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 | d1dnpa2 | DNA photolyase | Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase, N-terminal 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 <-- 0.643 --> HitDALI alignment (Z-score: 7.1 Raw score:582.10) d1qyca_ 1 gsrSRILLIGATG--yigRHVAKASLDLG-HPTFLLVRE------------sTASS-NSE 44 :::::::::: ::::::::::: ::::::::: :::: ::: d1dnpa2 1 ---TTHLVWFRQDlrlhdNLALAAACRNSsARVLALYIAtprqwathnmsprQAELiNAQ 57 d1qyca_ 45 KAQLLESFKASGANIVHG----siDDHASLVEAVK--NVDVVISTVGSL--QIESQVNII 96 :::::::::::::::::: ::::::::::: :::::::::::: ::::::::: d1dnpa2 58 LNGLQIALAEKGIPLLFRevddfvASVEIVKQVCAenSVTHLFYNYQYEvnERARDVEVE 117 d1qyca_ 97 KAIkevGTVKrFFPSEF--GNDVDNVH----AVEPaksvfevkakvrraieaegipytyv 150 ::: :::: :::::: :::::::: :::: d1dnpa2 118 RAL---RNVV-CEGFDDsvILPPGAVMtgnhEMYK------------------------- 148 d1qyca_ 151 ssncfagyflrslaqagltapprdkvvilgdgnaRVVFVKEEDigtftikavddprtlnk 210 ::::::::: d1dnpa2 149 ---------------------vftpfknawlkrlREGMPECVA----------------- 170 d1qyca_ 211 tlylrlpantlslnelvalwekkidktlekayvpeeevlkliadtpfpanisiaishsif 270 d1dnpa2 171 ------------------------------------------------------------ 171 d1qyca_ 271 vkgdqtnfeigpagveasqlypdvkyttvdeylsnfv 307 d1dnpa2 171 -------apkvrssgsiepspsitlnyprqsfdtahf 200 FAST alignment (Normalized score: 3.06 Raw score:758.20) d1qyca_ 1 GSRSRILLIGATGYIG----------RHVAKASLD-LGHPTFLLVRESTASS-------- 41 ::::: ::::::::: ::::::::: d1dnpa2 1 ---TTHLV--------WFRQDLRLHDNLALAAACRNSSARVLALY-------IATPRQWA 42 d1qyca_ 42 ------------NSEKAQLLESFKASGANIVHGSIDDHASLVEAVKNVDVVISTVGSL-- 87 :::::::::::::::::::::: d1dnpa2 43 THNMSPRQAELINAQLNGLQIALAEKGIPLLFRE------------------------VD 78 d1qyca_ 88 QIES-QVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEP----AKSVFEVKAKVRRAIEA 142 :::: :::::::::: :::::::: :::::::::::::: d1dnpa2 79 DFVASVEIVKQVCAE-NSVTHLFY---------------NYQYEVNERARDVEVERA--- 119 d1qyca_ 143 -EGIPYTYVSSNCFAGYFLRS---------------LAQAGLTAPPRDKVVILGDGNAR- 185 ::::::::: :::: d1dnpa2 120 LRNVVCEGFD-----------DSVILPPGAVMTGNHEMYK-------------------V 149 d1qyca_ 186 -------------VVFVKEEDIGTFTIKAVDDPRTLNKTLYLRLPANTLSLNELVALWEK 232 ::::: d1dnpa2 150 FTPFKNAWLKRLREGMPE------------------------------------------ 167 d1qyca_ 233 KIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYP 292 d1dnpa2 168 ------------------------------------------------------------ 168 d1qyca_ 293 DVKYTTVDEYLSNFV--------------------------------- 307 d1dnpa2 168 ---------------CVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHF 200 TMalign alignment (TM-score: 0.36 Raw score:109.49) d1qyca_ 1 GSRSRILLIGATGYIGR-H-VAKASLDLG-HPTFLLVREST-----------ASS--NSE 44 :::::::::::::: : ::::::::: ::::::::::: ::: ::: d1dnpa2 1 ---TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQ 57 d1qyca_ 45 KAQLLESFKASGANIVHG-S--I-DDHASLVEAVK--NVDVVISTVGSL--QIESQVNII 96 :::::::::::::::::: : : ::::::::::: :::::::::::: ::::::::: d1dnpa2 58 LNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVE 117 d1qyca_ 97 KAIKEVGTVKRFFPSEF---GNDVDNVH----AVEPA---KSVFEVKAKVRRAIEAEGIP 146 :::: : : ::::::: :::::::: ::::: d1dnpa2 118 RALR--N-V-VCEGFDDSVILPPGAVMTGNHEMYKVFTPF-------------------- 153 d1qyca_ 147 YTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARV--VFVKEEDIGT-------- 196 :::::::: ::::::: :: d1dnpa2 154 --------------------------------KNAWLKRLREGMPECVA-APKVRSSGSI 180 d1qyca_ 197 --------------------FTIKAVDDPRTLNKTLYLRLPANTLSLNELVALWEKKIDK 236 d1dnpa2 181 EPSPSITLNYPRQSFDTAHF---------------------------------------- 200 d1qyca_ 237 TLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKY 296 d1dnpa2 201 ------------------------------------------------------------ 201 d1qyca_ 297 TTVDEYLSNFV 307 d1dnpa2 201 ----------- 201 HHsearch alignment (Probability: 0.05 E-value:0.23) d1qyca_ 86 SLQIESQVNIIKAIKEVG--TVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAE 143 :::::::::::::::::: ::::::::::::: :::::::::::::::::::::::::: d1dnpa2 10 DLRLHDNLALAAACRNSSARVLALYIATPRQWA-THNMSPRQAELINAQLNGLQIALAEK 68 d1qyca_ 144 GIPYTYVS 151 :::::::: d1dnpa2 69 GIPLLFRE 76