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 <-- 1.893 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1fcda2) 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 d1fcda2 Flavocytochrome c sulfide dehydrogenase,​ FCSD,​ flavin-​binding subunitFAD/​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 <-- 1.893 --> Hit
DALI alignment (Z-score: 9.5 Raw score:570.80) d1onfa2 1 fppvkGIEN-----TISSD-------EFFN-IKES---KKIGIVG------sGYIAVELI 38 :::: ::::: :::: :::: ::::::: :::::::: d1fcda2 1 -----GYSEeaaakLPHAWkageqtaILRKqLEDMadgGTVVIAPpaapfrcPPGPYERA 55 d1onfa2 39 NVIKRLG------IDSYIFARGNRILrkfdesVINVLENDMKKNN--------INIVTF- 83 ::::::: ::::::::::::: ::::::::::::: :::::: d1fcda2 56 SQVAYYLkahkpmSKVIILDSSQTFS------KQSQFSKGWERLYgfgtenamIEWHPGp 109 d1onfa2 84 -ADVV-EIKKVsdknLSIHLSDGRIYEhFDHVIYCV- 117 :::: ::::: :::::::::::: :::::::: d1fcda2 110 dSAVVkVDGGE----MMVETAFGDEFK-ADVINLIPp 141 FAST alignment (Normalized score: 7.49 Raw score:962.30) d1onfa2 1 FPPVK-----GIENTI-------SSDEFF-NIKES----KKIGIVGS---------GYIA 34 :::::: :::::: :::: ::::: :::: d1fcda2 1 -----GYSEEAAAKLPHAWKAGEQTAILRKQLED-MADGGTVVI---APPAAPFRCPPGP 51 d1onfa2 35 VELINVIKR------LGIDSYIFARGNRILRKFDE-SVINVLENDMKK--------NNIN 79 ::::::::: ::::::::::::: :::::::::::: :::: d1fcda2 52 YERASQVAYYLKAHKPMSKVIILDSSQT-------FSKQSQFSKGWERLYGFGTENAMIE 104 d1onfa2 80 IVTFAD-------VVEIKKVSDKN--LSIHLSDGRIYEHFDHVIYCV--- 117 :: ::::: ::::::::::: ::::::: d1fcda2 105 WH----PGPDSAVVKVDG------GEMMVETAFGDEF-KADVINL--IPP 141 TMalign alignment (TM-score: 0.68 Raw score:79.70) d1onfa2 1 FPPVKGI--E--NTISS------D-EFFNI-KES---KKIGIVG-------SGY--IAVE 36 ::: : ::::: : ::::: ::: ::::::: ::: :::: d1fcda2 1 ----GYSEEAAAKLPHAWKAGEQTAILRKQLEDMADGGTVVIAPPAAPFRCPPGPYERAS 56 d1onfa2 37 LINVIKRLG---IDSYIFARGNRILRKFDESVINVLEND---MK-K--NNINIVTF--AD 85 ::::::::: ::::::::::: ::: :::::::: : :: : :::::::: :: d1fcda2 57 QVAYYLKAHKPMSKVIILDSSQT--FSK-QSQFSKGW-ERLYGFGTENAMIEWHPGPDSA 112 d1onfa2 86 VV-EIKKVSDKNLSIHLSDGRIYEHFDHVIYCV- 117 :: ::::: :::::::::::: :::::::: d1fcda2 113 VVKVDGGE----MMVETAFGDEFK-ADVINLIPP 141 HHsearch alignment (Probability: 0.96 E-value:0.00) d1onfa2 18 NIKESKKIGIV-GSGYI-----AVEL----INVIKRLGID--SYIFARGN--RILRKFDE 63 ::::::::::: ::::: :::: :::::::::: :::::::: :::::::: d1fcda2 29 DMADGGTVVIAPPAAPFRCPPGPYERASQVAYYLKAHKPMSKVIILDSSQTFSKQSQFSK 88 d1onfa2 64 SVINVLENDMKKNNINIVTFADVVEIKKVSDKNLSIHLSDGRIYEHFDHVIY 115 :::::::::::::::::::::::::::: ::::::::::::::: ::::::: d1fcda2 89 GWERLYGFGTENAMIEWHPGPDSAVVKV-DGGEMMVETAFGDEF-KADVINL 138