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 <-- 2.154 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ju2a1) 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 d1ju2a1 Hydroxynitrile lyaseFAD/​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 <-- 2.154 --> Hit
DALI alignment (Z-score: 4.6 Raw score:468.00) d1onfa2 1 ----fppvkgientissdeffnikeskKIGIVGSGYIAVELINVIKRlGIDSYIFARGNR 56 :::::::::::::::::::: :::::::::::: d1ju2a1 1 lattsdhdfsylsfaydatdlelegsyDYVIVGGGTSGCPLAATLSE-KYKVLVLERGSL 59 d1onfa2 57 -------------------------------------------ILRKFDE---------- 63 ::::::: d1ju2a1 60 ptaypnvltadgfvynlqqeddgktpverfvsedgidnvrgrvLGGTSIInagvyarant 119 d1onfa2 64 ------------------------------------------------------------ 64 d1ju2a1 120 siysasgvdwdmdlvnqtyewvedtivykpnsqswqsvtktafleagvhpnhgfsldhee 179 d1onfa2 64 --------------SVINvLENDM-kKNNINIVTFADVVEIKKV---sDKNLSIHLS--- 102 :::: ::::: :::::::::::::::::: ::::::::: d1ju2a1 180 gtritgstfdnkgtRHAAdELLNKgnSNNLRVGVHASVEKIIFSnapgLTATGVIYRdsn 239 d1onfa2 103 -DGRIYEH--fDHVIYCV------------------------------------------ 117 ::::::: ::::::: d1ju2a1 240 gTPHQAFVrskGEVIVSAgtigtpqllllsgvgpesylsslnipvvlshpyvgqclvgkv 299 d1onfa2 118 ---------------------------------------------------- 118 d1ju2a1 300 ldgdfrvtginalrvvdgstfpytpashpqgfylmlgryvgikilqersasd 351 FAST alignment (Normalized score: 4.37 Raw score:885.00) d1onfa2 1 FPPVKGIENTISSDEFFNIKESK---------------------------KIGIVGSGYI 33 :::::::::: d1ju2a1 1 -----------------------LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTS 37 d1onfa2 34 AVELINVIKRLGIDSYIFARG--------------------------------------- 54 ::::::::: ::::::::::: d1ju2a1 38 GCPLAATLS-EKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGID 96 d1onfa2 55 ----NRILRKFDE----------------------------------------------- 63 :::::: d1ju2a1 97 NVRGRVLGGT---SIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQS 153 d1onfa2 64 -----------------------------------------SVINVLENDMK--KNNINI 80 ::::::::: :::::: d1ju2a1 154 WQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNK--GNSNNLRV 211 d1onfa2 81 VTFADVVEIKKVSDKN---------LSIHL----SDGRIYEHF-----DHVIYCV----- 117 :::::::::: ::::: :::::: ::::: d1ju2a1 212 GVHASVEKII------FSNAPGLTATGVIYRDSNGTPHQA---FVRSKGEVIV--SAGTI 260 d1onfa2 118 ------------------------------------------------------------ 118 d1ju2a1 261 GTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQCLVGKVLDGDFRVTGINALRVVDGSTF 320 d1onfa2 118 ------------------------------- 118 d1ju2a1 321 PYTPASHPQGFYLMLGRYVGIKILQERSASD 351 TMalign alignment (TM-score: 0.31 Raw score:36.13) d1onfa2 1 --------------------------------FPPVKGIEN---TI-SSDEFF-N----- 18 : :: ::::: : d1ju2a1 1 LATTSDHDFSYLSFAYDATDLELEGSYDYVIV--------GGGTSGC-PLAATLSEKYKV 51 d1onfa2 19 -I-------------------------------------------------KES-K---- 23 : ::: : d1ju2a1 52 LVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINA 111 d1onfa2 24 --K-IG----I----V-GSGYIAVELINVIKRLGID-----------------------S 48 : :: : : ::::::::::::::::::: d1ju2a1 112 GVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPN- 170 d1onfa2 49 YIFARGNRILRKFDESVINVLEN-DMKKNNINI--------------------------- 80 : :: :::: d1ju2a1 171 ----------------------HG--FS-LDHEEGTRITGSTFDNKGTRHAADELLNKGN 205 d1onfa2 81 --------------------------------------------------VTFADVVEI- 89 : d1ju2a1 206 SNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIV--------SA 257 d1onfa2 90 KKVSD----------------------------------------------------KNL 97 ::::: ::: d1ju2a1 258 GTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQCLVGKVLDGDFRVTGINALRVVDG 317 d1onfa2 98 SIHLSDGRIY---EH--FDHVI--Y-CV--------- 117 :::: ::: :: ::::: : :: d1ju2a1 318 STFP---YTPASHPQGFYLMLGRYVGIKILQERSASD 351 HHsearch alignment (Probability: 0.94 E-value:0.00) d1onfa2 18 NIKESKKIGIVGSGYIAVELINVIKRLGIDSYIFARGNRILR 59 :::::::::::::::::::::::::: ::::::::::::::: d1ju2a1 22 ELEGSYDYVIVGGGTSGCPLAATLSE-KYKVLVLERGSLPTA 62