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 | d1gcaa_ | Galactose/glucose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | 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 <-- 1.794 --> HitDALI alignment (Z-score: 5.7 Raw score:700.50) d1qyca_ 1 gsRSRILLIG-ATGY-IGRHVAKASLDLG-----HPTFLLVRestassnsekaqllesfk 53 :::::::: :::: ::::::::::::: :::::::: d1gcaa_ 1 -aDTRIGVTIyKYDDnFMSVVRKAIEKDGksapdVQLLMNDS------------------ 41 d1qyca_ 54 asganivhGSIDdhaSLVEAVK-NVDVVISTVGslQIESQVNIIKAIKeVGTVkRFFPSE 112 :::: ::::::: :::::::::: ::::::::::::: :::: :::::: d1gcaa_ 42 ---qndqsKQND---QIDVLLAkGVKALAINLV--DPAAAGTVIEKAR-GQNV-PVVFFN 91 d1qyca_ 113 fgndvdnvhavepaksvfevkakVRRAIEAEGiPYTYVSSN------------------- 153 ::::::::: :::::::: d1gcaa_ 92 --------------------kepSRKALDSYD-KAYYVGTDskesgviqgdliakhwqan 130 d1qyca_ 154 ------------------------------------------------------------ 154 d1gcaa_ 131 qgwdlnkdgkiqyvllkgepghpdaearttyvvkelndkgiqteqlaldtamwdtaqakd 190 d1qyca_ 154 -----------------cfagyflrslaqagltapprDKVVI-------------lgdgn 183 ::::: d1gcaa_ 191 kmdawlsgpnankievvianndamamgavealkahnkSSIPVfgvdalpealalvksgam 250 d1qyca_ 184 arVVFVKEEDIGTFTIKAVDD----PRTL--------nKTLYLRLpaNTLSlnelvalwe 231 ::::::::::::::::::: :::: ::::::: :::: d1gcaa_ 251 agTVLNDANNQAKATFDLAKNlaegKGAAdgtswkienKIVRVPY--VGVD--------- 299 d1qyca_ 232 kkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfeigpagveasqly 291 d1gcaa_ 300 ------------------------------------------------------------ 300 d1qyca_ 292 pdvkyttvDEYLSNfv 307 :::::: d1gcaa_ 300 ----kdnlSEFTQK-- 309 FAST alignment (Normalized score: 3.93 Raw score:1210.00) d1qyca_ 1 G--SRSRILLIGATGYIGRHVAKASLD-------LGHPTFLLVRESTASSNSEKAQLLES 51 :::::::::::::::::::::::: :::::::: d1gcaa_ 1 -ADTRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDS------------------ 41 d1qyca_ 52 FKASGANIVHGSI-DDHASLVEAVK-----NVDVVISTVGSL-QIESQVNIIKAIKEVGT 104 ::::::::::: ::::::::: :::::::::::::::: d1gcaa_ 42 -------------QNDQSKQNDQIDVLLAKGVKALAINL---VDPAAAGTVIEKARGQN- 84 d1qyca_ 105 VKRFFPSEFGNDVDNVHAVEPAKSVFEV-----KAKVRRAIEAEG-IPYTYVSSN----- 153 ::::: ::::::: ::::: d1gcaa_ 85 -VPVVF----------------------FNKEPSRKALDS-----YDKAYY----VGTDS 112 d1qyca_ 154 ------------------------------------------------------------ 154 d1gcaa_ 113 KESGVIQGDLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQ 172 d1qyca_ 154 -------------------------------------CFAGYFLRSLAQAGLTAP----- 171 :::::::: d1gcaa_ 173 TEQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMG----------AVEAL 222 d1qyca_ 172 -PRDKVVILGDGN----------------------ARVVFVKEEDIGTFTIKAVDDPRTL 208 ::::: :::::::::::::::::::: d1gcaa_ 223 KAHNKS-------SIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAK----- 270 d1qyca_ 209 N------------------KTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLK 250 ::::::: d1gcaa_ 271 -NLAEGKGAADGTSWKIENKIVRVPY---------------------------------- 295 d1qyca_ 251 LIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV--- 307 d1gcaa_ 296 ---------------------------------------------------------VGV 298 d1qyca_ 308 ----------- 308 d1gcaa_ 299 DKDNLSEFTQK 309 TMalign alignment (TM-score: 0.37 Raw score:112.62) d1qyca_ 1 G-SRSRILLIGATGY-IGRHVAKASLDLG-----H-PTFLLV---RES---TASSNSEKA 46 : :::::::::::: ::::::::::::: : :::::: ::: : d1gcaa_ 1 AD-TRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQND--------Q 51 d1qyca_ 47 ----------QLLESFKASGANIV-HGS-IDDHASLVEAV--KNVDVVISTVGSLQIESQ 92 :::: ::: ::::::::::: ::::::::: : : d1gcaa_ 52 IDVLLAKGVK----------ALAINLVDPAAAGTVIEKARGQNVPVVFFNK-----E--P 94 d1qyca_ 93 VNIIKAIKEVGTVKRFFPSEFGNDVDNVHA---------------------VEP-A---- 126 : :::::::::: :::::::::::::::: ::: : d1gcaa_ 95 S--RKALDSYDKA-YYVGTDSKESGVIQGDLIAKHWQANQGWDLNKDGKIQYVLLKGEPG 151 d1qyca_ 127 --KSVFEVKA-----------------------------------------------KVR 137 :::::::: d1gcaa_ 152 HPDAEARTTYVVKELNDKGIQTEQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVI--- 208 d1qyca_ 138 RAIEAEGIPYTYVSSNCFAGYFLRSLAQAGLTAPP-RDKVVILGDGNARVVFVKE----- 191 ::::::: : :::::::: :::::: : :::::::: d1gcaa_ 209 ---------------ANNDAMA--M--GAVEALKAH-NKSSIP--V-FGVDALPEALALV 245 d1qyca_ 192 ---------EDIGTFTIKAV-D--------------DPRTLN---KTLYLRLPANTLSLN 224 ::::::::::: : :::::: ::::::: ::: : d1gcaa_ 246 KSGAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVG---VDK-D 301 d1qyca_ 225 ELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAG 284 :: : d1gcaa_ 302 NL--S------------------------------------------------------- 304 d1qyca_ 285 VEASQLYPDVKYTTVDEYLSNFV 307 : :::: d1gcaa_ 305 ---E--------FTQK------- 309 HHsearch alignment (Probability: 0.46 E-value:0.23) d1qyca_ 75 KNVDVVISTVGSLQIESQVNIIKAIKEVGTVKRFF 109 :::::::::::::: ::::::::::::::::::: d1gcaa_ 58 KGVKALAINLVDPA--AAGTVIEKARGQNVPVVFF 90