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 | d1jx7a_ | Hypothetical protein YchN | YchN-like | YchN-like | α/β |
| Hit | d1ve9a1 | D-aminoacid oxidase, N-terminal domain | Nucleotide-binding domain | Nucleotide-binding domain | α/β |
Query <-- 1.887 --> IntermediateDALI alignment (Z-score: 13.0 Raw score:806.90) query 1 gmeNKKMNLLLFSGDY--DKALASLIIANAAREME--IEVTIFCAFWGLLLLRDPekasq 56 ::::::::::::: ::::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYgsESLFNSLRLAIALREQEsnLDLRLFLMSDAVTAGLRG----- 52 query 57 edkslyeqafssltpreaeelplskmnlggigkkmlLEMMkeekaPKLSDLLSGARKKEV 116 :::: ::::::::::::::: d1jx7a_ 53 ----------------------------------qkPGEG-----YNIQQMLEILTAQNV 73 query 117 KFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 74 PVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 FAST alignment (Normalized score: 12.96 Raw score:1774.00) query 1 GMENKKMNLLLFSGD---YDKALASLIIANAARE--MEIEVTIFCAFWGLLLLRDPEKAS 55 ::::::::::: :::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGA-PYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGL------ 50 query 56 QEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEE------KAPKLSDLLS 109 :::::::::: d1jx7a_ 51 --------------------------------------------RGQKPGEGYNIQQMLE 66 query 110 GARKKEVKFYAXQLSVEIMGFKKE-ELFPEVQIMDVKEYLKNALESDLQLFI-- 160 :::::::::::::::::::: ::: ::::::::::::::::::::::::: d1jx7a_ 67 ILTAQNVPVKLCKTCTDGRG-ISTLPLIDGVEIGTLVELAQWTLSADKVL--TF 117 TMalign alignment (TM-score: 0.61 Raw score:97.67) query 1 GMENKKMNLLLFSGDY--DKALASLIIANAARE-M-EIEVTIFCAFWGLLLLRDPEKASQ 56 ::::::::::::: ::::::::::::::: : ::::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRG----- 52 query 57 EDKSLYEQAFSSLTPREAEE-LPLSKMNLGGIGKKMLLEMMKEEKAPKLS-DLLSGARKK 114 : :: : : ::: ::::::::: d1jx7a_ 53 ----------------Q-KPG-------------E--G---------YNIQQMLEILTAQ 71 query 115 EVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 72 NVPVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 HHsearch alignment (Probability: 0.99 E-value:0.00) query 5 KKMNLLLFSG--DYDKALASLIIANAAREMEI--EVTIFCAFWGLLLLRDPEKASQEDKS 60 :::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1jx7a_ 2 QKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPG----- 56 query 61 LYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYA 120 ::::::::::::::::::::: d1jx7a_ 57 ---------------------------------------EGYNIQQMLEILTAQNVPVKL 77 query 121 XQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQL 158 :::::::::::::::::::::::::::::::::::::: d1jx7a_ 78 CKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVL 115
Intermediate <-- 1.696 --> HitDALI alignment (Z-score: 5.2 Raw score:421.90) d1jx7a_ 1 mQKIVIVAngapygsesLFNSLRLAIALREQES----NLDLRLFLMsdaVTAG------- 49 ::::::: :::::::::::::::: ::::::::: :::: d1ve9a1 1 -MRVVVIG--------aGVIGLSTALCIHERYHsvlqPLDVKVYAD---RFTPftttdva 48 d1jx7a_ 50 -----------------------------------lrGQKP------------------- 55 :::: d1ve9a1 49 aglwqpytsepsnpqeanwnqqtfnyllshigspnaaNMGLtpvsgynlfreavpdpywk 108 d1jx7a_ 56 -----------------------------GEGY--NIQQMLEILTAQNVPVKLCktctdg 84 :::: ::::::::::::::::::: d1ve9a1 109 dmvlgfrkltpreldmfpdyrygwfntslILEGrkYLQWLTERLTERGVKFFLR------ 162 d1jx7a_ 85 rgistlplidgveigTLVELAQWTL-SADKVLTF-------------------------- 117 :::::::::: :::::::: d1ve9a1 163 ---------------KVESFEEVARgGADVIINCtgvwagvlqpdplqvrlereqlrfgs 207 d1jx7a_ 118 ---------------------------------------- 118 d1ve9a1 208 sntevihnyghggygltihwgcalevaklfgkvleernll 247 FAST alignment (Normalized score: 3.93 Raw score:667.50) d1jx7a_ 1 MQKIVIVANGAPYGSES---LFNSLRLAIALREQE-----SNLDLRLFLMSDAVTAGL-- 50 ::::: :::::::::::::: ::::::::: d1ve9a1 1 -MRVVV-----------IGAGVIGLSTALCIHER-YHSVLQPLDVKVYA---------DR 38 d1jx7a_ 51 -------RGQKPGEGY-------------------------------------------- 59 ::::: d1ve9a1 39 FTPFTTTDVAAG----LWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSG 94 d1jx7a_ 60 -------------------------------------------------NIQQMLEILTA 70 ::::::::::: d1ve9a1 95 YNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTE 154 d1jx7a_ 71 QNVPVKLCKTCTDGRGISTLPLIDGVEIG-TLVELAQWTLSADKVLTF------------ 117 :::::: :::: ::::::: :::::::: d1ve9a1 155 RGVKFF-------------------LRKVESFEEVAR--GGADVIIN-CTGVWAGVLQPD 192 d1jx7a_ 118 ------------------------------------------------------- 118 d1ve9a1 193 PLQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 247 TMalign alignment (TM-score: 0.33 Raw score:38.69) d1jx7a_ 1 ---------MQKIV---I------------------------------V------ANGAP 12 : : : ::::: d1ve9a1 1 MRVVVIGAG----VIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYT 56 d1jx7a_ 13 --Y--G--SESLFNSLRLAIALREQESNLD-LRL-----FLMSDAVTAGLR-----GQKP 55 : : :::::::::::::::: ::::: ::: ::: :::: d1ve9a1 57 SEPSNPQEANWNQQTFNYLLSHIG-SPNAANMGLTPVSG---------YNLFREAVPDPY 106 d1jx7a_ 56 GEGYNIQQM--------------------LEILTAQNVPVKLCKTCTDGRGISTLPLIDG 95 ::::::: :::: ::: d1ve9a1 107 --WKDMVLGFRKLTPRELDMFPDYRYGWFNTSL-----ILE------------------- 140 d1jx7a_ 96 VEIGTLVELAQWTLSADKV----------------------------------------- 114 : :::::::: d1ve9a1 141 --------G--RKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQ 190 d1jx7a_ 115 --------------------------------L--TF-------------------- 117 : :: d1ve9a1 191 PDPLQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 247 HHsearch alignment (Probability: 0.01 E-value:0.25) d1jx7a_ 21 SLRLAIALREQES 33 ::::::::::::: d1ve9a1 12 GLSTALCIHERYH 24