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 <-- 1.613 --> Intermediate <-- 1.887 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1h6va2) through the intermediate protein (d1ps9a3) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ps9a3 2,​4-​dienoyl-​CoA reductase,​ middle domainNucleotide-​binding domainNucleotide-​binding domainα/β
Hit d1h6va2 Mammalian thioredoxin reductaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β

Supporting Alignments

Query <-- 1.613 --> Intermediate
DALI alignment (Z-score: 4.1 Raw score:393.70) query 1 ---------------------------------------GMENKKMNLLLfsgdydkALA 21 ::::::::::: ::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQKKNLAVVG------aGPA 54 query 22 SLIIANAAREMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreaeELPLsk 81 :::::::::::::::::::: :::: :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA---HSEI------------------------ggqFNIA-- 85 query 82 mnlgGIGKKmllemmkeekaPKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqI 141 ::::: :::::::::::::::::::: : d1ps9a3 86 --kqIPGKE--------efyETLRYYRRMIEVTGVTLKLN------------------hT 117 query 142 MDVKEYlknaLESDLQLFI----------------------------------------- 160 :::::: ::::::::: d1ps9a3 118 VTADQL----QAFDETILAsgipnralaqplidsgktvhliggcdvameldarraiaqgt 173 query 161 ------ 161 d1ps9a3 174 rlalei 179 FAST alignment (Normalized score: 3.87 Raw score:654.60) query 1 GME------------------------------------------NKKMNLLLFSGDYDK 18 :::::: d1ps9a3 1 ---INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV--------- 48 query 19 ---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLT-PREA 74 :::::::::::::::::::::: :::: d1ps9a3 49 VGAGPAGLAFAINAAARGHQVTLFD------------------------------AHSEI 78 query 75 EELPLSKMNLGGIGKKMLLEMMKEEKAP------------------KLSDLLSGARKKEV 116 :::::::::::::: d1ps9a3 79 ----------------------------GGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 query 117 KFYAXQLSVEIMGFKKEELFPE-VQIMDVKEYLKNA-LESDLQLFI-------------- 160 ::: :::::::: ::::::: d1ps9a3 111 TLK-------------------LNHTVTADQ-----LQAFDETI--LASGIPNRALAQPL 144 query 161 ----------------------------------- 161 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 TMalign alignment (TM-score: 0.44 Raw score:70.82) query 1 ---------------------------------------GMENKKMNLLLFSGDYDKALA 21 ::::::::::: :::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREA-EELPLS 80 :::::::::::::::::::: ::::: : :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA--HSEIG-------------------------GQ-FNIA- 85 query 81 KMNLGGIGKKMLLE-MMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEV 139 : :::::: :: ::::::::::::::::::::: : d1ps9a3 86 --K-QIPGKE--EFY-------ETLRYYRRMIEVTGVTLKLNH-T--------------- 117 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 :::::: :::::::::: d1ps9a3 118 ----VTADQL-QAFDETILASGIPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQG 172 query 161 ------- 161 d1ps9a3 173 TRLALEI 179 HHsearch alignment (Probability: 0.10 E-value:0.01) query 2 MENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 ::::::::::::: :::::::::::::::::::: d1ps9a3 40 AVQKKNLAVVGAG-----PAGLAFAINAAARGHQVTLF 72
Intermediate <-- 1.887 --> Hit
DALI alignment (Z-score: 6.4 Raw score:473.00) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQK-KNLAVVGAGPAGLAFA 59 :::: :::::::::::::::: d1h6va2 1 ------------------------pgdkeycissddlfsLPYCpGKTLVVGASYVALECA 36 d1ps9a3 60 INAAARGHQVTLFDAHsEIGGQFniakqipgkeeFYETLRYYRRMIEVTGVTLKLNHTVT 119 :::::::::::::::: :::::: :::::::::::::::::::::::::: d1h6va2 37 GFLAGIGLDVTVMVRS-ILLRGF-----------DQDMANKIGEHMEEHGIKFIRQFVPT 84 d1ps9a3 120 AD-----------------------QLQAFDETILASGipnralaqplidsgktvhligg 156 :: ::::::::::::: d1h6va2 85 KIeqieagtpgrlkvtakstnseetIEDEFNTVLLAVG---------------------- 122 d1ps9a3 157 cdvameldarraiaqgtrlalei 179 d1h6va2 123 ----------------------- 123 FAST alignment (Normalized score: 6.20 Raw score:915.80) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP---------------AVQK-K 44 :::: : d1h6va2 1 ---------------------------------------PGDKEYCISSDDLFSLPYCPG 21 d1ps9a3 45 NLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEE-FYETLRYYRR 103 ::::::::::::::::::::::::::::: ::::::: :::::::::: d1h6va2 22 KTLVVGASYVALECAGFLAGIGLDVTVMV-RSILLRG------------FDQDMANKIGE 68 d1ps9a3 104 MIEVTGVTLKLNHTVTAD--------------------------QLQAFDETILASGIPN 137 ::::::::::::::: :::::::::::: d1h6va2 69 HMEEHGIKFIRQFVP---TKIEQIEAGTPGRLKVTAKSTNSEETIEDEFNTVLLAV---- 121 d1ps9a3 138 RALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI- 179 d1h6va2 122 ------------------------------------------G 122 TMalign alignment (TM-score: 0.40 Raw score:71.49) d1ps9a3 1 -----------------INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQK 43 ::: d1h6va2 1 PGDKEYCISSDDLFSLP----------------------------------------YCP 20 d1ps9a3 44 KNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRR 103 :::::::::::::::::::::::::::::::: ::: :: : :::::::::: d1h6va2 21 GKTLVVGASYVALECAGFLAGIGLDVTVMVRS-ILL-RG---F-------DQDMANKIGE 68 d1ps9a3 104 MIEVTGVTLKLNHTVTAD-------------Q----------LQAFDETILASGIPNRAL 140 :::::::::::::::::: : ::::::::::: d1h6va2 69 HMEEHGIKFIRQFVPTKIEQIEAGTPGRLKVTAKSTNSEETIEDEFNTVLLAV------- 121 d1ps9a3 141 AQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 : d1h6va2 122 ---------------G----------------------- 122 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 37 ILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYE 96 ::::::::::::::::::::::::::::::::::::::::::: ::::: d1h6va2 14 FSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLR------------GFDQD 61 d1ps9a3 97 TLRYYRRMIEVTGVTLKLNHTVTAD 121 ::::::::::::::::::::::::: d1h6va2 62 MANKIGEHMEEHGIKFIRQFVPTKI 86