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 | d1u5ta1 | Vacuolar sorting protein SNF8 | (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 <-- 0.696 --> HitDALI alignment (Z-score: 3.7 Raw score:163.60) d1ri7a1 1 ------------------------------------------------------------ 1 d1u5ta1 1 vnktilekqsvelrdqlmvfqerlvefakkhnselqaspefrskfmhmcssigidplslf 60 d1ri7a1 1 ------------lDEIDKKIIKILQND-----gKAPLREISKITG----LAESTIHERIR 39 :::::::::::::: :::::::::::: ::::::::::: d1u5ta1 61 drdkhlftvndfyYEVCLKVIEICRQTkdmnggVISFQELEKVHFrklnVGLDDLEKSID 120 d1ri7a1 40 KLRESGVIK----------kfTAIIdpealg 60 ::::::::: :::: d1u5ta1 121 MLKSLECFEifqirgkkflrsVPNE------ 145 FAST alignment (Normalized score: 3.58 Raw score:334.00) d1ri7a1 1 L----------------------------------------------------------- 1 d1u5ta1 1 -VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSL 59 d1ri7a1 2 --------------DEIDKKIIKILQN-----DGKAPLREISKI----TGLAESTIHERI 38 ::::::::::::: :::::::::::: :::::::::::: d1u5ta1 60 FDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKVHFRKLNVGLDDLEKSI 119 d1ri7a1 39 RKLRESGVIKKFTAIIDPEALG------------------ 60 :::::::: d1u5ta1 120 DMLKSLEC--------------FEIFQIRGKKFLRSVPNE 145 TMalign alignment (TM-score: 0.58 Raw score:34.79) d1ri7a1 1 ------------------------------------------------------------ 1 d1u5ta1 1 VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLF 60 d1ri7a1 1 ----------L--DEIDKKIIKILQ--N----DGKAPLREIS-KIT---GLAESTIHERI 38 : :::::::::::: : : :::::::: ::: ::::::::::: d1u5ta1 61 DRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGG-VISFQELEKVHFRKLNVGLDDLEKSI 119 d1ri7a1 39 RKLRESGVIKKF--------------TAIIDPEALG 60 :::: :: ::: ::: d1u5ta1 120 DMLK--SL-ECFEIFQIRGKKFLRSVPNE------- 145 HHsearch alignment (Probability: 0.00 E-value:0.49) d1ri7a1 14 NDGKAPLREISK----ITGLAESTIHERIRKLRESGVIKKFTAI 53 :::::::::::: :::::::::::::::::::: ::::: d1u5ta1 91 NGGVISFQELEKVHFRKLNVGLDDLEKSIDMLKSLE---CFEIF 131