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 <-- 2.350 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1trba1) 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 d1trba1 Thioredoxin reductaseFAD/​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 <-- 2.350 --> Hit
DALI alignment (Z-score: 7.3 Raw score:526.50) d1onfa2 1 fppvkgientissdeffnikeskKIGIVGSGYIAVELINVIKRLGIDSYIFARGNRILRK 60 ::::::::::::::::::::::::::::::::::::: d1trba1 1 -----------------gttkhsKLLILGSGPAGYTAAVYAARANLQPVLITGMEKGGQL 43 d1onfa2 61 F----------------DESVINVLENDMKKNNINIVTfADVVEIKKVSDkNLSIHLSDg 104 : ::::::::::::::::::::: ::::::::::: :::::::: d1trba1 44 TtttevenwpgdpndltGPLLMERMHEHATKFETEIIF-DHINKVDLQNR-PFRLNGDN- 100 d1onfa2 105 RIYEhFDHVIYCV----------------------------------------------- 117 :::: :::::::: d1trba1 101 GEYT-CDALIIATgasaryhspntaifegqlelengyikvqsgihgnatqtsipgvfaag 159 d1onfa2 118 ------------------------------ 118 d1trba1 160 dvmdhiyrqaitsagtgcmaaldaeryldg 189 FAST alignment (Normalized score: 6.87 Raw score:1022.00) d1onfa2 1 FPPVKGIENTISSDEFFNIKESK------KIGIVGSGYIAVELINVIKRLGIDSYIFARG 54 ::::::::::::::::::::::::::::::: d1trba1 1 -----------------------GTTKHSKLLILGSGPAGYTAAVYAARANLQPVLITGM 37 d1onfa2 55 NRILRKF---------------------DESVINVLENDMKKNNINIVTFADVVEIKKVS 93 :: :::::::::::::::::::: ::::::::::: d1trba1 38 EK-----GGQLTTTTEVENWPGDPNDLTGPLLMERMHEHATKFETEII-FDHINKVDLQN 91 d1onfa2 94 DKNLSIHLSDGRIYEHFDHVIYCV------------------------------------ 117 : :::::::: ::: ::::::: d1trba1 92 R-PFRLNGDN-GEY-TCDALII--ATGASARYHSPNTAIFEGQLELENGYIKVQSGIHGN 146 d1onfa2 118 ------------------------------------------- 118 d1trba1 147 ATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG 189 TMalign alignment (TM-score: 0.59 Raw score:68.69) d1onfa2 1 -----FPPVKGIENTISSDEFFNIKESKKIGIVGSGYIAVELINVIKRLGIDSYIFARGN 55 ::::::::::::::::::::::::::::::::: d1trba1 1 GTTKH----------------------SKLLILGSGPAGYTAAVYAARANLQPVLITGME 38 d1onfa2 56 RILRKF----------------DESVINVLENDMKKNNINIVTFADVVEIKKVSDKNLSI 99 :::::: ::::::::::::::::::::: ::::::::::: :::: d1trba1 39 KGGQLTTTTEVENWPGDPNDLTGPLLMERMHEHATKFETEIIF-DHINKVDLQNR-PFRL 96 d1onfa2 100 HLSDGRIYEHFDHVIYCV------------------------------------------ 117 :: :::::: :::::::: d1trba1 97 NG-DNGEYT-CDALIIATGASARYHSPNTAIFEGQLELENGYIKVQSGIHGNATQTSIPG 154 d1onfa2 118 ----------------------------------- 118 d1trba1 155 VFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG 189 HHsearch alignment (Probability: 0.99 E-value:0.00) d1onfa2 20 KESKKIGIVGSGYIAVELINVIKRLGIDSYIFARGNRI----------------LRKFDE 63 :::::::::::::::::::::::::::::::::::::: :::::: d1trba1 3 TKHSKLLILGSGPAGYTAAVYAARANLQPVLITGMEKGGQLTTTTEVENWPGDPNDLTGP 62 d1onfa2 64 SVINVLENDMKKNNINIVTFADVVEIKKVSDKNLSIHLSDGRIYEHFDHVIYCV 117 ::::::::::::::::::::: ::::::::: :::::::::::: :::::::: d1trba1 63 LLMERMHEHATKFETEIIFDH-INKVDLQNR--PFRLNGDNGEYT-CDALIIAT 112