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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1ps9a3 | 2,4-dienoyl-CoA reductase, middle domain | Nucleotide-binding domain | Nucleotide-binding domain | α/β |
| Hit | d5nula_ | Flavodoxin | Flavoproteins | Flavodoxin-like | α/β |
Query <-- 1.613 --> IntermediateDALI 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 <-- 1.428 --> HitDALI alignment (Z-score: 4.6 Raw score:401.80) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkknLAVVG------aGPA 54 ::::: ::: d5nula_ 1 ---------------------------------------------MKIVYwsgtgntEKM 15 d1ps9a3 55 GLAFAINAAARGHQVTLFDAhseiggqfniakqipgkeefyetlryyrrmievtgvtlkl 114 :::::::::::::::::::: d5nula_ 16 AELIAKGIIESGKDVNTINV---------------------------------------- 35 d1ps9a3 115 nHTVTADQLQAFDETILaSGIP----------nraLAQPLIDSG--KTVHLIGGcdVAME 162 :::::::::::::::: :::: ::::::::: :::::::: :::: d5nula_ 36 -SDVNIDELLNEDILIL-GCSAmtdevleesefepFIEEISTKIsgKKVALFGS--YGWG 91 d1ps9a3 163 --------------------------LDAR-raIAQGTRLALEI--- 179 :::: ::::::::::: d5nula_ 92 dgkwmrdfeermngygcvvvetplivQNEPdeaEQDCIEFGKKIani 138 FAST alignment (Normalized score: 2.96 Raw score:465.30) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGA--------- 51 d5nula_ 1 ---------------------------------------------------MKIVYWSGT 9 d1ps9a3 52 ---GPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVT 108 ::::::::::::::::::::: d5nula_ 10 GNTEKMAELIAKGIIESGKDVNTI------------------------------------ 33 d1ps9a3 109 GVTLKLNH---TVTADQ-LQAFDETILASGIPN--------------------------- 137 ::::: ::::::::::: d5nula_ 34 --------NVSDVNID-ELLNEDILILGC----SAMTDEVLEESEFEPFIEEISTKISGK 80 d1ps9a3 138 ----------------RALAQPLIDSGKTVHLIGGCDVAMEL-------------DARRA 168 :::::::::::::: ::::: d5nula_ 81 KVALFGSYGWGDGKWMRDFEERMNGYGCVV------------VETPLIVQNEPDEAEQDC 128 d1ps9a3 169 IAQGTRLALEI-- 179 :::::::: d5nula_ 129 IEFGKKIA---NI 138 TMalign alignment (TM-score: 0.36 Raw score:64.37) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAI 60 d5nula_ 1 ------------------------------------------------------------ 1 d1ps9a3 61 NAAARGHQVTLFDAHSEIGGQFN-IAKQIPGKEEFYETL-RYY--RRM---IEVTGVTLK 113 : : ::::::::::::: :: :: : ::::::: d5nula_ 1 --M-----K-IVYWSGTGNTEKMA-------------ELI-AKGI--IESG--KDVNTIN 34 d1ps9a3 114 LN----------------------------HTV-TADQLQ-AF--DETILASGI----P- 136 :: ::: :::::: :: ::::::::: : d5nula_ 35 VSDVNIDELLNEDILILGCSAMTDEVLEESEFEPFIEEISTKISGKKVALFGSYGWGDGK 94 d1ps9a3 137 NR-ALAQPLIDSGKTVH-LIGGCDVA----MELDARRAIAQGTRLALEI 179 :: :::::::::::::: ::::: : :::::::::::::: :: d5nula_ 95 WMRDFEERMNGYGCVVVETPLIV--QNEPD--EAEQDCIEFGKKIA-NI 138 HHsearch alignment (Probability: 0.51 E-value:0.00) d1ps9a3 94 FYETLRYYRRMIEVTGVTLKLNH--TVTADQLQAFDETILASGIP 136 ::::::::::::::::::::::: :::::::::::::::::::: d5nula_ 12 TEKMAELIAKGIIESGKDVNTINVSDVNIDELLNEDILILGCSAM 56