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 | d2foka2 | Restriction endonuclease FokI, N-terminal (recognition) domain | (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 <-- 0.705 --> HitDALI alignment (Z-score: 3.2 Raw score:189.60) d1ri7a1 1 --------------LDEIDKKIIKILQNDGKAPLREISKITG------------------ 28 :::::::::::::::::::::::::::: d2foka2 1 gsaiekeilieaisSYPPAIRILTLLEDGQHLTKFDLGKNLGfsgesgftslpegilldt 60 d1ri7a1 29 ------------------lAESTIHERIRKLRESGVIKKF-------------------- 50 ::::::::::::::::::::: d2foka2 61 lanampkdkgeirnnwegsSDKYARMIGGWLDKLGLVKQGkkefiiptnkefishafkit 120 d1ri7a1 51 --------taiidpealg 60 d2foka2 121 geglkvlrrakgstkftr 138 FAST alignment (Normalized score: 4.09 Raw score:372.00) d1ri7a1 1 --------------LDEIDKKIIKILQND--GKAPLREISKITGL--------------- 29 ::::::::::::: ::::::::::: d2foka2 1 GSAIEKEILIEAISSYPPAIRILTLLE--DGQHLTKFDLGKN---LGFSGESGFTSLPEG 55 d1ri7a1 30 ------------------------AESTIHERIRKLRESGVIKKFTAIIDPEALG----- 60 ::::::::::::::::: :::: d2foka2 56 ILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGL-VKQG---------KKEFI 105 d1ri7a1 61 --------------------------------- 61 d2foka2 106 IPTNKEFISHAFKITGEGLKVLRRAKGSTKFTR 138 TMalign alignment (TM-score: 0.30 Raw score:18.22) d1ri7a1 1 LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESG-VIK----------- 48 ::::::::::::::::: : : d2foka2 1 ----------------------------GSAIEKEILIEAISSYPPA-IRILTLLEDGQH 31 d1ri7a1 49 ------------------------------------------------------------ 49 d2foka2 32 LTKFDLGKNLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWL 91 d1ri7a1 49 ----------------------------------KFT----------AIIDPEALG 60 ::: d2foka2 92 DKLGLVKQGKKEFIIPTNKEFISHAFKITGEGLKVLRRAKGSTKFTR--------- 138 HHsearch alignment (Probability: 0.02 E-value:0.08) d1ri7a1 6 KKIIKILQNDGKAPLREISKITGLAE 31 :::::::::::::::::::::::::: d2foka2 20 IRILTLLEDGQHLTKFDLGKNLGFSG 45