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 | d1qyca_ | Phenylcoumaran benzylic ether reductase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1ehia1 | D-alanine:D-lactate ligase VanA, N-domain | PreATP-grasp domain | PreATP-grasp domain | α/β |
Query <-- 0.813 --> IntermediateDALI alignment (Z-score: 4.9 Raw score:359.30) query 1 gMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAfwglllLRDPekasqedks 60 :::::::::: ::::::::::::::::::::::: :::: d1qyca_ 1 -GSRSRILLIG-----atGYIGRHVAKASLDLGHPTFLLVR-----eSTAS--------- 40 query 61 lyeqafssltpREAEelplskmnlggigkkmllemmkeekapkLSDLLSGARKKEVKFY- 119 :::: :::::::::::::::: d1qyca_ 41 -----------SNSE----------------------------KAQLLESFKASGANIVh 61 query 120 AXQLsveimgfkkeelfpevqimDVKEYLKNALESDLQLFI------------------- 160 :::: :::::::::::::::::: d1qyca_ 62 GSID-------------------DHASLVEAVKNVDVVISTvgslqiesqvniikaikev 102 query 161 ------------------------------------------------------------ 161 d1qyca_ 103 gtvkrffpsefgndvdnvhavepaksvfevkakvrraieaegipytyvssncfagyflrs 162 query 161 ------------------------------------------------------------ 161 d1qyca_ 163 laqagltapprdkvvilgdgnarvvfvkeedigtftikavddprtlnktlylrlpantls 222 query 161 ------------------------------------------------------------ 161 d1qyca_ 223 lnelvalwekkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfeigp 282 query 161 ------------------------- 161 d1qyca_ 283 agveasqlypdvkyttvdeylsnfv 307 FAST alignment (Normalized score: 3.09 Raw score:685.40) query 1 GMENKKMNLLLFSGDYDK----ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQ 56 :::::::: ::::::::::::::::::::::: d1qyca_ 1 -GSRSRILL---------IGATGYIGRHVAKASLDLGHPTFLLVR--------------- 35 query 57 EDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP--------KLSDLL 108 :::::: d1qyca_ 36 ----------------------------------------------ESTASSNSEKAQLL 49 query 109 SGARKKEVKFYAXQLSVEIMGFKKEELFPEVQI----MDVKEYLKNALESDLQLFI---- 160 ::::::::::: ::::::::::::::::: d1qyca_ 50 ESFKASGANIV----------------------HGSIDDHASLVEAVKNVDVVI--STVG 85 query 161 ------------------------------------------------------------ 161 d1qyca_ 86 SLQIESQVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGI 145 query 161 ------------------------------------------------------------ 161 d1qyca_ 146 PYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEEDIGTFTIKAVDDP 205 query 161 ------------------------------------------------------------ 161 d1qyca_ 206 RTLNKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAI 265 query 161 ------------------------------------------ 161 d1qyca_ 266 SHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV 307 TMalign alignment (TM-score: 0.36 Raw score:58.19) query 1 GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKS 60 :: ::::::::::::::::::::::::: : ::::::: :: d1qyca_ 1 GS--RSRILLIGATGYIGRHVAKASLDLG----H-PTFLLVR--ES-------------- 37 query 61 LYEQAFSSLTPR-EAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFY 119 ::::::: ::: : :: ::::: :::: d1qyca_ 38 -----TASSNSEKAQL-L--------------------------ES-FKASG----ANIV 60 query 120 AXQLSVE-IMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI------------------ 160 ::::: : :::::::::: : ::::: d1qyca_ 61 HGSID-DH---------------ASLVEAVKNV--D-VVISTVGSLQIESQVNIIKAIKE 101 query 161 ------------------------------------------------------------ 161 d1qyca_ 102 VGTVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYFLR 161 query 161 ------------------------------------------------------------ 161 d1qyca_ 162 SLAQAGLTAPPRDKVVILGDGNARVVFVKEEDIGTFTIKAVDDPRTLNKTLYLRLPANTL 221 query 161 ------------------------------------------------------------ 161 d1qyca_ 222 SLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIG 281 query 161 -------------------------- 161 d1qyca_ 282 PAGVEASQLYPDVKYTTVDEYLSNFV 307 HHsearch alignment (Probability: 0.02 E-value:0.33) query 89 KKMLLEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYL 148 ::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::: d1qyca_ 245 EEEVLKLIADTPF-PANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYL 303 query 149 KN 150 :: d1qyca_ 304 SN 305
Intermediate <-- 1.050 --> HitDALI alignment (Z-score: 5.0 Raw score:333.70) d1qyca_ 1 gsRSRILLIG--------aTGYIGRHVAKASLDLG-HPTFLLVRES--tassnsekaQLL 49 :::::::: :::::::::::::::: :::::::::: ::: d1ehia1 1 --KKRVALIFggnssehdvSKRSAQNFYNAIEATGkYEIIVFAIAQngffldtesskKIL 58 d1qyca_ 50 ES-------fkasganivhgsidDHASLveavkNVDVVISTVGslqIESQ--VNIIKAIK 100 :: ::::: :::::::::: :::: :::::::: d1ehia1 59 ALedeqpivdafmktvdasdplaRIHAL-ksagDFDIFFPVVH---GNLGedGTLQGLFK 114 d1qyca_ 101 EVGTvkRFFPsefgndvdnvhavepaksvfevkakvrraieaegipytyvssncfagyfl 160 :::: :::: d1ehia1 115 LLDK--PYVG-------------------------------------------------- 122 d1qyca_ 161 rslaqagltapprdkvvilgdgnarvvfvkeedigtftikavddprtlnktlylrlpant 220 d1ehia1 123 ------------------------------------------------------------ 123 d1qyca_ 221 lslnelvalwekkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfei 280 d1ehia1 123 ------------------------------------------------------------ 123 d1qyca_ 281 gpagveasqlypdvkyttvdeylsnfv 307 d1ehia1 123 -----------------aplrghavsf 132 FAST alignment (Normalized score: 2.27 Raw score:456.60) d1qyca_ 1 GSRSRILLIGAT--------GYIGRHVAKASLD-----LGHPTFLLVRESTASSNS---- 43 :::::: ::::::::::::: :::::::::: d1ehia1 1 --KKRVAL----IFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAI--------AQNG 46 d1qyca_ 44 ---------------EKAQLLESFKASGANIVHGSID--------------DHASLVEAV 74 :::::: ::::: d1ehia1 47 FFLDTESSKKILALEDEQPIV----------------DAFMKTVDASDPLARIHAL---- 86 d1qyca_ 75 K----NVDVVISTVGSLQIESQ----VNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEPA 126 :::::::::::: ::::::::::: d1ehia1 87 -KSAGDFDIFFPVVHGN-----LGEDGTLQGLFKLLD----------------------- 117 d1qyca_ 127 KSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARV 186 d1ehia1 118 ------------------------------------------------------------ 118 d1qyca_ 187 VFVKEEDIGTFTIKAVDDPRTLNKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEE 246 d1ehia1 118 ------------------------------------------------------------ 118 d1qyca_ 247 EVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNF 306 d1ehia1 118 ------------------------------------------------------------ 118 d1qyca_ 307 V--------------- 307 d1ehia1 118 -KPYVGAPLRGHAVSF 132 TMalign alignment (TM-score: 0.24 Raw score:73.54) d1qyca_ 1 GSRSRILLIGA--------TGYIGRHVAKASLDLG-HPTFLLVRES-----------TAS 40 ::::::::: :::::::::::::::: :::::::::: d1ehia1 1 --KKRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNGFFLDTESSK--- 55 d1qyca_ 41 SNSEKAQLLE--------SFKASGANIVH----------GSIDDHASLVEAVKNVDVVIS 82 :::::: : :::::: ::::::::::: d1ehia1 56 ----KILALEDEQPIVDA----------FMKTVDASDPL---ARIHAL-KSAGDFDIFFP 97 d1qyca_ 83 TVGSLQ-IESQVNIIKAIKEVGTVKRFFPSE--FGNDVDNVHAVEPAKSVFEVKAKVR-R 138 :::::: :: :: ::::::::: : :::: : :::::: d1ehia1 98 VVHGNLGED-GT-LQGLFKLLD-K-PYVG-APL-------------------RGHAVSF- 132 d1qyca_ 139 AIEAEGIPYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEEDIGTFT 198 d1ehia1 133 ------------------------------------------------------------ 133 d1qyca_ 199 IKAVDDPRTLNKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFP 258 d1ehia1 133 ------------------------------------------------------------ 133 d1qyca_ 259 ANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV 307 d1ehia1 133 ------------------------------------------------- 133 HHsearch alignment (Probability: 0.31 E-value:0.01) d1qyca_ 3 RSRILLIGA-TG-------YIGRHVAKASLDL-GHPTFLLVRESTA 39 ::::::::: :: ::::::::::::: ::::::::::::: d1ehia1 1 KKRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNG 46