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 | d1mx3a1 | Transcription corepressor CtbP | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.511 --> HitDALI alignment (Z-score: 6.3 Raw score:370.50) d1q1ra2 1 rplpvasgavgkannfrylrtlEDAECIRR------------------------------ 30 :::::::: d1mx3a1 1 -----------------eetadSTLCHILNlyrratwlhqalregtrvqsveqirevasg 43 d1q1ra2 31 -qlIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARvlervtappvsAFYEHLHRe 89 ::::::::::::::::::::::::::::::::::::: :::::::: d1mx3a1 44 aarIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLS-----------DGVERALG- 91 d1q1ra2 90 agVDIRtgTQVCgfemstdqqkvtavlcedgtrLPADLVIAGIG---------------- 133 :::: :::: ::::::::::: d1mx3a1 92 --LQRV--STLQ------------------dllFHSDCVTLHCGlnehnhhlindftvkq 129 d1q1ra2 134 ------------------------------------------------------------ 134 d1mx3a1 130 mrqgaflvntargglvdekalaqalkegrirgaaldvhesepfsfsqgplkdapnlictp 189 d1q1ra2 134 ---- 134 d1mx3a1 190 haaw 193 FAST alignment (Normalized score: 4.53 Raw score:725.30) d1q1ra2 1 RPLPVASGAVGKANNFRYLR---TLEDAECIRRQL------------------------- 32 :::::::::: d1mx3a1 1 --------------------EETADSTLCHILN--LYRRATWLHQALREGTRVQSVEQIR 38 d1q1ra2 33 --------IADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPV--SAF 82 :::::::::::::::::::::::::::::::::: ::: d1mx3a1 39 EVASGAARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDP-------------YLSDG 85 d1q1ra2 83 YEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTR------LPADLVIAGIG--- 133 :::: ::::::: ::::::::: d1mx3a1 86 VERA---LGLQRVS--------------------------TLQDLLFHSDCVTLH--CGL 114 d1q1ra2 134 ------------------------------------------------------------ 134 d1mx3a1 115 NEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSF 174 d1q1ra2 134 ------------------- 134 d1mx3a1 175 SQGPLKDAPNLICTPHAAW 193 TMalign alignment (TM-score: 0.48 Raw score:64.48) d1q1ra2 1 -RPLPVASGAVGKANNFRYLRTLEDAECIRR-Q--------------------------- 31 :::::::::::: : d1mx3a1 1 E------------------ETADSTLCHILNLYRRATWLHQALREGTRVQSVEQIREVAS 42 d1q1ra2 32 ---LIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHR 88 ::::::::::::::::::::::::::::::::::::::: : :::::: d1mx3a1 43 GAARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSD----------G-VERALG 91 d1q1ra2 89 EAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIG--------------- 133 :::: ::: :: ::::::::::::: d1mx3a1 92 ---LQRV--STL---------------QD---LLFHSDCVTLHCGLNEHNHHLINDFTVK 128 d1q1ra2 134 ------------------------------------------------------------ 134 d1mx3a1 129 QMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFSQGPLKDAPNLICT 188 d1q1ra2 134 ----- 134 d1mx3a1 189 PHAAW 193 HHsearch alignment (Probability: 0.89 E-value:0.00) d1q1ra2 33 IADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARV 70 :::::::::::::::::::::::::::::::::::::: d1mx3a1 47 IRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSD 84