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 | d1tjya_ | AI-2 receptor LsrB | 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 <-- 0.863 --> HitDALI alignment (Z-score: 5.6 Raw score:609.00) d1qyca_ 1 gsRSRILLIG------aTGYIGRHVAKASLDLGHPTFLLVREStassnsekaqllesfka 54 :::::::: :::::::::::::::::::::::::: d1tjya_ 1 gsAERIAFIPklvgvgfFTSGGNGAQEAGKALGIDVTYDGPTE----------------- 43 d1qyca_ 55 sganivhgsIDDHASL-VEAVK-NVDVVISTvgslQIESQVNIIKAIKeVGTVkRFFPSE 112 ::::::: ::::: :::::::: ::::::::::::: :::: :::::: d1tjya_ 44 -------psVSGQVQLvNNFVNqGYDAIIVS--avSPDGLCPALKRAM-QRGV-KILTWD 92 d1qyca_ 113 fgndvdnvhavepaksvfevkakVRRAIeaegipYTYVSSN------------------- 153 ::::: ::::::: d1tjya_ 93 ---------------------sdTKPEC-----rSYYINQGtpkqlgsmlvemaahqvdk 126 d1qyca_ 154 ------------------------------------------------------------ 154 d1tjya_ 127 ekakvaffyssptvtdqnqwvkeakakisqehpgweivttqfgyndatkslqtaegiika 186 d1qyca_ 154 --------------------cfagyflrslaqagltapprdkvvilgdgnarvvfVKEED 193 ::::: d1tjya_ 187 ypdldaiiapdanalpaaaqaaenlkrnnlaivgfstpnvmrpyvqrgtvkefglWDVVQ 246 d1qyca_ 194 IGTFTIKAV---DDPR------------------------------tLNKTLYLRLpant 220 ::::::::: :::: ::::::::: d1tjya_ 247 QGKISVYVAnalLKNMpmnvgdsldipgigkvtvspnseqgyhyeakGNGIVLLPE---- 302 d1qyca_ 221 lslnelvalwekkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfei 280 d1tjya_ 303 ------------------------------------------------------------ 303 d1qyca_ 281 gpagveasqlypdvkyttvdeylsnfv 307 d1tjya_ 303 -------------rvifnkdnidkydf 316 FAST alignment (Normalized score: 3.08 Raw score:961.00) d1qyca_ 1 GS--RSRILL--IGATGYIGRHVAKASLD----LGHPTFLLVRESTASSNSEKAQLLESF 52 :::::: ::::::::::::::::: ::::::: d1tjya_ 1 --GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTY-------------------- 38 d1qyca_ 53 KASGANIVHGSIDDHASLVEAVKNVDVVISTVGSL------QIESQVNIIKAIKEVGTVK 106 :::::::::::::: :::: d1tjya_ 39 -----------------------------------DGPTEPSVSGQVQLVNNFVN-QGYD 62 d1qyca_ 107 RFFPSEFGNDVDNVHAVEPAKS----VFEVKAKVRRAIEAEGIPYTYVSSNCF------- 155 ::: :::::::::::::::::::: d1tjya_ 63 AII-------------------VSAVSPDGLCPALKRAMQRGVKIL-------TWDSDTK 96 d1qyca_ 156 ------------------------------------------------------------ 156 d1tjya_ 97 PECRSYYINQGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQ 156 d1qyca_ 156 ----------------------------------------AGYFLRSLAQAGLTAPPRDK 175 :::::: d1tjya_ 157 EHPGWEIVTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALP-------------- 202 d1qyca_ 176 VV---------ILGDGNARVV-------------------FVKEEDIGTFTIKAVDDPRT 207 :::::::::: :::::::::::::::: d1tjya_ 203 --AAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKEFGLWDVVQQGKISVYVAN---- 256 d1qyca_ 208 -------------------------------------LNKTLYLRLPANTLSLNELVALW 230 ::::::: d1tjya_ 257 ALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLL---------------- 300 d1qyca_ 231 EKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQL 290 d1tjya_ 301 ------------------------------------------------------------ 301 d1qyca_ 291 YPDVKYTTVDEYLSNFV---------------- 307 d1tjya_ 301 -----------------PERVIFNKDNIDKYDF 316 TMalign alignment (TM-score: 0.40 Raw score:121.87) d1qyca_ 1 --GSRSRILLIG-AT-GYIGRHVAKASLDL-G---HPTFLLVRESTASSNSEK--AQLLE 50 :::::::: :: :::::::::::::: : :::::::: : : : d1tjya_ 1 GS--AERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGP-T----E--PSV----- 46 d1qyca_ 51 SFKASGANIVHGSIDDHASLVEAV-KNVDVVISTVGSLQIESQVNIIKAIKEVGTVKRFF 109 ::::: :::::: ::::::::::: :::::::::::::: ::: ::: d1tjya_ 47 -----------SGQVQ--LVNNFVNQGYDAIIVSAV--SPDGLCPALKRAMQ-RGV-KIL 89 d1qyca_ 110 PSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGIPYTYVSSNCF-AGYFLRSLAQAGL 168 : ::: : :: :::: ::::::::: ::::::::::: d1tjya_ 90 T-WDS--D---------------TK--PECR------SYYINQGTPKQLGSMLVEMAA-- 121 d1qyca_ 169 TAPPRDKVV-------------------------IL-GDG-------------------- 182 :: :::: :: ::: d1tjya_ 122 --HQ-VDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIVTTQFGYNDATKSLQ 178 d1qyca_ 183 ------------------------------------------------------------ 183 d1tjya_ 179 TAEGIIKAYPDLDAIIAPDANALPAAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKE 238 d1qyca_ 183 -NARVVFVKEEDIGTFTIKAVDD---PRTLNKTLYL----RLP--------ANTLSLNEL 226 :::::::::::::::::: :::::::::: :: d1tjya_ 239 F----GLWDVVQQGKISVYVANALLKNMPMNVGDSLDIPG-IGKVTVSPNS--------- 284 d1qyca_ 227 VALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQT---NFEIGP- 282 ::: ::: d1tjya_ 285 -----------------------------------------------EQGYHY---EAKG 294 d1qyca_ 283 AGVEASQLYPDVKYTTVDEYL-SNFV---- 307 :::::: ::::: :: :::: d1tjya_ 295 NGIVLL-------PERVI-FNKDNIDKYDF 316 HHsearch alignment (Probability: 0.85 E-value:0.07) d1qyca_ 1 GSRSRILLIGATG---Y---IGRHVAKASLDLGHPTFLLVRESTASSNSEKAQLLESFKA 54 ::::::::::::: : ::::::::::::::::::::::::: :::::::::::: d1tjya_ 1 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPS--VSGQVQLVNNFV- 57 d1qyca_ 55 SGANIVHGSIDDHASLVEAVKNVDVVISTVGSLQIESQVNIIKAIKEVGTVKRFFPSEFG 114 ::::::::::: ::::::::::::::::::::::::::: d1tjya_ 58 -------------------NQGYDAIIVSA--VSPDGLCPALKRAMQRGVKILTWDSDT- 95 d1qyca_ 115 NDVDNVHAVEPAKSVFEVKAKVRRAIEAE 143 ::::::::::::::::::::::::::::: d1tjya_ 96 KPECRSYYINQGTPKQLGSMLVEMAAHQV 124