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 | d1li4a1 | S-adenosylhomocystein hydrolase | 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 <-- 1.465 --> HitDALI alignment (Z-score: 4.1 Raw score:347.50) d1q1ra2 1 rplpvasgavgkannfrylrtlEDAECIR---rqlIADNRLVVIGGGYIGLEVAATAIKA 57 ::::::: ::::::::::::::::::::::::: d1li4a1 1 --------------dnlygcreSLIDGIKratdvmIAGKVAVVAGYGDVGKGCAQALRGF 46 d1q1ra2 58 NMHVTLLDTAARVlervtappvsafYEHLHReagVDIRtgtqvcgfemstdqqkvtavlc 117 ::::::::::::: :::::: :::: d1li4a1 47 GARVIITEIDPIN----------alQAAMEG---YEVT---------------------- 71 d1q1ra2 118 edgTRLP--ADLVIAGIG------------------------------------------ 133 :::: ::::::::: d1li4a1 72 -tmDEACqeGNIFVTTTGcidiilgrhfeqmkddaivcnighfdveidvkwlnenavekv 130 d1q1ra2 134 --------------------------------- 134 d1li4a1 131 nikpqvdryrlkngrriillaegrlvnlgcamg 163 FAST alignment (Normalized score: 5.06 Raw score:745.50) d1q1ra2 1 RPLPVASGAVGKANNFRYLR------TLEDAECIRRQL-----IADNRLVVIGGGYIGLE 49 :::::::::: ::::::::::::::::: d1li4a1 1 --------------------DNLYGCRESLIDGIKR--ATDVMIAGKVAVVAGYGDVGKG 38 d1q1ra2 50 VAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQ 109 ::::::::::::::::: ::::::::::::::: d1li4a1 39 CAQALRGFGARVIITEI-------------DPINALQAAMEGYEV--------------- 70 d1q1ra2 110 QKVTAVLCEDGTR-------LPADLVIAGIG----------------------------- 133 ::::::::: d1li4a1 71 -------------TTMDEACQEGNIFVTT--TGCIDIILGRHFEQMKDDAIVCNIGHFDV 115 d1q1ra2 134 ------------------------------------------------ 134 d1li4a1 116 EIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMG 163 TMalign alignment (TM-score: 0.47 Raw score:63.02) d1q1ra2 1 -----RPLPVASGAVGKANNFRYL--RTLEDAECIR---RQLIADNRLVVIGGGYIGLEV 50 : : :::::: ::::::::::::::::::::: d1li4a1 1 DNLYG------------------CRE--S-LIDGIKRATDVMIAGKVAVVAGYGDVGKGC 39 d1q1ra2 51 AATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQ 110 :::::::::::::::::::: :::::: :: :::: : : d1li4a1 40 AQALRGFGARVIITEIDPIN---------ALQAAM-EG---YEVT--T-M---------- 73 d1q1ra2 111 KVTAVLCEDGTR-LPADLVIAGIG------------------------------------ 133 : :: ::::::::::: d1li4a1 74 ------D---EACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNE 124 d1q1ra2 134 --------------------------------------- 134 d1li4a1 125 NAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMG 163 HHsearch alignment (Probability: 0.96 E-value:0.00) d1q1ra2 27 CIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARV 70 :::::::::::::::::::::::::::::::::::::::::::: d1li4a1 16 RATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPIN 59