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 | d1kpga_ | CmaA1 | 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 <-- 1.657 --> HitDALI alignment (Z-score: 3.4 Raw score:385.10) d1q1ra2 1 -------------rplpvasgavgkannfryLRTL--------------EDAECIRRQ-L 32 :::: ::::::::: : d1kpga_ 1 delkphfanvqahydlsddffrlfldptqtySCAYferddmtlqeaqiaKIDLALGKLgL 60 d1q1ra2 33 IADNRLVVIGGGYigLEVAATAIK-ANMHVTLLDTAARVlervtappvsAFYEHLHREA- 90 ::::::::::::: ::::::::: :::::::::::::: :::::::::: d1kpga_ 61 QPGMTLLDVGCGW--GATMMRAVEkYDVNVVGLTLSKNQ---------aNHVQQLVANSe 109 d1q1ra2 91 ---GVDIRTgTQVCgfemstdqqkvtavlcedgTRLPADLVIAGIG-------------- 133 :::::: :::: ::::::::::::: d1kpga_ 110 nlrSKRVLL-AGWE------------------qFDEPVDRIVSIGAfehfgherydaffs 150 d1q1ra2 134 ------------------------------------------------------------ 134 d1kpga_ 151 lahrllpadgvmllhtitglhpkeiherglpmsftfarflkfivteifpggrlpsipmvq 210 d1q1ra2 134 ------------------------------------------------------------ 134 d1kpga_ 211 ecasangftvtrvqslqphyaktldlwsaalqankgqaialqseevyerymkyltgcaem 270 d1q1ra2 134 --------------- 134 d1kpga_ 271 frigyidvnqftcqk 285 FAST alignment (Normalized score: 3.39 Raw score:660.80) d1q1ra2 1 RPLPVASGAVGKANNFRYLR---------------------------------------- 20 d1kpga_ 1 --------------------DELKPHFANVQAHYDLSDDFFRLFLDPTQTYSCAYFERDD 40 d1q1ra2 21 ---TLEDAECIRR-----QLIADNRLVVIGGGYIG-LEVAATAI-KANMHVTLLDTAARV 70 :::::::::: :::::::::::::: :::::::: ::::::::::::: d1kpga_ 41 MTLQEAQIAKIDLALGKLGLQPGMTLLDVGCG---WGATMMRAVEKYDVNVVGLTLSK-- 95 d1q1ra2 71 LERVTAPPVS--AFYEHLHRE-----AGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRL 123 ::::::::: ::::: ::::: ::::: d1kpga_ 96 ----------NQANHVQQLVANSENLRSKRV-LLAGW------------------EQFDE 126 d1q1ra2 124 PADLVIAGIG-------------------------------------------------- 133 ::::::: d1kpga_ 127 PVDRIVS---IGAFEHFGHERYDAFFSLAHRLLPADGVMLLHTITGLHPKEIHERGLPMS 183 d1q1ra2 134 ------------------------------------------------------------ 134 d1kpga_ 184 FTFARFLKFIVTEIFPGGRLPSIPMVQECASANGFTVTRVQSLQPHYAKTLDLWSAALQA 243 d1q1ra2 134 ------------------------------------------ 134 d1kpga_ 244 NKGQAIALQSEEVYERYMKYLTGCAEMFRIGYIDVNQFTCQK 285 TMalign alignment (TM-score: 0.50 Raw score:66.96) d1q1ra2 1 -------------------------------RPLPVASGAVGKANNFRYLRT-L------ 22 :::: : d1kpga_ 1 DELKPHFANVQAHYDLSDDFFRLFLDPTQTY-----------------SCAYFERDDMTL 43 d1q1ra2 23 ------EDAECIRR-QLIADNRLVVIGGGYIGLEVAATAIK-ANMHVTLLDTAARVLERV 74 :::::::: ::::::::::::::: ::::::::: :::::::::::::: d1kpga_ 44 QEAQIAKIDLALGKLGLQPGMTLLDVGCGW--GATMMRAVEKYDVNVVGLTLSKNQ---- 97 d1q1ra2 75 TAPPVSAFYEHLHREA----GVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIA 130 ::::::::::: :::::: :::: : :::::::::: d1kpga_ 98 -----ANHVQQLVANSENLRSKRVLL-AGWE---------------Q---FDEPVDRIVS 133 d1q1ra2 131 G-I-G------------------------------------------------------- 133 : : : d1kpga_ 134 IGAFEHFGHERYDAFFSLAHRLLPADGVMLLHTITGLHPKEIHERGLPMSFTFARFLKFI 193 d1q1ra2 134 ------------------------------------------------------------ 134 d1kpga_ 194 VTEIFPGGRLPSIPMVQECASANGFTVTRVQSLQPHYAKTLDLWSAALQANKGQAIALQS 253 d1q1ra2 134 -------------------------------- 134 d1kpga_ 254 EEVYERYMKYLTGCAEMFRIGYIDVNQFTCQK 285 HHsearch alignment (Probability: 0.06 E-value:0.05) d1q1ra2 21 TLEDAE-----CIRRQ--LIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLE 72 :::::: ::::: ::::::::::::::::::: ::::::::::::::::::::: d1kpga_ 42 TLQEAQIAKIDLALGKLGLQPGMTLLDVGCGWGATMM-RAVEKYDVNVVGLTLSKNQAN 99