Normalized score: 4.62 Raw score:632.20) query 1 -----------------GMEN-KKMNLLLFSGDYDK---ALASLIIANAAREMEIEVTIF 39 :::: ::::: ::::::::::::::::::::: d1onfa2 1 FPPVKGIENTISSDEFFNIKESKKIGI---------VGSGYIAVELINVIKRLGIDSYIF 51 query 40 CAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEE 99 :: d1onfa2 52 AR---------------------------------------------------------- 53 query 100 KAP-----------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYL 148 ::::::::::::::::: ::::: d1onfa2 54 ---GNRILRKFDESVINVLENDMKKNNINIV--------------------TFADV---- 86 query 149 KN--------------------ALESDLQLFI--- 160 :::::::: d1onfa2 87 --VEIKKVSDKNLSIHLSDGRIYEHFDHVI--YCV 117 TMalign alignment (TM-score: 0.39 Raw score:61.66) query 1 -------------------GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCA 41 :: :::::::: : ::::::::::::::::::::::: d1onfa2 1 FPPVKGIENTISSDEFFNIKE-SKKIGIVG-S-----GYIAVELINVIKRLGIDSYIFAR 53 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEEL-PLSKMNLGGIGKKMLLEMMKEEK 100 ::::: : :::: d1onfa2 54 ---GNRIL---------------------R--KFDES----------------------- 64 query 101 APKLS-DLLSGARKKEVKFYAXQLS------------VEIMGFKKEELFPEVQIMDV--K 145 :: ::::::::::::::::::: ::: : d1onfa2 65 ---VINVLENDMKKNNINIVTFADVVEIKKVSDKNLS-----------------IHLSDG 104 query 146 EYLKNALESDLQLFI- 160 :: :: :::::::: d1onfa2 105 RI-YE--HFDHVIYCV 117 HHsearch alignment (Probability: 0.09 E-value:0.01) query 20 LASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPL 79 :::::::::::::::::::::::::::: d1onfa2 32 YIAVELINVIKRLGIDSYIFARGNRILR-------------------------------- 59 query 80 SKMNLGGIGKKMLLEMMKEEKA 101 ::::::::::::::::::: d1onfa2 60 ---KFDESVINVLENDMKKNNI 78
Intermediate <-- 1.799 --> Hit
DALI alignment (Z-score: 6.0 Raw score:459.80) d1onfa2 1 fppvkgientissdeffniKESKKIGIVGSGYIAVELINVIKRLGI-DSYIFARGNRILR 59 ::::::::::::::::::::::::::: ::::::::::::: d1h7wa4 1 ------------------eAYSAKIALLGAGPASISCASFLARLGYsDITIFEKQEYVGG 42 d1onfa2 60 KF---------DESVINVLENDMKKNNINIVTFADVV----EIKKvsdknlsihlsdgri 106 :: :::::::::::::::::::::::::: :::: d1h7wa4 43 LStseipqfrlPYDVVNFEIELMKDLGVKIICGKSLSeneiTLNT-------------lk 89 d1onfa2 107 yEHFDHVIYCV------------------------------------------------- 117 :::::::::: d1h7wa4 90 eEGYKAAFIGIglpevlrdpkvkealspikfnrwdlpevdpetmqtsepwvfaggdivgm 149 d1onfa2 118 ----------------------------------------------- 118 d1h7wa4 150 anttvesvndgkqaswyihkyiqaqygasvsakpelplfytpvdlvd 196 FAST alignment (Normalized score: 6.28 Raw score:951.10) d1onfa2 1 FPPVKGIENTISSDEFFNIKE---SKKIGIVGSGYIAVELINVIKRLG-IDSYIFARGNR 56 :::::::::::::::::::::::: ::::::::::: d1h7wa4 1 ---------------------EAYSAKIALLGAGPASISCASFLARLGYSDITIFEKQEY 39 d1onfa2 57 ILRK---------FDESVINVLENDMKKNNINIVTFADVVEIKKVSDKNLSIHLSDGRIY 107 :::: ::::::::::::::::::::::::: d1h7wa4 40 VGGLSTSEIPQFRLPYDVVNFEIELMKDLGVKIICGKS---------------------- 77 d1onfa2 108 -------------EHFDHVIYCV------------------------------------- 117 :::::::: d1h7wa4 78 LSENEITLNTLKEEGYKAAFI--GIGLPEVLRDPKVKEALSPIKFNRWDLPEVDPETMQT 135 d1onfa2 118 ------------------------------------------------------------ 118 d1h7wa4 136 SEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKYIQAQYGASVSAKPELPLFYTPVDLV 195 d1onfa2 118 - 118 d1h7wa4 196 D 196 TMalign alignment (TM-score: 0.58 Raw score:68.13) d1onfa2 1 -FPPVKGIENTISSDEFFNIKES-KKIGIVGSGYIAVELINVIKRLGI-DSYIFARGNRI 57 :: :::::::::::::::::::::::: ::::::::::: d1h7wa4 1 E--------------------AYSAKIALLGAGPASISCASFLARLGYSDITIFEKQEYV 40 d1onfa2 58 LRKF---------DESVINVLENDMKKNNINIVTFADV---VEI--K-KVSDKNLSIHLS 102 :::: ::::::::::::::::::::::::: ::: : :: : d1h7wa4 41 GGLSTSEIPQFRLPYDVVNFEIELMKDLGVKIICGKSLSENEITLNTLKE-----E---- 91 d1onfa2 103 DGRIYEHFDHVIYCV--------------------------------------------- 117 ::::::::: d1h7wa4 92 ------GYKAAFIGIGLPEVLRDPKVKEALSPIKFNRWDLPEVDPETMQTSEPWVFAGGD 145 d1onfa2 118 --------------------------------------------------- 118 d1h7wa4 146 IVGMANTTVESVNDGKQASWYIHKYIQAQYGASVSAKPELPLFYTPVDLVD 196 HHsearch alignment (Probability: 0.99 E-value:0.00) d1onfa2 21 ESKKIGIVGSGYIAVELINVIKRLGI-DSYIFARGNRILRKFDESVINVLENDMKKNNIN 79 :::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::: d1h7wa4 3 YSAKIALLGAGPASISCASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEI 62 d1onfa2 80 IVTFADVVEIKKVSDK-NLSIHLSDGRIYEHFDHVIYC 116 :::::::::::::::: :::::::::::: :::::::: d1h7wa4 63 ELMKDLGVKIICGKSLSENEITLNTLKEE-GYKAAFIG 99