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 | d1q1ra2 | Putidaredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1o54a_ | Hypothetical protein TM0748 | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | α/β |
Query <-- 1.466 --> IntermediateDALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 0.982 --> HitDALI alignment (Z-score: 4.6 Raw score:385.90) d1q1ra2 1 ------------------------------------------------------------ 1 d1o54a_ 1 hhhvgkvadtlkpgdrvllsfedeseflvdlekdkklhthlgiidlnevfekgpgeiirt 60 d1q1ra2 1 -------rplpvasgavgkannfryLRTLEDAECIRRQ-LIADNRLVVIGGGYigLEVAA 52 ::::::::::::: :::::::::::::: ::::: d1o54a_ 61 sagkkgyilipslideimnmkrtqiVYPKDSSFIAMMLdVKEGDRIIDTGVGS--GAMCA 118 d1q1ra2 53 TAIKAN---MHVTLLDTAARVlervtappvsAFYEHLHR----EAGVDIRTgTQVCGFem 105 :::::: :::::::::::: :::::::: :::::::: :::::: d1o54a_ 119 VLARAVgssGKVFAYEKREEF---------aKLAESNLTkwglIERVTIKV-RDISEG-- 166 d1q1ra2 106 stdqqkvtavlcedgTRLP-ADLVIAGIG------------------------------- 133 :::: ::::::::: d1o54a_ 167 ---------------FDEKdVDALFLDVPdpwnyidkcwealkgggrfatvcpttnqvqe 211 d1q1ra2 134 ------------------------------------------------------ 134 d1o54a_ 212 tlkklqelpfirievweslfrpykpvperlrpvdrmvahtaymifatkvcrree 265 FAST alignment (Normalized score: 3.21 Raw score:603.00) d1q1ra2 1 RPLPVASGAVGKANNFRYLR---------------------------------------- 20 d1o54a_ 1 --------------------HHHVGKVADTLKPGDRVLLSFEDESEFLVDLEKDKKLHTH 40 d1q1ra2 21 -----------------------------------------------TLEDAECIRR-QL 32 :::::::::: :: d1o54a_ 41 LGIIDLNEVFEKGPGEIIRTSAGKKGYILIPSLIDEIMNMKRTQIVYPKDSSFIAMMLDV 100 d1q1ra2 33 IADNRLVVIGG--GYIGLEVAATAIK--ANMHVTLLDTAARVLERVTAPP-VSAFYEHLH 87 ::::::::::: :::::::::: :::::::::::: ::::::::: d1o54a_ 101 KEGDRIIDTGVGSGAMCAVLARA---VGSSGKVFAYEKRE----------EFAKLAESNL 147 d1q1ra2 88 REA----GVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTR-LPADLVIAGIG--------- 133 ::: ::::: ::::: :::: ::::::::: d1o54a_ 148 TKWGLIERVTIK-VRDIS-----------------EGFDEKDVDALFLD--VPDPWNYID 187 d1q1ra2 134 ------------------------------------------------------------ 134 d1o54a_ 188 KCWEALKGGGRFATVCPTTNQVQETLKKLQELPFIRIEVWESLFRPYKPVPERLRPVDRM 247 d1q1ra2 134 ------------------ 134 d1o54a_ 248 VAHTAYMIFATKVCRREE 265 TMalign alignment (TM-score: 0.48 Raw score:64.45) d1q1ra2 1 ------------------------------------------------------------ 1 d1o54a_ 1 HHHVGKVADTLKPGDRVLLSFEDESEFLVDLEKDKKLHTHLGIIDLNEVFEKGPGEIIRT 60 d1q1ra2 1 -------------------------RPLPVASGAVGKANNFRYLRTLEDAECIRR-QLIA 34 :::::::::::: :::: d1o54a_ 61 SAGKKGYILIPSLIDEIMNMKRTQI------------------VYPKDSSFIAMMLDVKE 102 d1q1ra2 35 DNRLVVIGGGY-IGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHL---HREA 90 ::::::::::: :::::::::::::::::::::::::: : :::::: : :: : d1o54a_ 103 GDRIIDTGVGSGAMCAVLARAVGSSGKVFAYEKREEFA-----K-LAESNL-TKWGLI-E 154 d1q1ra2 91 GVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLP-ADLVIAGIG---------------- 133 :::::: ::::: :: ::: ::::::::: d1o54a_ 155 RVTIKV-RDISE-------------GF----DEKDVDALFLDVPDPWNYIDKCWEALKGG 196 d1q1ra2 134 ------------------------------------------------------------ 134 d1o54a_ 197 GRFATVCPTTNQVQETLKKLQELPFIRIEVWESLFRPYKPVPERLRPVDRMVAHTAYMIF 256 d1q1ra2 134 --------- 134 d1o54a_ 257 ATKVCRREE 265 HHsearch alignment (Probability: 0.12 E-value:0.01) d1q1ra2 31 QLIADNRLVVIGGGYIGLEV--AATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHR 88 :::::::::::::::::::: ::::: :::::::::::::::: ::::::::::: d1o54a_ 99 DVKEGDRIIDTGVGSGAMCAVLARAVG-SSGKVFAYEKREEFAK-----LAESNLTKWGL 152 d1q1ra2 89 EAGVDIRTGTQVCGF 103 ::::::::::::::: d1o54a_ 153 IERVTIKVRDISEGF 167