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 | d1vg0a1 | Rab escort protein 1 | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 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 <-- 1.910 --> HitDALI alignment (Z-score: 8.1 Raw score:731.90) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkkNLAVVGAGPAGLAFAI 60 :::::::::::::::: d1vg0a1 1 -------------------------------------dnlpsdfDVIVIGTGLPESIIAA 23 d1ps9a3 61 NAAARGHQVTLFDAHSEIGGQFNI------------------------------------ 84 :::::::::::::::::::::::: d1vg0a1 24 ACSRSGQRVLHVDSRSYYGGNWASfsfsgllswlkeyqmwqeqileneeaiplsskdkti 83 d1ps9a3 85 ---------------------------AKQI----------------------------- 88 :::: d1vg0a1 84 qhvevfcyasqritysqiikegrrfniDLVSkllysrgllidlliksnvsryaefknitr 143 d1ps9a3 89 ------------------------------------------------------------ 89 d1vg0a1 144 ilafregtveqvpcsradvfnskqltmvekrmlmkfltfcveyeehpdeyrayegttfse 203 d1ps9a3 89 --------------------------------------------------pgKEEFYETL 98 :::::::: d1vg0a1 204 ylktqkltpnlqyfvlhsiamettsctvdglkatkkflqclgrygntpflfpLYGQGELP 263 d1ps9a3 99 RYYRRMIEVTGVTLKLNHTVTAD-----------------QLQAFDETILASgiPNRA-- 139 ::::::::::::::::::::::: :::::::::::: :::: d1vg0a1 264 QCFCRMCAVFGGIYCLRHSVQCLvvdkesrkckavidqfgQRIISKHFIIED--SYLSen 321 d1ps9a3 140 --------laQPLIdsgKTVHLIGGcdvAMELDARRAIAQGTRLALEI----------- 179 :::: :::::::: :::::::::::::::::::: d1vg0a1 322 tcsrvsrdcyNDLP---SNVYVCSG--pDSGLGNDNAVKQAETLFQQIcpnedfcpapp 375 FAST alignment (Normalized score: 5.22 Raw score:1353.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKK-------NLAVVGAGP 53 ::::::::: d1vg0a1 1 --------------------------------------------DNLPSDFDVIVIGTGL 16 d1ps9a3 54 AGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEE-------------------- 93 ::::::::::::::::::::::::::::: d1vg0a1 17 PESIIAAACSRSGQRVLHVDSRSYYGGNW-----------ASFSFSGLLSWLKEYQMWQE 65 d1ps9a3 94 ------------------------------------------------------------ 94 d1vg0a1 66 QILENEEAIPLSSKDKTIQHVEVFCYASQRITYSQIIKEGRRFNIDLVSKLLYSRGLLID 125 d1ps9a3 94 ------------------------------------------------------------ 94 d1vg0a1 126 LLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVE 185 d1ps9a3 94 ------------------------------------------------------------ 94 d1vg0a1 186 YEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSIAMETTSCTVDGLKATKKFLQCLG 245 d1ps9a3 94 ----------FYETLRYYRRMI---EVTGVTLKLNHTVTAD------------------- 121 :::::::::::: ::::::::::::: d1vg0a1 246 RYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSV---QCLVVDKESRKCKAVIDQF 302 d1ps9a3 122 -QLQAFDETILASGIPNRALAQPLIDSG---------------------KTVHLIGGCDV 159 ::::::::::: :::::: d1vg0a1 303 GQRIISKHFIIE----------------DSYLSENTCSRVSRDCYNDLPSNVYVC----- 341 d1ps9a3 160 AMEL-------DARRAIAQGTRLALEI------------ 179 ::::::::::::::: d1vg0a1 342 ----SGPDSGLGNDNAVKQAETLFQQ-ICPNEDFCPAPP 375 TMalign alignment (TM-score: 0.26 Raw score:47.13) d1ps9a3 1 ------INTCIGCNQACLDQIFVGKVT----------SCLVNP----RACHETKM-PI-- 37 :: ::: :::::: ::::::: :: d1vg0a1 1 DNLPSD-------------FD---VIVIGTGLPESIIAAACSRSGQR-VLHVDSRSYYGG 43 d1ps9a3 38 --LPA----V-------------------------------------------------- 41 ::: : d1vg0a1 44 NWASFSFSGLLSWLKEYQMWQEQILENEEAIPLSSKDKTIQHVEVFCYASQRITYSQIIK 103 d1ps9a3 42 -----QKK--NLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEF 94 ::: ::::::::: : ::: :: d1vg0a1 104 EGRRFNIDLVSKLLYSRGL-L----------------------IDL-LI----------- 128 d1ps9a3 95 YETLRYYRRMIEVTGVTLK----------------LNH---------------------- 116 : : ::: :::: :::: : d1vg0a1 129 K-S-NVS-RYAE---FKNITRILAFREGTVEQVPC--SRADVFNSKQLTMVEKRMLMKFL 180 d1ps9a3 117 ---T---------------------------------VT-ADQLQ---------AFDETI 130 : : ::::: d1vg0a1 181 TFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYF-VLHSIAMETTSCTVDG------ 233 d1ps9a3 131 LASGIPNRAL-------------------------------------------------- 140 :::: d1vg0a1 234 ------LKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLV 287 d1ps9a3 141 ---------------------------------------------------------AQP 143 d1vg0a1 288 VDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVSRDCYNDLPSNVYVCSGP--- 344 d1ps9a3 144 LIDSGKTVH-LIGGCDVAMELDARRA--------------IAQGTRLALEI 179 ::: ::::::: :::::: d1vg0a1 345 ------DSGLGNDNAVK---QAETLFQQICPNEDFCPAPP----------- 375 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 41 VQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNI 84 :::::::::::::::::::::::::::::::::::::::::::: d1vg0a1 4 PSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWAS 47