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: 542d3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1ri7a1 | Putative transcriptional regulator PH1519 | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α |
| Hit | d1lvaa3 | C-terminal fragment of elongation factor SelB | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α |
Query <-- 0.715 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:159.80) query 1 pDYPVLDAILELYVDRD-TGADAIVAA-gYDRELVVKTLRMVDTAEykrrqyppgtkisa 58 :::::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 1 -LDEIDKKIIKILQNDGkAPLREISKItgLAESTIHERIRKLRESG-----------vik 48 query 59 KGFGkdrrlpitnrwregh 77 :::: d1ri7a1 49 KFTA-------iidpealg 60 FAST alignment (Normalized score: 4.52 Raw score:307.00) query 1 PDYPVLDAILELYVDR-DTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISA 58 ::::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 1 -LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRE---------------- 43 query 59 KGFGKDRRLPITNRWREGH----------------- 77 d1ri7a1 44 -------------------SGVIKKFTAIIDPEALG 60 TMalign alignment (TM-score: 0.42 Raw score:32.51) query 1 PDYPVLDAILELYVDRD--TGADAIVAAGYDR-ELVVKTLRM-VDTAE--YKRRQYPPGT 54 :: :::::::::: ::: ::::::::::::: ::::::::: : ::: : d1ri7a1 1 LD-EIDKKIIKIL-QNDGKAPLREISKITGLAESTIHERIRKLR-ESGVI--K------- 48 query 55 KISAKGFGKDRR--------LPITNRWREGH 77 :: :: d1ri7a1 49 ------KF--TAIIDPEALG----------- 60 HHsearch alignment (Probability: 0.05 E-value:0.06) query 4 PVLDAILELYVDRD--TGADAIVAA-GYDRELVVKTLRMVDTA 43 :::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 2 DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES 44
Intermediate <-- 0.827 --> HitDALI alignment (Z-score: 5.1 Raw score:189.90) d1ri7a1 1 ----LDEIDKKIIKILQND--gKAPLREISKITGLAESTIHERIRKLRESGVIKKFTaii 54 ::::::::::::::: ::::::::::::::::::::::::::::::::::: d1lvaa3 1 fsetQKKLLKDLEDKYRVSrwqPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKIN--d 58 d1ri7a1 55 dpealg 60 d1lvaa3 59 efywhr 64 FAST alignment (Normalized score: 6.55 Raw score:406.20) d1ri7a1 1 ----LDEIDKKIIKILQNDG--KAPLREISKITGLAESTIHERIRKLRESGVIKKFTAII 54 :::::::::::::::: :::::::::::::::::::::::::::::::: d1lvaa3 1 FSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLV------ 54 d1ri7a1 55 DPEALG---------- 60 d1lvaa3 55 ------KINDEFYWHR 64 TMalign alignment (TM-score: 0.59 Raw score:35.60) d1ri7a1 1 L----DEIDKKIIKILQNDG--KAPLREISKITGLAESTIHERIRKLRESGVIKK----- 49 : ::::::::::::::: ::::::::::::::::::::::::::: ::::: d1lvaa3 1 FSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVR-EGVLVKINDE 59 d1ri7a1 50 --FT-AIIDPEALG 60 :: d1lvaa3 60 FYWHR--------- 64 HHsearch alignment (Probability: 0.87 E-value:0.00) d1ri7a1 4 IDKKIIKILQNDGKA--PLREISKITGLAESTIHERIRKLRESGVIKKFT 51 ::::::::::::::: ::::::::::::::::::::::::::::::::: d1lvaa3 8 LLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKIN 57