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 | d7reqb2 | Methylmalonyl-CoA mutase beta subunit, C-terminal domain | Cobalamin (vitamin B12)-binding domain | Flavodoxin-like | 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 <-- 0.918 --> HitDALI alignment (Z-score: 5.7 Raw score:591.20) d1qyca_ 1 --------------------------------gsRSRILLIG-----atGYIGRHVAKAS 23 :::::::: ::::::::::: d7reqb2 1 tkpfpaaparkglawhrdsevfeqlmdrstsvseRPKVFLAClgtrrdfGGREGFSSPVW 60 d1qyca_ 24 LDLGHPTFLLVRestassnsekaqllesfkasganivhgsidDHASLVEAVK--NVDVVI 81 :::::::::::: :::::::::: :::::: d7reqb2 61 HIAGIDTPQVEG-----------------------------gTTAEIVEAFKksGAQVAD 91 d1qyca_ 82 STVGSLQIE-SQVNIIKAIKEVgTVKRFFPSEfgndvdnvhavepaksvfEVKAKVRRAI 140 ::::::::: :::::::::::: ::::::::: :::::::::: d7reqb2 92 LCSSAKVYAqQGLEVAKALKAA-GAKALYLSG----------------afKEFGDDAAEA 134 d1qyca_ 141 EAegIPYTYVSSNcfagyflrslaqagltapprdkvvilgdgnarvvfvkeedIGTFTIK 200 :: ::::::::: ::::::: d7reqb2 135 EK--LIDGRLFMG---------------------------------------mDVVDTLS 153 d1qyca_ 201 AVDDPrtlnktlylrlpantlslnelvalwekkidktlekayvpeeevlkliadtpfpan 260 ::::: d7reqb2 154 STLDI------------------------------------------------------- 158 d1qyca_ 261 isiaishsifvkgdqtnfeigpagveasqlypdvkyttvdeylsnfv 307 d7reqb2 159 ------------------------------------------lgvak 163 FAST alignment (Normalized score: 4.66 Raw score:1043.00) d1qyca_ 1 GS----------------------------------RSRILLIGAT---------GYIGR 17 :::::: ::::: d7reqb2 1 --TKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFL----ACLGTRRDFGGREG 54 d1qyca_ 18 HVAKASLDLGHPTFLLVRESTASSNSEKAQLLESFKASGANIVHGSIDDHASLVEAVK-- 75 :::::::::::::::: ::::::::::::: d7reqb2 55 FSSPVWHIAGIDTPQV-----------------------------EGGTTAEIVEAFKKS 85 d1qyca_ 76 NVDVVISTVGSLQI-ESQVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEPAKSVFEV-- 132 :::::::::::::: :::::::::::: :::::::: d7reqb2 86 GAQVADLCSSAKVYAQQGLEVAKALKA-AGAKALYL----------------------SG 122 d1qyca_ 133 ----KAKVRRAIEAEGIP--YTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARV 186 :::::::::: :::: d7reqb2 123 AFKEFGDDAAEAEK----LIDGRL------------------------------------ 142 d1qyca_ 187 VFVKEED----IGTFTIKAVDDPRTLNKTLYLRLPANTLSLNELVALWEKKIDKTLEKAY 242 ::::::::: d7reqb2 143 -------FMGMDVVDTLSST---------------------------------------- 155 d1qyca_ 243 VPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEY 302 d7reqb2 156 ------------------------------------------------------------ 156 d1qyca_ 303 LSNFV-------- 307 d7reqb2 156 -----LDILGVAK 163 TMalign alignment (TM-score: 0.32 Raw score:99.23) d1qyca_ 1 -------------------------G--S-----RSRILLIG---A--TGYIGRHVAKAS 23 : : :::::::: : :::::::::::: d7reqb2 1 TKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLGTRRDFGGREGFSSPVW 60 d1qyca_ 24 LDLGHPTFLLVRESTASSNSEKAQLLESFKASGANIVHGSIDDHASLVEAVK--NVDVVI 81 :::::::::::: : :::::::::: :::::: d7reqb2 61 HIAGIDTPQVEG---------------------------G--TTAEIVEAFKKSGAQVAD 91 d1qyca_ 82 STVGSLQIE-SQVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAI 140 ::::::::: ::::::::::::: ::::::::: : ::::::::::: d7reqb2 92 LCSSAKVYAQQGLEVAKALKAAG-AKALYLSGA---F------------KEFGDDAAEAE 135 d1qyca_ 141 EAEGIPYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEEDIGTF-TI 199 : :::::: : : : :::: :: d7reqb2 136 K---LIDGRL-F--M---------------------------------G----MDVVDTL 152 d1qyca_ 200 KAVDDP-----RTLNKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLKLIAD 254 :::::: d7reqb2 153 SSTLDILGVAK------------------------------------------------- 163 d1qyca_ 255 TPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV 307 d7reqb2 164 ----------------------------------------------------- 164 HHsearch alignment (Probability: 0.39 E-value:0.02) d1qyca_ 211 TLYLRLPA 218 :::::::: d7reqb2 89 VADLCSSA 96