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 <-- 2.245 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1pj5a2) 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 d1pj5a2 N,​N-​dimethylglycine oxidaseFAD/​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 <-- 2.245 --> Hit
DALI alignment (Z-score: 6.9 Raw score:560.80) d1onfa2 1 fppvkgientissdeffnikeSKKIGIVGSGYIAVELINVIKRLGI-DSYIFARGNR--I 57 ::::::::::::::::::::::::: :::::::::: : d1pj5a2 1 ---------------------TPRIVIIGAGIVGTNLADELVTRGWnNITVLDQGPLnmP 39 d1onfa2 58 LRKF-------------------------------------------------------- 61 :::: d1pj5a2 40 GGSTshapglvfqtnpsktmasfakytvekllsltedgvscfnqvgglevattetrladl 99 d1onfa2 62 -----------------------------------------------DESVINVLENDMK 74 ::::::::::::: d1pj5a2 100 krklgyaaawgiegrllspaecqelyplldgenilgglhvpsdglasAARAVQLLIKRTE 159 d1onfa2 75 KNNINIVTFADVVEIKKVSDKNLSIHLSdGRIYEhFDHVIYCV----------------- 117 :::::::::::::::::::::::::::: ::::: :::::::: d1pj5a2 160 SAGVTYRGSTTVTGIEQSGGRVTGVQTA-DGVIP-ADIVVSCAgfwgakigamigmavpp 217 d1onfa2 118 ------------------------------------------------------------ 118 d1pj5a2 218 dggpllgeskeldgfyvaeavwvthsagvakamaellttgrsetdlgecditrfedvqlt 277 d1onfa2 118 ---------------------------- 118 d1pj5a2 278 peyvsetsqqnfveiydvlhplqprlsp 305 FAST alignment (Normalized score: 6.17 Raw score:1166.00) d1onfa2 1 FPPVKGIENTISSDEFFNIKESKKIGIVGSGYIAVELINVIKRLG-IDSYIFARGNRILR 59 :::::::::::::::::::::::: ::::::::: d1pj5a2 1 ---------------------TPRIVIIGAGIVGTNLADELVTRGWNNITVLDQG----- 34 d1onfa2 60 KF---------------------------------------------------------- 61 d1pj5a2 35 --PLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATT 92 d1onfa2 62 ------------------------------------------------------DESVIN 67 :::::: d1pj5a2 93 ETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQ 152 d1onfa2 68 VLENDMKKNNINIVTFADVVEIKKVSDK-NLSIHLSDGRIYEHFDHVIYCV--------- 117 ::::::::::::::::::::::::::: :::::::: ::: ::::::: d1pj5a2 153 LLIKRTESAGVTYRGSTTVTGIEQSGG-RVTGVQTAD-GVI-PADIVVS--CAGFWGAKI 207 d1onfa2 118 ------------------------------------------------------------ 118 d1pj5a2 208 GAMIGMAVPPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECD 267 d1onfa2 118 -------------------------------------- 118 d1pj5a2 268 ITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSP 305 TMalign alignment (TM-score: 0.64 Raw score:75.46) d1onfa2 1 FPPVKGIENTISSDEFFNIKESKKIGIVGSGYIAVELINVIKRLGI-DSYIFARGNRILR 59 ::::::::::::::::::::::::: ::::::::::::: d1pj5a2 1 ---------------------TPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMP 39 d1onfa2 60 ----K------------------------------------------------------- 60 : d1pj5a2 40 GGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADL 99 d1onfa2 61 ------------------------------------------------FDESVINVLEND 72 ::: :: ::::: d1pj5a2 100 KRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARA-VQ-LLIKR 157 d1onfa2 73 MKKNNINIVTFADVVEIKKVSDKNLSIHLSDGRIYEHFDHVIYCV--------------- 117 :::::::::::::::::::::::::::::: ::::: :::::::: d1pj5a2 158 TESAGVTYRGSTTVTGIEQSGGRVTGVQTA-DGVIP-ADIVVSCAGFWGAKIGAMIGMAV 215 d1onfa2 118 ------------------------------------------------------------ 118 d1pj5a2 216 PPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQ 275 d1onfa2 118 ------------------------------ 118 d1pj5a2 276 LTPEYVSETSQQNFVEIYDVLHPLQPRLSP 305 HHsearch alignment (Probability: 0.98 E-value:0.00) d1onfa2 23 KKIGIVGSGYIAVELINVIKRLGI-DSYIFARGNRILR------------K--FDES--- 64 :::::::::::::::::::::::: ::::::::::::: : :::: d1pj5a2 2 PRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMAS 61 d1onfa2 65 ------------------------------------------------------------ 65 d1pj5a2 62 FAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAEC 121 d1onfa2 65 ----------------------------VINVLENDMKKNNINIVTFADVVEIKKVSDKN 96 :::::::::::::::::::::::::::::::: d1pj5a2 122 QELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRV 181 d1onfa2 97 LSIHLSDGRIYEHFDHVIYC 116 :::::::::: :::::::: d1pj5a2 182 TGVQTADGVI--PADIVVSC 199