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 <-- 2.142 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d3lada1) 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 d3lada1 Dihydrolipoamide dehydrogenaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​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 <-- 2.142 --> Hit
DALI alignment (Z-score: 6.8 Raw score:548.60) d1onfa2 1 fppvkgientissdeffnikeskKIGIVGSGYIAVELINVIKRLGIDSYIFARG------ 54 ::::::::::::::::::::::::::::::: d3lada1 1 -------------------sqkfDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYkgkegk 41 d1onfa2 55 NRILRKF-------------------------------------------------DESV 65 ::::::: :::: d3lada1 42 TALGGTClnvgcipskalldssykfheahesfklhgistgevaidvptmiarkdqiVRNL 101 d1onfa2 66 INVLENDMKKNNINIVTfADVVeIKKVsdknLSIHLS----DGRIYEhFDHVIYCV---- 117 ::::::::::::::::: :::: :::: :::::: :::::: :::::::: d3lada1 102 TGGVASLIKANGVTLFE-GHGK-LLAG----KKVEVTaadgSSQVLD-TENVILASgskp 154 d1onfa2 118 ------------------------------------------------------------ 118 d3lada1 155 veiprrpvttdllaadsgvtldergfiyvddycatsvpgvyaigdvvrgamlahkaseeg 214 d1onfa2 118 --------------- 118 d3lada1 215 vvvaeriaghkaqmn 229 FAST alignment (Normalized score: 6.24 Raw score:1021.00) d1onfa2 1 FPPVKGIENTISSDEFFNIKESK----KIGIVGSGYIAVELINVIKRLGIDSYIFARG-- 54 :::::::::::::::::::::::::::::: d3lada1 1 -----------------------SQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEK-YK 36 d1onfa2 55 -----NRILRKF------------------------------------------------ 61 :::::: d3lada1 37 GKEGKTALGGT-CLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKD 95 d1onfa2 62 --DESVINVLENDMKKNNINIVTFADVV-EIKKVSDKNLSIHLSDGRIY-EHFDHVIYCV 117 ::::::::::::::::::::: :::::::::::::::::::: :::::::: d3lada1 96 QIVRNLTGGVASLIKANGVTLFE-----GHGKLLAGKKVEVTAADGSSQVLDTENVIL-- 148 d1onfa2 118 ------------------------------------------------------------ 118 d3lada1 149 ASGSKPVEIPRRPVTTDLLAADSGVTLDERGFIYVDDYCATSVPGVYAIGDVVRGAMLAH 208 d1onfa2 118 --------------------- 118 d3lada1 209 KASEEGVVVAERIAGHKAQMN 229 TMalign alignment (TM-score: 0.65 Raw score:75.86) d1onfa2 1 ---FPPVKGIENTISSDEFFNIKESKKIGIVGSGYIAVELINVIKRLGIDSYIFARG--- 54 :::::::::::::::::::::::::::::::: d3lada1 1 SQK----------------------FDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGK 38 d1onfa2 55 ---NRILR-KF------------------------------------------------D 62 ::::: :: : d3lada1 39 EGKTALGGTCLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIV 98 d1onfa2 63 ESVINVLENDMKKNNINIVTFADVVEIKKVSDKNLSIHLS---DGRIYEHFDHVIYCV-- 117 :::::::::::::::::::: :::::::: :::::: ::::::::::::::: d3lada1 99 RNLTGGVASLIKANGVTLFE-GHGKLLAG-----KKVEVTAADGSSQVLDTENVILASGS 152 d1onfa2 118 ------------------------------------------------------------ 118 d3lada1 153 KPVEIPRRPVTTDLLAADSGVTLDERGFIYVDDYCATSVPGVYAIGDVVRGAMLAHKASE 212 d1onfa2 118 ----------------- 118 d3lada1 213 EGVVVAERIAGHKAQMN 229 HHsearch alignment (Probability: 0.97 E-value:0.00) d1onfa2 23 KKIGIVGSGYIAVELINVIKRLGIDSYIFARGN 55 ::::::::::::::::::::::::::::::::: d3lada1 4 FDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYK 36