HorA Server Result

References:
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 link
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 link
Comments and suggestions to: grishin@chop.swmed.edu


Query:
542d3.pdb
Mode:
Database search, accurate
Database:
SCOP1.69 less than 40% identity from ASTRAL
 
Scores:
dali   daliZ   gdtts   tmscore   rmsd   AHM   LBcontactA   LBcontactB   LHM   identity   blosum   compass   pearson  
Searches:
DALI   FAST   TMalign   HHsearch
Multiple sequence alignment
HHsearch hidden markov model

Mouse: rotate:Left; translate:Ctrl+Right; zoom:Middle

Downloads: 
PDB file 
PyMOL


Summary of Hits

Hits are found by three methods: Combined Score, SVM model and HHsearch. Hits are ordered by the combined score (Comb score). The combined scores is a similarity measure from sequence and structural similarities. A higher combined score (Comb score) indicates a higher probablity that the hit is homologous to the query.

top hits.
  
SVM score above .


Click the hit # to scroll down to alignments.   Download tab-delimited summary table.
Hit
#
SCOP Id Pro​tein Name SCOP​ Superfamily SCOP​ Fold SCOP
Class
Comb score SVM score HH prob DALI Z FAST SN TM​score
Domains with score better than the threshold ( Comb score > 2.0 OR SVM score > 0.6 OR HH prob > 0.9 )
1 d1ri7a1 Putative transcriptional regulator PH1519 "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 2.97 1.406 0.05 3.0 4.5 0.42
2 d1je8a_ Nitrate/​nitrite response regulator (NarL) C-​terminal effector domain of the bipartite response regulators DNA/​RNA-​binding 3-​helical bundle All α 2.57 0.907 0.04 3.2 5.0 0.44
3 d1uhsa_ Homeodomain-​only protein,​ Hop Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 2.49 0.632 0.03 3.5 4.2 0.49
4 d1a9xa1 Carbamoyl phosphate synthetase,​ large subunit connection domain Carbamoyl phosphate synthetase,​ large subunit connection domain Carbamoyl phosphate synthetase,​ large subunit connection domain All α 2.37 0.994 0.03 2.9 3.7 0.51
5 d1hcra_ HIN recombinase (DNA-​binding domain) Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 2.34 1.399 0.02 2.4 3.8 0.42
6 d1sfua_ 34L "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 2.18 0.905 0.02 3.3 4.8 0.46
7 d1u5ta2 Vacuolar sorting protein SNF8 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 2.05 0.901 0.01 2.7 3.9 0.43
8 d1mkma1 Transcriptional regulator IclR,​ N-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 2.04 0.908 0.11 2.3 4.9 0.46
9 d1fsea_ Germination protein GerE C-​terminal effector domain of the bipartite response regulators DNA/​RNA-​binding 3-​helical bundle All α 2.02 0.906 0.04 1.8 4.9 0.44
10 d1l3la1 Quorum-​sensing transcription factor TraR,​ C-​terminal domain C-​terminal effector domain of the bipartite response regulators DNA/​RNA-​binding 3-​helical bundle All α 1.94 0.899 0.04 1.9 5.0 0.43
11 d1sfxa_ Hypothetical protein AF2008 "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.92 0.901 0.03 3.0 4.1 0.45
12 d1igna1 DNA-​binding domain of rap1 Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.86 0.729 0.01 2.0 3.2 0.46
13 d1fjla_ Paired protein Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.85 0.728 0.01 2.8 4.5 0.48
14 d1on2a1 Manganese transport regulator MntR "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.80 1.311 0.04 1.6 4.6 0.41
15 d1lvaa3 C-​terminal fragment of elongation factor SelB "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.77 0.723 0.03 2.6 4.8 0.44
16 d1sfea1 Ada DNA repair protein Methylated DNA-​protein cysteine methyltransferase,​ C-​terminal domain DNA/​RNA-​binding 3-​helical bundle All α 1.59 0.724 0.01 1.9 3.1 0.44
17 d1qbja_ Z-​alpha domain of dsRNA-​specific adenosine deaminase,​ ADAR1 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.52 1.021 0.02 2.0 4.9 0.46
18 d1ldda_ Anaphase promoting complex (APC) ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.48 0.897 0.03 1.8 3.8 0.44
19 d1t56a1 Ethr repressor Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.45 0.902 0.03 2.3 2.8 0.40
20 d1in4a1 Holliday junction helicase RuvB "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.42 0.906 0.02 0.9 3.8 0.41
21 d1bl0a2 MarA Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.40 0.641 0.05 1.3 2.9 0.38
22 d1r71a_ Transcriptional repressor protein KorB DNA-​binding domain KorB DNA-​binding domain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.34 0.898 0.17 0.2 3.2 0.38
23 d1o57a1 N-​terminal domain of Bacillus PurR "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.29 0.895 0.01 0.8 4.6 0.46
24 d1biaa1 Biotin repressor,​ N-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.29 1.297 0.02 1.5 4.2 0.40
25 d1qdma1 (Pro)phytepsin Saposin Saposin-​like All α 1.25 0.726 0.02 1.8 3.2 0.43
26 d1j75a_ Dlm-​1 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.23 0.900 0.08 1.1 4.4 0.43
27 d1hlva1 DNA-​binding domain of centromere binding protein B (CENP-​B) Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.22 1.591 0.04 1.1 3.8 0.39
28 d1mgta1 O6-​alkylguanine-​DNA alkyltransferase Methylated DNA-​protein cysteine methyltransferase,​ C-​terminal domain DNA/​RNA-​binding 3-​helical bundle All α 1.22 0.903 0.00 1.6 3.7 0.42
29 d2bbya_ DNA-​binding domain from rap30 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.21 0.897 0.01 1.1 4.3 0.44
30 d1pb6a1 Hypothetical transcriptional regulator YcdC Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.18 0.904 0.02 1.9 3.0 0.26
31 d1j5ya1 Putative transcriptional regulator TM1602,​ N-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.18 1.541 0.10 1.2 4.7 0.44
32 d1rp3a1 Sigma factor sigma-​28 (FliA) Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/​RNA-​binding 3-​helical bundle All α 1.18 0.895 0.03 1.6 3.9 0.36
33 d1or7a1 SigmaE factor (RpoE) Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/​RNA-​binding 3-​helical bundle All α 1.17 1.037 0.05 5.4 0.42
34 d1dpua_ C-​terminal domain of RPA32 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.15 0.994 0.04 0.5 4.7 0.45
35 d1d5ya2 Rob transcription factor,​ N-​terminal domain Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.14 0.901 0.03 1.3 2.8 0.37
36 d1hsta_ Histone H5,​ globular domain ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.12 0.907 0.01 1.3 2.8 0.38
37 d1ufma_ COP9 signalosome complex subunit 4,​ GSN4 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.11 0.729 0.01 0.4 3.6 0.41
38 d1p6ra_ Penicillinase repressor BlaI "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.09 0.910 0.01 0.8 3.8 0.42
39 d1ucra_ Dissimilatory sulfite reductase DsvD "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.04 0.906 0.01 1.5 3.7 0.39
40 d1sd4a_ Penicillinase repressor BlaI "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 1.02 0.911 0.03 1.1 3.2 0.44
41 d1gdta1 gamma,​delta resolvase (C-​terminal domain) Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 0.95 1.647 0.15 4.6 0.39
42 d1bjaa_ Transcription factor MotA,​ activation domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.93 0.905 0.01 1.3 4.0 0.45
43 d1lvaa1 C-​terminal fragment of elongation factor SelB "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.91 0.723 0.01 0.1 4.5 0.44
44 d2foka2 Restriction endonuclease FokI,​ N-​terminal (recognition) domain ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.88 0.712 0.01 0.9 2.7 0.33
45 d1pdnc_ Paired protein (prd) Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 0.88 0.843 0.04 0.0 3.9 0.47
46 d1u78a2 Transposase tc3a1-​65 Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 0.88 1.664 0.02 4.9 0.40
47 d1u5tb2 Vacuolar protein sorting-​associated protein VPS36 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.78 0.899 0.01 0.7 4.4 0.44
48 d2foka3 Restriction endonuclease FokI,​ N-​terminal (recognition) domain ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.76 0.896 0.01 0.8 3.9 0.39
49 d1tqia1 Rio2 serine protein kinase N-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.75 0.906 0.05 0.5 3.7 0.42
50 d1rp3a2 Sigma factor sigma-​28 (FliA) Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/​RNA-​binding 3-​helical bundle All α 0.73 1.099 0.07 0.0 5.4 0.41
51 d1hw1a1 Fatty acid responsive transcription factor FadR,​ N-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.70 0.896 0.05 3.6 0.42
52 d1ft9a1 CO-​sensing protein CooA,​ C-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.69 0.910 0.02 0.5 3.5 0.42
53 d1tc3c_ Transposase tc3a1-​65 Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 0.68 1.664 0.01 4.9 0.42
54 d1hkqa_ Replication protein A,​ repA "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.58 0.728 0.01 1.0 1.9 0.44
55 d1smyf1 Sigma70 Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/​RNA-​binding 3-​helical bundle All α 0.54 0.906 0.03 3.7 0.37
56 d1lnwa_ MexR repressor "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.39 0.901 0.05 1.1 2.1 0.43
57 d1hq1a_ Signal sequence binding protein Ffh Signal peptide-​binding domain Signal peptide-​binding domain All α 0.37 0.866 0.01 0.0 4.0 0.44
58 d1gvda_ c-​Myb,​ DNA-​binding domain Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 0.33 0.896 0.01 0.0 3.6 0.41
59 d1fnna1 CDC6,​ C-​terminal domain "​Winged helix"​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.26 0.905 0.01 0.5 2.4 0.42
60 d1kqpa_ NH3-​dependent NAD+-​synthetase Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β 0.17 -0.531 0.94 0.0 1.5 0.35
61 d1mswd_ T7 RNA polymerase DNA/​RNA polymerases DNA/​RNA polymerases multi 0.12 0.897 0.01 0.9 1.0 0.33
62 d1u5ta1 Vacuolar sorting protein SNF8 ​(​Winged helix​(​ DNA-​binding domain DNA/​RNA-​binding 3-​helical bundle All α 0.09 0.703 0.00 0.4 1.2 0.36
63 d6paxa2 Pax-​6 Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 0.03 1.285 0.02 0.0 5.0 0.45
64 d1e3oc1 Oct-​1 POU Homeodomain Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α -0.03 0.763 0.01 0.0 4.1 0.46
65 d1ru8a_ Putative N-​type ATP pyrophosphatase PF0828 Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.08 -0.488 0.94 0.0 0.9 0.35
66 d1jgta1 beta-​Lactam synthetase Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.15 -0.566 0.94 0.0 1.1 0.38
67 d1q15a1 beta-​Lactam synthetase Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.19 -0.600 0.94 0.0 1.7 0.39
68 d1ni5a1 Putative cell cycle protein MesJ,​ N-​terminal domain Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.28 -0.485 0.94 0.0 0.9 0.35
69 d1ct9a1 Asparagine synthetase B,​ C-​terminal domain Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.30 -0.676 0.94 0.0 1.0 0.37
70 d1k92a1 Argininosuccinate synthetase,​ N-​terminal domain Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.43 -0.257 0.94 0.0 1.1 0.37
71 d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domain Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.44 -0.289 0.94 0.0 1.3 0.38
72 d1sura_ Phosphoadenylyl sulphate (PAPS) reductase Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.56 -0.424 0.94 0.0 1.0 0.28
73 d1gpma1 GMP synthetase,​ central domain Adenine nucleotide alpha hydrolases-​like Adenine nucleotide alpha hydrolase-​like α/β -0.70 -0.281 0.94 0.0 1.0 0.29
SCOP domains with score worse than the threshold
74 d1mija_ Homeo-​prospero domain of Prospero protein Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.47 0.558 0.01 3.0 2.9 0.55
75 d2ezha_ Transposase Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.35 -0.699 0.01 1.7 3.2 0.43
76 d1wdka1 Fatty oxidation complex alpha subunit,​ C-​terminal domain 6-​phosphogluconate dehydrogenase C-​terminal domain-​like 6-​phosphogluconate dehydrogenase C-​terminal domain-​like All α 1.32 -1.348 0.03 1.2 1.4 0.47
77 d1t4ga1 DNA repair protein Rad51,​ N-​terminal domain Rad51 N-​terminal domain-​like SAM domain-​like All α 1.29 -1.092 0.05 0.0 3.5 0.43
78 d1c20a_ DNA-​binding domain from the dead ringer protein ARID-​like DNA/​RNA-​binding 3-​helical bundle All α 1.23 -1.201 0.02 0.9 2.1 0.44
79 d2ezla_ Ibeta subdomain of the mu end DNA-​binding domain of phage mu transposase Homeodomain-​like DNA/​RNA-​binding 3-​helical bundle All α 1.13 -0.841 0.01 1.8 2.5 0.37
80 d1ikpa3 Exotoxin A,​ middle domain Exotoxin A,​ middle domain Toxins'​ membrane translocation domains mem 1.12 -0.854 0.02 1.1 2.8 0.49
81 d1kb4b_ Vitamin D3 receptor,​ VDR,​ DNA-​binding domain Glucocorticoid receptor-​like (DNA-​binding domain) Glucocorticoid receptor-​like (DNA-​binding domain) small 1.09 -1.282 0.01 1.0 1.9 0.38
82 d1f14a1 Short chain L-​3-​hydroxyacyl CoA dehydrogenase 6-​phosphogluconate dehydrogenase C-​terminal domain-​like 6-​phosphogluconate dehydrogenase C-​terminal domain-​like All α 1.04 -0.973 0.02 1.3 1.7 0.46
83 d1u9la_ Transcription elongation protein NusA Rad51 N-​terminal domain-​like SAM domain-​like All α 1.03 -1.425 0.10 0.8 3.5 0.42


Alignments and Scores

hit structures.    
residues per line.
   
all residues in one line.


hit structures. 
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1: d1ri7a1 Putative transcriptional regulator PH1519 (svm: 1.406)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.63  Contact: 208
Modified z-scores:
dali:0.96 daliz:0.96 gdtts:0.94 tmscore:0.95 rmsd:0.38 AHM:0.45 LBcontacta:0.85 LBcontactb:0.82 LHM:0.19
id:0.74 blosum:0.58 compass:0.69 pearson:0.96
Scaled scores:
dali:0.66 daliz:0.43 gdtts:0.54 tmscore:0.43 rmsd:0.66 AHM:0.56 LBcontacta:0.31 LBcontactb:0.35 LHM:0.34
id:0.03 blosum:0.10 compass:0.29 pearson:0.29

hit structure      alignment
DALI 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


hit structure      alignment
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


hit structure      alignment
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


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.06)
DALI match       ..............  *********  ****************
Query          4 PVLDAILELYVDRD--TGADAIVAA-GYDRELVVKTLRMVDTA     43
d1ri7a1        2 DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES     44



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2: d1je8a_ Nitrate/​nitrite response regulator (NarL) (svm: 0.907)

SCOP Superfamily: C-​terminal effector domain of the bipartite response regulators  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.53  Contact: 186
Modified z-scores:
dali:0.95 daliz:0.95 gdtts:0.91 tmscore:0.94 rmsd:0.43 AHM:0.31 LBcontacta:0.94 LBcontactb:0.95 LHM:0.32
id:0.85 blosum:0.43 compass:0.67 pearson:0.95
Scaled scores:
dali:0.73 daliz:0.52 gdtts:0.55 tmscore:0.46 rmsd:0.60 AHM:0.64 LBcontacta:0.49 LBcontactb:0.58 LHM:0.02
id:0.05 blosum:0.06 compass:0.27 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 3.2 Raw score:153.30)
Query          1 ----pdypvlDAILELYvDRDTGADAIVAA-GYDRELVVKTLRMVDTAEykrrqyppgtk     55
d1je8a_        1 rdvnqltpreRDILKLI-AQGLPNKMIARRlDITESTVKVHVKHMLKKM----klksrve     55

Query         56 isAKGFGKDRrlpitnrwregh     77
d1je8a_       56 aaVWVHQERI-----------f     66


hit structure      alignment
FAST alignment (Normalized score: 4.99 Raw score:355.50)
Query          1 PD------YPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG     53
d1je8a_        1 --RDVNQLTPRERDILKLI-AQGLPNKMIARRLDITESTVKVHVKHMLKK----------     47

Query         54 TKISAKGFGKDRRLPITNRWREGH---------------     77
d1je8a_       48 ---------------MKLK-----SRVEAAVWVHQERIF     66


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.82)
Query          1 -----PDYPVLDAILELYVDRDTGADAIVAA-GYDRELVVKTLRM--VD--TAEY--KR-     47
d1je8a_        1 RDVNQ-LTPRERDILKLI-AQGLPNKMIARRLDITESTVKVHV-KHMLKKMKLKSRV-EA     56

Query         48 -----RQYPPGTKIS-AKGFGKDRRLPITNRWREGH     77
d1je8a_       57 AVWVH------QERIF--------------------     66


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.09)
DALI match       ******.............****************
Query          8 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDT     42
d1je8a_       12 DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLK     46



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3: d1uhsa_ Homeodomain-​only protein,​ Hop (svm: 0.632)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.61  Contact: 179
Modified z-scores:
dali:0.95 daliz:0.96 gdtts:0.95 tmscore:0.96 rmsd:0.28 AHM:0.30 LBcontacta:0.92 LBcontactb:0.92 LHM:0.29
id:0.84 blosum:0.57 compass:0.66 pearson:0.96
Scaled scores:
dali:0.71 daliz:0.52 gdtts:0.59 tmscore:0.50 rmsd:0.75 AHM:0.69 LBcontacta:0.41 LBcontactb:0.48 LHM:0.29
id:0.05 blosum:0.09 compass:0.08 pearson:0.22

hit structure      alignment
DALI alignment (Z-score: 3.5 Raw score:178.30)
Query          1 -------PDYPVLDAILELYVDRD-----tGADAIVA-aGYDRELVVKTLRMVDTAEYKR     47
d1uhsa_        1 gsegaatMTEDQVEILEYNFNKVNkhpdptTLCLIAAeaGLTEEQTQKWFKQRLAEWRRS     60

Query         48 RQYppgtkisakgfgkdrrlpitnrwregh     77
d1uhsa_       61 EGL------------------psecrsvtd     72


hit structure      alignment
FAST alignment (Normalized score: 4.24 Raw score:316.00)
Query          1 -------PDYPVLDAILELYVDRDT-------GADAIVA-AGYDRELVVKTLRMVDTAEY     45
d1uhsa_        1 GSEGAATMTEDQVEILEYNFNKV--NKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR     58

Query         46 KRRQYPPGTKISAKGFGKDRRLPITNRWREGH------------     77
d1uhsa_       59 RS------------------------------EGLPSECRSVTD     72


hit structure      alignment
TMalign alignment (TM-score: 0.49 Raw score:37.70)
Query          1 -------PDYPVLDAILELYVDRDT-GAD-AIVAA-G---YDRELVVKTLRMVDTA-EYK     46
d1uhsa_        1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR-     59

Query         47 RRQYPPGTKISAKGFGKDRRLPITN------RWREGH     77
d1uhsa_       60 -S-----------------EGLPSECRSVTD------     72


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.17)
DALI match       ......... *      ******* ........................         
Query          8 AILELYVDR-DT-----GADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK     59
d1uhsa_       14 EILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECRSVT     71



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4: d1a9xa1 Carbamoyl phosphate synthetase,​ large subunit connection domain (svm: 0.994)

SCOP Superfamily: Carbamoyl phosphate synthetase,​ large subunit connection domain  |  SCOP Fold: Carbamoyl phosphate synthetase,​ large subunit connection domain  |  SCOP Class: All alpha proteins

Consensus: 0.49  Contact: 192
Modified z-scores:
dali:0.96 daliz:0.97 gdtts:0.94 tmscore:0.95 rmsd:0.45 AHM:0.53 LBcontacta:0.91 LBcontactb:0.90 LHM:0.36
id:0.87 blosum:0.73 compass:0.61 pearson:0.96
Scaled scores:
dali:0.76 daliz:0.55 gdtts:0.59 tmscore:0.52 rmsd:0.64 AHM:0.57 LBcontacta:0.43 LBcontactb:0.44 LHM:0.22
id:0.04 blosum:0.13 compass:0.26 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 2.9 Raw score:187.80)
Query          1 ----------------------------pDYPVLDAILELYVdRDTGADAIVAAG-YDRE     31
d1a9xa1        1 evgatgfdpkvslddpealtkirrelkdaGADRIWYIADAFR-AGLSVDGVFNLTnIDRW     59

Query         32 LVVKTLRMVDTA-EYKR--------------------------RQYPPGT----------     54
d1a9xa1       60 FLVQIEELVRLEeKVAEvgitglnadflrqlkrkgfadarlakLAGVREAeirklrdqyd    119

Query         55 -----------kisakgfgkdrrlpitnrwregh     77
d1a9xa1      120 lhpvykrvdtcaaefatdtaymystyeeeceanp    153


hit structure      alignment
FAST alignment (Normalized score: 3.74 Raw score:406.40)
Query          1 PDY-------------------------------PVLDAILELYVDRDTGADAIVA-AGY     28
d1a9xa1        1 ---EVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFR-AGLSVDGVFNLTNI     56

Query         29 DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-----------     77
d1a9xa1       57 DRWFLVQIEELVRLEEKVAEV----------------------------GITGLNADFLR     88

Query         78 ------------------------------------------------------------     78
d1a9xa1       89 QLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEE    148

Query         78 -----     78
d1a9xa1      149 CEANP    153


hit structure      alignment
TMalign alignment (TM-score: 0.51 Raw score:39.02)
Query          1 ------PD-----------------------YPVLDAILELYVDRDTGADAIVAAGYD-R     30
d1a9xa1        1 EVGATG-FDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRA-GLSVDGVFNLTNIDR     58

Query         31 ELVVKTLRMVDTA-EYKRR-Q-------------------------YPP-----------     52
d1a9xa1       59 WFLVQIEELVRLEEK-VAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQ    117

Query         53 ------------------------------------GTKISAKGFGKDRRLPITNRWREG     76
d1a9xa1      118 YDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANP------------------------    153

Query         77 H     77
d1a9xa1      154 -    154


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.17)
DALI match       ...... ********** ..****************.
Query          9 ILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAE     44
d1a9xa1       36 YIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEE     72



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5: d1hcra_ HIN recombinase (DNA-​binding domain) (svm: 1.399)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.56  Contact: 150
Modified z-scores:
dali:0.94 daliz:0.94 gdtts:0.92 tmscore:0.95 rmsd:0.28 AHM:0.34 LBcontacta:0.92 LBcontactb:0.94 LHM:0.17
id:0.86 blosum:0.57 compass:0.64 pearson:0.90
Scaled scores:
dali:0.67 daliz:0.41 gdtts:0.54 tmscore:0.42 rmsd:0.75 AHM:0.63 LBcontacta:0.40 LBcontactb:0.53 LHM:0.31
id:0.07 blosum:0.11 compass:0.07 pearson:0.18

hit structure      alignment
DALI alignment (Z-score: 2.4 Raw score:121.00)
Query          1 -----PDYPVLDAILELYVdRDTGADAIVAaGYDRElvVKTLRMVDtaeykrrqyppgtk     55
d1hcra_        1 grpraINKHEQEQISRLLE-KGHPRQQLAI-IFGIG-vSTLYRYFP--------------     43

Query         56 isakgfgkdrrLPITNRwregh     77
d1hcra_       44 ----------aSSIKKR---mn     52


hit structure      alignment
FAST alignment (Normalized score: 3.79 Raw score:240.20)
Query          1 P------DYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG     53
d1hcra_        1 -GRPRAINKHEQEQISRLLE-KGHPRQQLAIIFGIGVSTLYRYF----------------     42

Query         54 TKISAKGFGKDRRLPITNRWREGH----------     77
d1hcra_       43 ------------------------PASSIKKRMN     52


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.12)
Query          1 -----PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVKTLRMVDTAEYKRRQYPPGT     54
d1hcra_        1 GRPRAINKHEQEQISRLLEK-GHPRQQLAIIFGIGVSTLYRYFP--AS------------     45

Query         55 KISAKGFGKDRRLPITNRWR----EGH     77
d1hcra_       46 -----------------SIKKRMN---     52


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.10)
DALI match       ....... **********.
Query          8 AILELYVDRDTGADAIVAA     26
d1hcra_       12 EQISRLLEKGHPRQQLAII     30



hit structures. 
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6: d1sfua_ 34L (svm: 0.905)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.54  Contact: 219
Modified z-scores:
dali:0.94 daliz:0.95 gdtts:0.93 tmscore:0.95 rmsd:0.22 AHM:0.26 LBcontacta:0.84 LBcontactb:0.77 LHM:0.21
id:0.85 blosum:0.77 compass:0.69 pearson:0.93
Scaled scores:
dali:0.71 daliz:0.52 gdtts:0.64 tmscore:0.54 rmsd:0.77 AHM:0.70 LBcontacta:0.37 LBcontactb:0.43 LHM:0.30
id:0.06 blosum:0.13 compass:0.08 pearson:0.19

hit structure      alignment
DALI alignment (Z-score: 3.3 Raw score:163.90)
Query          1 ---pDYPVLDAILELyVDRD-----TGADAIVAA-GYDRELVVKTLRMVDTAEykrrqyp     51
d1sfua_        1 ctvnDAEIFSLVKKE-VLSLntndyTTAISLSNRlKINKKKINQQLYKLQKED--tvkmv     57

Query         52 pgtkisakGFGKdrrlpitnrwregh     77
d1sfua_       58 psnppkwfKNYN-------------c     70


hit structure      alignment
FAST alignment (Normalized score: 4.85 Raw score:355.90)
Query          1 ---PDYPVLDAILELYVD-----RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYP     51
d1sfua_        1 CTVNDAEIFSLVKKEVL-SLNTNDYTTAISLSNRLKINKKKINQQLYKLQK---------     50

Query         52 PGTKISA--------------KGFGKDRRLPITNRWREGH--     77
d1sfua_       51 -------EDTVKMVPSNPPKWFKNY---------------NC     70


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.51)
Query          1 ----PDYPVLDAILELYVDR----DTGADAIVAA-GYDRELVVKTLRMVDTAEYKR----     47
d1sfua_        1 CTVNDAE-IFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKED--TVKMV     57

Query         48 --------RQYPPGTKISAKGFGKDRR-LPITNRWREGH     77
d1sfua_       58 PSNPPKWF------------KN---YNC-----------     70


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.21)
DALI match       .......... .............  ******************           
Query          3 YPVLDAILELYVDRDTGADAIVAA--GYDRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1sfua_        9 FSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSNPPK     63



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7: d1u5ta2 Vacuolar sorting protein SNF8 (svm: 0.901)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.54  Contact: 175
Modified z-scores:
dali:0.93 daliz:0.95 gdtts:0.91 tmscore:0.93 rmsd:0.29 AHM:0.32 LBcontacta:0.92 LBcontactb:0.93 LHM:0.23
id:0.92 blosum:0.77 compass:0.67 pearson:0.95
Scaled scores:
dali:0.70 daliz:0.45 gdtts:0.58 tmscore:0.44 rmsd:0.69 AHM:0.62 LBcontacta:0.45 LBcontactb:0.63 LHM:0.24
id:0.09 blosum:0.12 compass:0.16 pearson:0.24

hit structure      alignment
DALI alignment (Z-score: 2.7 Raw score:142.40)
Query          1 pdYPVLDAILELY-vdRDTGADAIVAA-GYDRELVVKTLRMVDTAE--ykrrqyppgtki     56
d1u5ta2        1 -lTSDQTKILEICsilGYSSISLLKANlGWEAVRSKSALDEMVANGllwidyqggaealy     59

Query         57 saKGFGKdrrlpitnrwregh     77
d1u5ta2       60 wdPSWIT------------rq     68


hit structure      alignment
FAST alignment (Normalized score: 3.85 Raw score:278.80)
Query          1 PDYPVLDAILELYVD---RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKI     56
d1u5ta2        1 -LTSDQTKILEIC--SILGYSSISLLKANLGWEAVRSKSALDEMVA--------------     43

Query         57 SAKGFGKDRRLPITNRWREGH-------------------------     77
d1u5ta2       44 ---------------------NGLLWIDYQGGAEALYWDPSWITRQ     68


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:33.29)
Query          1 -PDYPVL-DAILELYVD--RDTGADAIVAA-GYDRELVVKTLRMVDTAEYKR--------     47
d1u5ta2        1 L-TS--DQTKILEIC-SILGYSSISLLKANLGWEAVRSKSALDEMVANG--LLWIDYQGG     54

Query         48 -----RQYPPGTKISAKGFG-KDR--RLPITNRWREGH     77
d1u5ta2       55 AEALY-----------WDPSW-ITRQ------------     68


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.30)
DALI match                
Query         20 ADAIVAAGY     28
d1u5ta2       38 LDEMVANGL     46



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8: d1mkma1 Transcriptional regulator IclR,​ N-​terminal domain (svm: 0.908)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.53  Contact: 138
Modified z-scores:
dali:0.86 daliz:0.86 gdtts:0.88 tmscore:0.90 rmsd:0.31 AHM:0.30 LBcontacta:0.79 LBcontactb:0.86 LHM:0.19
id:0.73 blosum:0.47 compass:0.66 pearson:0.92
Scaled scores:
dali:0.71 daliz:0.42 gdtts:0.53 tmscore:0.43 rmsd:0.72 AHM:0.68 LBcontacta:0.37 LBcontactb:0.51 LHM:0.36
id:0.03 blosum:0.05 compass:0.09 pearson:0.23

hit structure      alignment
DALI alignment (Z-score: 2.3 Raw score:125.50)
Query          1 --PDYPvLDAILE--lyvdrDTGADAIVAA-GYDRELVVKTLRMVDTAE-----------     44
d1mkma1        1 mnTLKK-AFEILDfivknpgDVSVSEIAEKfNMSVSNAYKYMVVLEEKGfvlrkkdkryv     59

Query         45 -yKRRQY--PPGTkisakgfgkdrrlpitnrwregh     77
d1mkma1       60 pgYKLIEygSFVL--------------------rrf     75


hit structure      alignment
FAST alignment (Normalized score: 4.87 Raw score:370.30)
Query          1 P--DYPVLDAILELYV--DRDTGADAIVA-AGYDRELVVKTLRMVDT-------------     42
d1mkma1        1 -MNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYV     59

Query         43 AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------     77
d1mkma1       60 PGYKLIE----------------------------YGSFVLRRF     75


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.56)
Query          1 -PDYPVLDAILELYVDR--DTGADAIVAA-GYDRELVVKTLRMVDTAE------------     44
d1mkma1        1 MNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVP     60

Query         45 --YKR-RQY-PPGT---KISAKGFGKDRRLPITNRWREGH     77
d1mkma1       61 GY--KLIEYGSFVLRRF-----------------------     75


hit structure      alignment
HHsearch alignment (Probability: 0.11 E-value:0.01)
DALI match       ****     .  ********* ******************                
Query          8 AILELYVDRD--TGADAIVAA-GYDRELVVKTLRMVDTAEY----KRRQYPPGTKI     56
d1mkma1        9 EILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKL     64



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9: d1fsea_ Germination protein GerE (svm: 0.906)

SCOP Superfamily: C-​terminal effector domain of the bipartite response regulators  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.46  Contact: 159
Modified z-scores:
dali:0.85 daliz:0.81 gdtts:0.83 tmscore:0.87 rmsd:0.40 AHM:0.41 LBcontacta:0.81 LBcontactb:0.83 LHM:0.22
id:0.74 blosum:0.41 compass:0.35 pearson:0.86
Scaled scores:
dali:0.62 daliz:0.31 gdtts:0.42 tmscore:0.33 rmsd:0.66 AHM:0.60 LBcontacta:0.31 LBcontactb:0.38 LHM:0.15
id:0.03 blosum:0.04 compass:0.15 pearson:0.13

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:124.80)
Query          1 ---pdYPVLDAILELYvDRDTGADAIVAAgYDRElVVKTLRMVDT-AEYKRR------qy     50
d1fsea_        1 skpllTKREREVFELL-VQDKTTKEIASE-LFIS-EKTVRNHISNaMQKLGVkgrsqavv     57

Query         51 ppgTKISakgfgkdrrlpitnrwregh     77
d1fsea_       58 ellRMGE-----------------lel     67


hit structure      alignment
FAST alignment (Normalized score: 4.91 Raw score:352.50)
Query          1 P----DYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1fsea_        1 -SKPLLTKREREVFELL-VQDKTTKEIASELFISEKTVRNHISNAMQK------------     46

Query         56 ISAKGFGKDRRLPITNRWREGH-----------------     77
d1fsea_       47 -------------LGVK-----GRSQAVVELLRMGELEL     67


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.58)
Query          1 ----PDYPVLDAILELYVDRDTGADAIVAA-GYDRELVVK-TL--RM----VDTA-E--Y     45
d1fsea_        1 SKPL-LTKREREVFELLV-QDKTTKEIASELFISEKTVRNHISNA-MQKLGVKGRSQAV-     56

Query         46 KRRQY--PPGTK-ISAKGFGKDRRLPITNRWREGH     77
d1fsea_       57 -V--ELL--RMGELEL-------------------     67


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.10)
DALI match       ******............. .... ..........
Query          8 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDT     42
d1fsea_       11 EVFELLVQDKTTKEIASELFISEKTVRNHISNAMQ     45



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10: d1l3la1 Quorum-​sensing transcription factor TraR,​ C-​terminal domain (svm: 0.899)

SCOP Superfamily: C-​terminal effector domain of the bipartite response regulators  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.52  Contact: 153
Modified z-scores:
dali:0.86 daliz:0.83 gdtts:0.81 tmscore:0.87 rmsd:0.41 AHM:0.41 LBcontacta:0.85 LBcontactb:0.88 LHM:0.22
id:0.63 blosum:0.23 compass:0.61 pearson:0.73
Scaled scores:
dali:0.64 daliz:0.33 gdtts:0.41 tmscore:0.34 rmsd:0.65 AHM:0.59 LBcontacta:0.35 LBcontactb:0.44 LHM:0.11
id:-0.01 blosum:-0.01 compass:0.02 pearson:0.05

hit structure      alignment
DALI alignment (Z-score: 1.9 Raw score:118.20)
Query          1 ---pdYPVLDAILELYvDRDTGADAIVAAgYDRElvVKTLRMVDT-AEYKRR-----qyp     51
d1l3la1        1 daawlDPKEATYLRWI-AVGKTMEEIADV-EGVK-yNSVRVKLREaMKRFDVrskahlta     57

Query         52 pgtKISAkgfgkdrrlpitnrwregh     77
d1l3la1       58 laiRRKL------------------i     65


hit structure      alignment
FAST alignment (Normalized score: 4.96 Raw score:351.20)
Query          1 P----DYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1l3la1        1 -DAAWLDPKEATYLRWI-AVGKTMEEIADVEGVKYNSVRVKLREAMKR------------     46

Query         56 ISAKGFGKDRRLPITNRWREGH---------------     77
d1l3la1       47 -------------FDVR-----SKAHLTALAIRRKLI     65


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:32.99)
Query          1 ----PDYPVLDAILELYVDRDTGADAIVAA-GYDRELVVKTLRM--VD--TAEY--KRR-     48
d1l3la1        1 DAAW-LDPKEATYLRWI-AVGKTMEEIADVEGVKYNSVRVKL-REAMKRFDVRSKA--HL     55

Query         49 QYPPGTKISAKGFG-------KDRRLPITNRWREGH     77
d1l3la1       56 -----------TALAIRRKLI---------------     65


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.09)
DALI match       ******............. ....  .........
Query          8 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDT     42
d1l3la1       11 TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMK     45



hit structures. 
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11: d1sfxa_ Hypothetical protein AF2008 (svm: 0.901)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.51  Contact: 172
Modified z-scores:
dali:0.89 daliz:0.90 gdtts:0.89 tmscore:0.91 rmsd:0.50 AHM:0.56 LBcontacta:0.77 LBcontactb:0.76 LHM:0.32
id:0.91 blosum:0.73 compass:0.68 pearson:0.95
Scaled scores:
dali:0.73 daliz:0.50 gdtts:0.52 tmscore:0.43 rmsd:0.59 AHM:0.47 LBcontacta:0.37 LBcontactb:0.43 LHM:0.20
id:0.08 blosum:0.12 compass:0.07 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 3.0 Raw score:170.00)
Query          1 ----------------pdYPVLDAILELYVD-RDTGADAIVAA-GYDRELVVKTLRMVDT     42
d1sfxa_        1 hmsnplgelvkaleklsfKPSDVRIYSLLLErGGMRVSEIARElDLSARFVRDRLKVLLK     60

Query         43 AE------------------------yKRRQY--PPGTkisakgfgkdrrlpitnrwreg     76
d1sfxa_       61 RGfvrreivekgwvgyiysaekpekvlKEFKSsiLGEI------------eriekmftdg    108

Query         77 h     77
d1sfxa_      109 s    109


hit structure      alignment
FAST alignment (Normalized score: 4.08 Raw score:374.00)
Query          1 PD------------------YPVLDAILELYVD-RDTGADAIVA-AGYDRELVVKTLRMV     40
d1sfxa_        1 --HMSNPLGELVKALEKLSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVL     58

Query         41 DT-------------------------AEYKRRQYPPGTKISAKGFGKDRRLPITNRWRE     75
d1sfxa_       59 LKRGFVRREIVEKGWVGYIYSAEKPEKVLKEFKS--------------------------     92

Query         76 GH-----------------     77
d1sfxa_       93 --SILGEIERIEKMFTDGS    109


hit structure      alignment
TMalign alignment (TM-score: 0.45 Raw score:34.40)
Query          1 -----------------PDYPVL-DAILELYVD-RD-TGADAIVAA-GYDRELVVKTLRM     39
d1sfxa_        1 HMSNPLGELVKALEKLSFKP--SDVRIYSLL-LERGGMRVSEIARELDLSARFVRDRLKV     57

Query         40 VDTAE------------------YKRRQYPPGTKISAKGFGK------------------     63
d1sfxa_       58 LLKRGFVRREIVEKGWVGYIYSA--------------EKPEKVLKEFKSSILGEIERIEK    103

Query         64 ------DRRLPITNRWREGH     77
d1sfxa_      104 MFTDGS--------------    109


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.08)
DALI match       ******** *********** ******************     
Query          8 AILELYVD-RDTGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQ     49
d1sfxa_       24 RIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE     67



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12: d1igna1 DNA-​binding domain of rap1 (svm: 0.729)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.40  Contact: 228
Modified z-scores:
dali:0.93 daliz:0.89 gdtts:0.90 tmscore:0.93 rmsd:0.43 AHM:0.51 LBcontacta:0.69 LBcontactb:0.63 LHM:0.22
id:0.77 blosum:0.20 compass:0.56 pearson:0.69
Scaled scores:
dali:0.65 daliz:0.32 gdtts:0.47 tmscore:0.38 rmsd:0.70 AHM:0.62 LBcontacta:0.20 LBcontactb:0.20 LHM:0.30
id:0.01 blosum:0.02 compass:0.01 pearson:0.03

hit structure      alignment
DALI alignment (Z-score: 2.0 Raw score:132.70)
Query          1 ---PDYPVLDAILELYVDRD---tGADAIVAAG------yDRELVVKTLRMVDTA-----     43
d1igna1        1 kasFTDEEDEFILDVVRKNPtrrtTHTLYDEIShyvpnhtGNSIRHRFRVYLSKRleyvy     60

Query         44 --eykrrqyppgTKISAKgfGKDRRlpitnrwregh     77
d1igna1       61 evdkfgklvrddDGNLIK--TKVLP--------psi     86


hit structure      alignment
FAST alignment (Normalized score: 3.23 Raw score:262.90)
Query          1 ---PDYPVLDAILELYVDRDT---------GADAIVA--AGYDRELVVKTL-RMVDTAEY     45
d1igna1        1 KASFTDEEDEFILDVVRK---NPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSK---     54

Query         46 KRRQYPPGTK--------------------ISAKGFGKDRRLPITNRWREGH-------     77
d1igna1       55 ----------RLEYVYEVDKFGKLVRDDDGNLIKT-----------------KVLPPSI     86


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.07)
Query          1 ---PDYPVLDAILELYVDRD--T-----GADAIVAAGY-DR-ELVVKTLRM--VDTA--E     44
d1igna1        1 KASFTDEEDEFILDVV-RKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLS--KRL-     56

Query         45 YKR------------------RQYPPGTKISAKGFGKDRRL--PITNRWREGH     77
d1igna1       57 --EYVYEVDKFGKLVRDDDGN---------LIKT-K-VLPPSI----------     86


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.15)
DALI match       ..........
Query          7 DAILELYVDR     16
d1igna1        9 DEFILDVVRK     18



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13: d1fjla_ Paired protein (svm: 0.728)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.48  Contact: 167
Modified z-scores:
dali:0.90 daliz:0.88 gdtts:0.93 tmscore:0.95 rmsd:0.30 AHM:0.42 LBcontacta:0.83 LBcontactb:0.88 LHM:0.28
id:0.49 blosum:0.33 compass:0.41 pearson:0.93
Scaled scores:
dali:0.68 daliz:0.41 gdtts:0.59 tmscore:0.50 rmsd:0.76 AHM:0.66 LBcontacta:0.34 LBcontactb:0.41 LHM:0.28
id:-0.02 blosum:0.03 compass:0.17 pearson:0.17

hit structure      alignment
DALI alignment (Z-score: 2.8 Raw score:142.00)
Query          1 ------PDYPvlDAILELYVDRD--------tGADAIVAA-GYDRELVVKTLRMVDTAEY     45
d1fjla_        1 kqrrsrTTFS--ASQLDELERAFertqypdiyTREELAQRtNLTEARIQVWFQNRRARLR     58

Query         46 KRRQYPPgtkisakgfgkdrrlpitnrwregh     77
d1fjla_       59 KQHTSVS-------------------------     65


hit structure      alignment
FAST alignment (Normalized score: 4.48 Raw score:317.00)
Query          1 --------PDYPVLDAILELYVDRDT---------GADAIVA-AGYDRELVVKTLRMVDT     42
d1fjla_        1 KQRRSRTTFSASQLDELERAF-----ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRA     55

Query         43 AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--     77
d1fjla_       56 RLRKQHTS---------------------------VS     65


hit structure      alignment
TMalign alignment (TM-score: 0.48 Raw score:37.10)
Query          1 --------PDYPVLDAILELYVDRD-TGAD-AIVAAGY-----DRELVVKTLRMVDTA-E     44
d1fjla_        1 KQRRSRTTFSASQLDELERA-FERTQYPDIYTRE-ELAQRTNLTEARIQVWFQNRRARLR     58

Query         45 YKRR--QYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1fjla_       59 KQ-HTSVS---------------------------     65


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.58)
DALI match                             
Query          2 DYPVLDAILELYVDRDTGADAI     23
d1fjla_       25 QYPDIYTREELAQRTNLTEARI     46



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14: d1on2a1 Manganese transport regulator MntR (svm: 1.311)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.56  Contact: 128
Modified z-scores:
dali:0.82 daliz:0.86 gdtts:0.84 tmscore:0.84 rmsd:0.27 AHM:0.34 LBcontacta:0.82 LBcontactb:0.84 LHM:0.14
id:0.91 blosum:0.88 compass:0.75 pearson:0.94
Scaled scores:
dali:0.64 daliz:0.45 gdtts:0.56 tmscore:0.40 rmsd:0.68 AHM:0.53 LBcontacta:0.43 LBcontactb:0.47 LHM:0.43
id:0.10 blosum:0.18 compass:0.26 pearson:0.34

hit structure      alignment
DALI alignment (Z-score: 1.6 Raw score:124.40)
Query          1 pDYPVLDAILELYVDRD-----TGADAIVAA-GYDRElvvKTLRMVDtaeykrrqyppgt     54
d1on2a1        1 -TTPSMEMYIEQIYMLIeekgyARVSDIAEAlAVHPSsvtKMVQKLD-------------     46

Query         55 kisakgfgkdrrlpitnrwregh     77
d1on2a1       47 --------kdeyliyekyrglvl     61


hit structure      alignment
FAST alignment (Normalized score: 4.60 Raw score:315.00)
Query          1 PDYPVLDAILELYVD-----RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGT     54
d1on2a1        1 -TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDK------------     47

Query         55 KISAKGFGKDRRLPITNRWREGH--------------     77
d1on2a1       48 -----------------------DEYLIYEKYRGLVL     61


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:31.75)
Query          1 -PDYPVL-DAILELYVDR-D-----TGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYP     51
d1on2a1        1 T-TP--SMEMYIEQI-YMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDE-------     49

Query         52 PGTKISAKGFGKDRRLPITN-RW---RE--GH     77
d1on2a1       50 ---------Y----LI---YE-KYRG-LVL--     61


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.09)
DALI match       .............. ********* *****   *******    
Query          4 PVLDAILELYVDRD-TGADAIVAA-GYDRELVVKTLRMVDTAEY     45
d1on2a1        7 MYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEY     50



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15: d1lvaa3 C-​terminal fragment of elongation factor SelB (svm: 0.723)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.61  Contact: 151
Modified z-scores:
dali:0.91 daliz:0.91 gdtts:0.91 tmscore:0.93 rmsd:0.21 AHM:0.23 LBcontacta:0.86 LBcontactb:0.74 LHM:0.15
id:0.73 blosum:0.69 compass:0.68 pearson:0.97
Scaled scores:
dali:0.60 daliz:0.46 gdtts:0.60 tmscore:0.49 rmsd:0.77 AHM:0.69 LBcontacta:0.39 LBcontactb:0.33 LHM:0.42
id:0.03 blosum:0.12 compass:0.06 pearson:0.32

hit structure      alignment
DALI alignment (Z-score: 2.6 Raw score:134.90)
Query          1 ---pDYPVLDAILELYVDR---DTGADAIVAA-GYDRELVVKTLRMVDTAEykrrqyppg     53
d1lvaa3        1 fsetQKKLLKDLEDKYRVSrwqPPSFKEVAGSfNLDPSELEELLHYLVREG---------     51

Query         54 tkisakgfgkdrrlpitnrwregh     77
d1lvaa3       52 -----------vlvkindefywhr     64


hit structure      alignment
FAST alignment (Normalized score: 4.79 Raw score:336.70)
Query          1 P----DYPVLDAILELYVDR----DTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYP     51
d1lvaa3        1 -FSETQKKLLKDLEDKYRV-SRWQPPSFKEVAGSFNLDPSELEELLHYLVR---------     49

Query         52 PGTKISAKGFGKDRRLPITNRWREGH---------------     77
d1lvaa3       50 --------------------------EGVLVKINDEFYWHR     64


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.74)
Query          1 ---PDYPVLDAILELYVD-R---DTGADAIVAAGYDR-ELVVKTLRMVDTAEYKRRQYPP     52
d1lvaa3        1 FSETQKKLLKDLEDKY-RVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREG--------     51

Query         53 GTKISAKGFGKDRRLPITNRWREG-----H     77
d1lvaa3       52 --------V----LV---K-INDEFYWHR-     64


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.04)
DALI match                                
Query         20 ADAIVAAGYDRELVVKTLRMVDTAE     44
d1lvaa3       13 EDKYRVSRWQPPSFKEVAGSFNLDP     37



hit structures. 
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16: d1sfea1 Ada DNA repair protein (svm: 0.724)

SCOP Superfamily: Methylated DNA-​protein cysteine methyltransferase,​ C-​terminal domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 177
Modified z-scores:
dali:0.90 daliz:0.93 gdtts:0.92 tmscore:0.93 rmsd:0.34 AHM:0.39 LBcontacta:0.73 LBcontactb:0.80 LHM:0.20
id:0.47 blosum:0.42 compass:0.42 pearson:0.88
Scaled scores:
dali:0.72 daliz:0.46 gdtts:0.60 tmscore:0.48 rmsd:0.69 AHM:0.61 LBcontacta:0.31 LBcontactb:0.43 LHM:0.33
id:-0.03 blosum:0.04 compass:0.17 pearson:0.18

hit structure      alignment
DALI alignment (Z-score: 1.9 Raw score:130.60)
Query          1 pDYPVLDAILELYVDR----dTGADAIVAAG---yDRELVVKTLRMVdtaeykrrqyppg     53
d1sfea1        1 -GTAFQQQVWQALRTIpcgetVSYQQLANAIgkpkAVRAVASACAAN----klaivipch     55

Query         54 tkisakgfgkdrrLPITNRW-----regh     77
d1sfea1       56 rvvrgdgslsgyrWGVSRKAqllrreaen     84


hit structure      alignment
FAST alignment (Normalized score: 3.09 Raw score:248.70)
Query          1 PDYPVLDAILELYVD-----RDTGADAIVA-AGY--DRELVVKTLRMVDT----------     42
d1sfea1        1 -GTAFQQQVWQALR-TIPCGETVSYQQLANAIGKPKAVRAVASACAA---NKLAIVIPCH     55

Query         43 --------------AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------     77
d1sfea1       56 RVVRGDGSLSGYRWGVSRKA-----------------------------QLLRREAEN     84


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:34.02)
Query          1 PDYPVLDAILELYVDRD----TG-ADAIVAA-GY--DRELVVKTLRMVDTAEYKRRQYPP     52
d1sfea1        1 -GTAFQQQVWQAL-RTIPCGETVSYQQLANAIGKPKAVRAVASACAAN--K---LA----     49

Query         53 GTKISAKGFGKDR-RL-----------PITNRW-R----------EGH     77
d1sfea1       50 -------IVI--PC-HRVVRGDGSLSGYRWGVSRKAQLLRREAEN---     84


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.78)
DALI match                   
Query         31 ELVVKTLRMVDT     42
d1sfea1        3 AFQQQVWQALRT     14



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17: d1qbja_ Z-​alpha domain of dsRNA-​specific adenosine deaminase,​ ADAR1 (svm: 1.021)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.55  Contact: 162
Modified z-scores:
dali:0.84 daliz:0.88 gdtts:0.90 tmscore:0.90 rmsd:0.20 AHM:0.18 LBcontacta:0.78 LBcontactb:0.69 LHM:0.10
id:0.89 blosum:0.86 compass:0.71 pearson:0.92
Scaled scores:
dali:0.66 daliz:0.50 gdtts:0.70 tmscore:0.53 rmsd:0.77 AHM:0.71 LBcontacta:0.42 LBcontactb:0.41 LHM:0.50
id:0.11 blosum:0.18 compass:0.15 pearson:0.28

hit structure      alignment
DALI alignment (Z-score: 2.0 Raw score:124.00)
Query          1 -PDYPVLDAILELyVDRD-----TGADAIVAA-GYDRelVVKTLRMVDtaeykrrqyppg     53
d1qbja_        1 sIYQDQEQRILKF-LEELgegkaTTAHDLSGKlGTPKkeINRVLYSLA------------     47

Query         54 tkisakgfgkdrrlpitnrwregh     77
d1qbja_       48 ------kkgklqkeagtpplwkia     65


hit structure      alignment
FAST alignment (Normalized score: 4.86 Raw score:343.60)
Query          1 -PDYPVLDAILELYV----DRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGT     54
d1qbja_        1 SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAK------------     48

Query         55 KISAKGFGKDRRLPITNRWREGH-----------------     77
d1qbja_       49 -----------------------KGKLQKEAGTPPLWKIA     65


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.53)
Query          1 PD-YPVLDAILELYVD-R----DTGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYPPG     53
d1qbja_        1 SIYQDQEQRILKFL-EELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKG---------     50

Query         54 TKISAKGFGKDRRLP-ITNRWR--EG----H     77
d1qbja_       51 -------K----LQKE----AGTPPLWKIA-     65


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.13)
DALI match       ****  *********                  
Query         27 GYDRELVVKTLRMVDTAEYKRRQY--PPGTKIS     57
d1qbja_       33 GTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIA     65



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18: d1ldda_ Anaphase promoting complex (APC) (svm: 0.897)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 186
Modified z-scores:
dali:0.85 daliz:0.81 gdtts:0.86 tmscore:0.88 rmsd:0.35 AHM:0.42 LBcontacta:0.80 LBcontactb:0.82 LHM:0.16
id:0.61 blosum:0.21 compass:0.56 pearson:0.54
Scaled scores:
dali:0.62 daliz:0.31 gdtts:0.48 tmscore:0.37 rmsd:0.73 AHM:0.62 LBcontacta:0.31 LBcontactb:0.40 LHM:0.35
id:0.01 blosum:0.02 compass:0.01 pearson:0.01

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:133.20)
Query          1 PDYPVLDAILELYVDRD---------tGADAIVAAG----yDRELvVKTLRMVDTA-EYK     46
d1ldda_        1 KYELTLQRSLPFIEGMLtnlgamklhkIHSFLKITVpkdwgYNRItLQQLEGYLNTlADE     60

Query         47 RrqyppgtkisakgfgkdrrlpiTNRW-regh     77
d1ldda_       61 G------------------rlkyIANGsyeiv     74


hit structure      alignment
FAST alignment (Normalized score: 3.82 Raw score:288.60)
Query          1 P-----DYPVLDAILELYVD-RDTGADAIVAA-------------GYDRELVVKTLRMVD     41
d1ldda_        1 -KYELTLQRSLPFIEGMLTNLGAMKLHKIHS-FLKITVPKDWGYNRITLQQLEGYLNTLA     58

Query         42 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------------     77
d1ldda_       59 D-----------------------------------EGRLKYIANGSYEIV     74


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.57)
Query          1 -PDYPVLDAILELYVDRDT----------GADAIVAA--G---YDRELVVKTLRM-VDTA     43
d1ldda_        1 KYEL-TLQRSLPFI-EGMLTNLGAMKLHKIHSFLKITVPKDWGYN-RITLQQLEGYL-NT     56

Query         44 -EYKRRQYPPGTKISAKGFGKDRRLPITNRWR----EGH     77
d1ldda_       57 LA-DEG------------R---LKYI--ANGSYEIV---     74


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.05)
DALI match                              
Query          1 PDY-----PVLDAILELYVDRDT     18
d1ldda_       40 WGYNRITLQQLEGYLNTLADEGR     62



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19: d1t56a1 Ethr repressor (svm: 0.902)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.27  Contact: 173
Modified z-scores:
dali:0.88 daliz:0.85 gdtts:0.85 tmscore:0.89 rmsd:0.52 AHM:0.67 LBcontacta:0.77 LBcontactb:0.71 LHM:0.23
id:0.81 blosum:0.29 compass:0.60 pearson:0.93
Scaled scores:
dali:0.66 daliz:0.36 gdtts:0.43 tmscore:0.35 rmsd:0.62 AHM:0.49 LBcontacta:0.33 LBcontactb:0.26 LHM:0.34
id:0.02 blosum:0.03 compass:0.16 pearson:0.20

hit structure      alignment
DALI alignment (Z-score: 2.3 Raw score:139.90)
Query          1 pDYPVLDAILELYVDRD-------tGADAIVA------aGYDR--ELVVKTLRMVDTAEY     45
d1t56a1        1 -GDDRELAILATAENLLedrpladiSVDDLAKgagisrpTFYFyfPSKEAVLLTLLDRVV     59

Query         46 KRRQY--PPGTkisakgfgkdrrlpitnrwregh     77
d1t56a1       60 NQADMalQTLA--------------------enp     73


hit structure      alignment
FAST alignment (Normalized score: 2.82 Raw score:211.40)
Query          1 P----DYPVLDAILELYVDRDTG------ADAIVAAGY---------------DRELVVK     35
d1t56a1        1 -GDDRELAILATAENLLEDR---PLADISVDDLAK---GAGISRPTFYFYFPSKEAVLLT     53

Query         36 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------     77
d1t56a1       54 LLDRVVNQADMALQ----------------------------TLAENP     73


hit structure      alignment
TMalign alignment (TM-score: 0.40 Raw score:30.83)
Query          1 PDYPVLDAILELYVDR-D-------TGADAIVAA-GYDRELVVK-TLRMVDTAE---YKR     47
d1t56a1        1 -GDDRELAILATA-ENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLL--D     56

Query         48 --RQYP--PGT--------KISAKGFGKDRRLPITNRWREGH     77
d1t56a1       57 RV--VNQADMALQTLAENP-----------------------     73


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.05)
DALI match                               
Query         20 ADAIVAAGYDRELVVKTLRMVDTA     43
d1t56a1       13 ENLLEDRPLADISVDDLAKGAGIS     36



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20: d1in4a1 Holliday junction helicase RuvB (svm: 0.906)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.47  Contact: 135
Modified z-scores:
dali:0.79 daliz:0.74 gdtts:0.75 tmscore:0.76 rmsd:0.41 AHM:0.39 LBcontacta:0.71 LBcontactb:0.58 LHM:0.23
id:0.94 blosum:0.81 compass:0.51 pearson:0.91
Scaled scores:
dali:0.58 daliz:0.24 gdtts:0.36 tmscore:0.23 rmsd:0.66 AHM:0.60 LBcontacta:0.28 LBcontactb:0.27 LHM:0.18
id:0.09 blosum:0.13 compass:0.19 pearson:0.17

hit structure      alignment
DALI alignment (Z-score: 0.9 Raw score:98.10)
Query          1 -pdYPVLDAILELYVDRD----TGADAIVAAgYDRElvVKTLR-MVDT-AEYK-------     46
d1in4a1        1 eglDEFDRKILKTIIEIYrggpVGLNALAAS-LGVE-aDTLSEvYEPYlLQAGflartpr     58

Query         47 ----rrqyppgtKISAkgfgkdrrlpitnrwregh     77
d1in4a1       59 grivtekaykhlKYEV------------------p     75


hit structure      alignment
FAST alignment (Normalized score: 3.81 Raw score:289.60)
Query          1 P--DYPVLDAILELYVD----RDTGADAIVA-AGYDRELVV-KTLRMVDTAEYKRRQYPP     52
d1in4a1        1 -EGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQ----------     49

Query         53 GTKISAKGFGKDRRLPITNRWREGH--------------------------     77
d1in4a1       50 -------------------------AGFLARTPRGRIVTEKAYKHLKYEVP     75


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:31.94)
Query          1 ---PDYPVLDAILELYVD----RD-TGADAIVAA-GYDRELVV-KTLRMVDTAE------     44
d1in4a1        1 EGL--DEFDRKILKTI-IEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLARTP     57

Query         45 ----------YKRRQYPPGTK--ISAKGFGKDRRLPITNRWREGH     77
d1in4a1       58 RGRIVTEKAY----------KHLKYEVP-----------------     75


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.13)
DALI match        ...............*********  ....  ....
Query          2 DYPVLDAILELYVDRDTGADAIVAA-GYDRELVVKTL     37
d1in4a1        7 DRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVY     43



hit structures. 
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21: d1bl0a2 MarA (svm: 0.641)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.48  Contact: 188
Modified z-scores:
dali:0.86 daliz:0.84 gdtts:0.90 tmscore:0.94 rmsd:0.35 AHM:0.48 LBcontacta:0.71 LBcontactb:0.68 LHM:0.33
id:0.52 blosum:0.40 compass:0.65 pearson:0.83
Scaled scores:
dali:0.58 daliz:0.29 gdtts:0.52 tmscore:0.41 rmsd:0.69 AHM:0.54 LBcontacta:0.23 LBcontactb:0.25 LHM:0.06
id:-0.00 blosum:0.06 compass:0.03 pearson:0.12

hit structure      alignment
DALI alignment (Z-score: 1.3 Raw score:100.70)
Query          1 pdyPVLDAILELYVDRDTGADAIVAAGYD--RELVVKTL------RMVDtaeykrrqypp     52
d1bl0a2        1 ---RKMTEIAQKLKESNEPILYLAERYGFesQQTLTRTFknyfdvPPHK-----------     46

Query         53 gtkisakGFGKdrrlpitnrwregh     77
d1bl0a2       47 -----yrMTNM----qgesrflhpl     62


hit structure      alignment
FAST alignment (Normalized score: 2.94 Raw score:203.10)
Query          1 PDYPVLDAILELYVDRDTGADAIVA-AGY-DRELVVKTLRMVDTAEYKRRQYPPGTKISA     58
d1bl0a2        1 ---RKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYF-----------------     40

Query         59 KGFGKDRRLPITNRWREGH----------------------     77
d1bl0a2       41 -------------------DVPPHKYRMTNMQGESRFLHPL     62


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:29.27)
Query          1 PDYPVLDAILELYVDRDTGADAIVAAGYD-R--ELVVK-T-------LRMVDTAEYKRRQ     49
d1bl0a2        1 ---RKMTEIAQKLKESNEPILYLAERYGFESQQT-LTRTFKNYFDVPPHKYRM-T-NMQ-     53

Query         50 Y--------PPGTKISAKGFGKDRRLPITNRWREGH     77
d1bl0a2       54 GESRFLHPL---------------------------     62


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.03)
DALI match       *********************
Query          6 LDAILELYVDRDTGADAIVAA     26
d1bl0a2        3 MTEIAQKLKESNEPILYLAER     23



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22: d1r71a_ Transcriptional repressor protein KorB DNA-​binding domain (svm: 0.898)

SCOP Superfamily: KorB DNA-​binding domain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.36  Contact: 142
Modified z-scores:
dali:0.68 daliz:0.55 gdtts:0.72 tmscore:0.80 rmsd:0.64 AHM:0.57 LBcontacta:0.60 LBcontactb:0.48 LHM:0.22
id:0.73 blosum:0.38 compass:0.53 pearson:0.77
Scaled scores:
dali:0.59 daliz:0.16 gdtts:0.34 tmscore:0.27 rmsd:0.60 AHM:0.59 LBcontacta:0.21 LBcontactb:0.16 LHM:0.28
id:0.02 blosum:0.06 compass:0.06 pearson:0.10

hit structure      alignment
DALI alignment (Z-score: 0.2 Raw score:99.90)
Query          1 ----------pDYPVldAILELYVDRD---TGADAIVAAgYDRElvVKTLRMVD-taEYK     46
d1r71a_        1 eadqvienlqrNELTprEIADFIGRELakgKKKGDIAKE-IGKS-pAFITQHVTlldLPE     58

Query         47 RRQY--PPGTkisakgfgkdrrLPITN------------------------rwregh     77
d1r71a_       59 KIADafNTGR-vrdvtvvnelvTAFKKrpeeveawldddtqeitrgtvkllreflde    114


hit structure      alignment
FAST alignment (Normalized score: 3.15 Raw score:295.60)
Query          1 P---------------DYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAE     44
d1r71a_        1 -EADQVIENLQRNELTPREIADFIGREL-AKGKKKGDIAKEIGKSPAFITQHVTLL----     54

Query         45 YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------------------------     77
d1r71a_       55 ---------------------------------DLPEKIADAFNTGRVRDVTVVNELVTA     81

Query         78 ---------------------------------     78
d1r71a_       82 FKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE    114


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:29.56)
Query          1 --------------PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVK-TLRMV-DTA     43
d1r71a_        1 EADQVIENLQRNELTPREIADFIGREL-AKGKKKGDIAKEIGKSPAFITQHV--TLL--D     55

Query         44 -EYK--------------------------------------------------------     46
d1r71a_       56 L--PEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLD    113

Query         47 -RRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1r71a_      114 E-------------------------------    114


hit structure      alignment
HHsearch alignment (Probability: 0.17 E-value:0.00)
DALI match       ........******* .. ....  ......... .
Query         10 LELYVDRDTGADAIV-AAGYDRELVVKTLRMVDTAE     44
d1r71a_       23 IGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPE     58



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23: d1o57a1 N-​terminal domain of Bacillus PurR (svm: 0.895)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.48  Contact: 116
Modified z-scores:
dali:0.64 daliz:0.70 gdtts:0.74 tmscore:0.69 rmsd:0.23 AHM:0.24 LBcontacta:0.61 LBcontactb:0.62 LHM:0.10
id:0.47 blosum:0.52 compass:0.74 pearson:0.91
Scaled scores:
dali:0.61 daliz:0.38 gdtts:0.56 tmscore:0.36 rmsd:0.74 AHM:0.61 LBcontacta:0.36 LBcontactb:0.43 LHM:0.48
id:-0.01 blosum:0.04 compass:0.22 pearson:0.31

hit structure      alignment
DALI alignment (Z-score: 0.8 Raw score:127.70)
Query          1 --PDYPVLDAILELyVDRD----TGADAIVAA-gYDRElvvKTLRMVDtaeykrrqyppg     53
d1o57a1        1 kfRRSGRLVDLTNY-LLTHphelIPLTFFSERyeSAKSsisEDLTIIK----------qt     49

Query         54 tkisakgfgkdrrlpitnrwregh     77
d1o57a1       50 feqqgigtlltvpgaaggvkyipk     73


hit structure      alignment
FAST alignment (Normalized score: 4.56 Raw score:341.80)
Query          1 P---DYPVLDAILELYVD---RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG     53
d1o57a1        1 -KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQ-------     52

Query         54 TKISAKGFGKDRRLPITNRWREGH---------------------     77
d1o57a1       53 ------------------------QGIGTLLTVPGAAGGVKYIPK     73


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.43)
Query          1 ---PDYPVLDAILELYVDRD---TGADAIVAAGYD-RELVVKTLRMVDTA-EYKRRQYPP     52
d1o57a1        1 KFRRS-GRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFE-QQG----     54

Query         53 GTKISAKGFGKDRRLPITNRWREGH----------     77
d1o57a1       55 --------I----GTL----LTVPGAAGGVKYIPK     73


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.24)
DALI match                                    
Query         10 LELYVDRDTGADAIVAAGYDRELVVKTLR     38
d1o57a1       25 LTFFSERYESAKSSISE--DLTIIKQTFE     51



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24: d1biaa1 Biotin repressor,​ N-​terminal domain (svm: 1.297)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.57  Contact: 168
Modified z-scores:
dali:0.81 daliz:0.83 gdtts:0.83 tmscore:0.84 rmsd:0.32 AHM:0.28 LBcontacta:0.69 LBcontactb:0.64 LHM:0.16
id:0.83 blosum:0.82 compass:0.73 pearson:0.91
Scaled scores:
dali:0.67 daliz:0.38 gdtts:0.54 tmscore:0.40 rmsd:0.70 AHM:0.66 LBcontacta:0.31 LBcontactb:0.36 LHM:0.33
id:0.08 blosum:0.16 compass:0.25 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 1.5 Raw score:88.70)
Query          1 -pDYPVLDAILELYV-dRDTGADAIVAA-gYDRElVVKTLRMVDtaeykrrqyppgtkis     57
d1biaa1        1 mkDNTVPLKLIALLAngEFHSGEQLGETlgMSRAaINKHIQTLR--dwgvdvftvpgkgy     58

Query         58 aKGFGkdrrlpitnrwregh     77
d1biaa1       59 sLPEP---------------     63


hit structure      alignment
FAST alignment (Normalized score: 4.22 Raw score:293.80)
Query          1 P--DYPVLDAILELYV-DRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKI     56
d1biaa1        1 -MKDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRD--------------     45

Query         57 SAKGFGKDRRLPITNRWREGH------------------     77
d1biaa1       46 ---------------------WGVDVFTVPGKGYSLPEP     63


hit structure      alignment
TMalign alignment (TM-score: 0.40 Raw score:30.63)
Query          1 --PDYPVLDAILELYVDR-D-TGADAIVAAGYDR-ELVVKTLRM-VDTAE-YKRR-----     48
d1biaa1        1 MK-DNTVPLKLIALL-ANGEFHSGEQLGETLGMSRAAINKHI-QTL--RDW-GVDVFTVP     54

Query         49 -------QYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1biaa1       55 GKGYSLP---------EP------------------     63


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.22)
DALI match       ************* ...........   **** *********  
Query          2 DYPVLDAILELYVDRDTGADAIVAA--GYDRELVVKTLRMVDTA     43
d1biaa1        3 DNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDW     46



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25: d1qdma1 (Pro)phytepsin (svm: 0.726)

SCOP Superfamily: Saposin  |  SCOP Fold: Saposin-​like  |  SCOP Class: All alpha proteins

Consensus: 0.43  Contact: 178
Modified z-scores:
dali:0.82 daliz:0.85 gdtts:0.89 tmscore:0.90 rmsd:0.24 AHM:0.29 LBcontacta:0.82 LBcontactb:0.77 LHM:0.16
id:0.35 blosum:0.47 compass:0.65 pearson:0.88
Scaled scores:
dali:0.68 daliz:0.45 gdtts:0.67 tmscore:0.54 rmsd:0.79 AHM:0.69 LBcontacta:0.39 LBcontactb:0.37 LHM:0.40
id:-0.02 blosum:0.05 compass:0.17 pearson:0.20

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:123.70)
Query          1 ----PDYPVLDAILELYVDR-------dtGADAIV-aagyDRELVVKTLRMVDTA-EYKR     47
d1qdma1        1 vvsqECKTIVSQYGQQILDLllaetqpkkICSQVGlcadpMCSACEMAVVWMQNQlAQNK     60

Query         48 rqyppgtkisakgfgkdrrlpitnrwregh     77
d1qdma1       61 -------------tqdlildyvnqlcnrlp     77


hit structure      alignment
FAST alignment (Normalized score: 3.22 Raw score:247.80)
Query          1 P---------DYPVLDAILELYVDRDTGADAIVAAGY--------DRELVVKTLRMVDTA     43
d1qdma1        1 -VVSQECKTIVSQYGQQILDLL-LAETQPKKICS---QVGLCADPMCSACEMAVVWMQN-     54

Query         44 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-----------------------     77
d1qdma1       55 ----------------------------------QLAQNKTQDLILDYVNQLCNRLP     77


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:33.13)
Query          1 --------PDYPVLDAILELYVDRDTGADAIVAA-GYD----RELVVKTLRMV-DTA--E     44
d1qdma1        1 VVSQECKTIVSQYGQQILDLLL-AETQPKKICSQVGLCADPMCSACEMAVVWMQN-QLAQ     58

Query         45 YKRRQYPPGTKISAKGF---------------GKDRRLPITNRWREGH     77
d1qdma1       59 N-K--T----------QDLILDYVNQLCNRLP----------------     77


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.08)
DALI match                       
Query         10 LELYVDRDTGADAIVA     25
d1qdma1       52 MQNQLAQNKTQDLILD     67



hit structures. 
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26: d1j75a_ Dlm-​1 (svm: 0.900)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.58  Contact: 132
Modified z-scores:
dali:0.74 daliz:0.71 gdtts:0.73 tmscore:0.73 rmsd:0.38 AHM:0.31 LBcontacta:0.76 LBcontactb:0.74 LHM:0.10
id:0.75 blosum:0.70 compass:0.68 pearson:0.94
Scaled scores:
dali:0.54 daliz:0.27 gdtts:0.40 tmscore:0.25 rmsd:0.63 AHM:0.62 LBcontacta:0.34 LBcontactb:0.39 LHM:0.53
id:0.04 blosum:0.10 compass:0.08 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:87.10)
Query          1 pdyPVLDAILELyVDRD---TGADAIVAAgYDRElVVKTLRMVDT-AEYKrrqyppgtki     56
d1j75a_        1 ---NLEQKILQV-LSDDggpVKIGQLVKK-CQVP-KKTLNQVLYRlKKED----------     44

Query         57 sakgfgkdrrlpitnrwregh     77
d1j75a_       45 --------rvsspepatwsig     57


hit structure      alignment
FAST alignment (Normalized score: 4.41 Raw score:292.00)
Query          1 PDYP-VLDAILELYV--DRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKI     56
d1j75a_        1 ----NLEQKILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKK--------------     42

Query         57 SAKGFGKDRRLPITNRWREGH---------------     77
d1j75a_       43 ---------------------EDRVSSPEPATWSIG     57


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:33.03)
Query          1 PDYPVLDAILELYVD-R-D-TGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYPPGTKI     56
d1j75a_        1 --N-LEQKILQVL-SDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKED------------     44

Query         57 SAKGFGKDRRL--PITNRWREG----H     77
d1j75a_       45 ----R----VSSP-----EPATWSIG-     57


hit structure      alignment
HHsearch alignment (Probability: 0.08 E-value:0.01)
DALI match       .. .... ............
Query         25 AAGYDRELVVKTLRMVDTAE     44
d1j75a_       25 KCQVPKKTLNQVLYRLKKED     44



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27: d1hlva1 DNA-​binding domain of centromere binding protein B (CENP-​B) (svm: 1.591)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.45  Contact: 103
Modified z-scores:
dali:0.78 daliz:0.78 gdtts:0.73 tmscore:0.74 rmsd:0.44 AHM:0.50 LBcontacta:0.79 LBcontactb:0.83 LHM:0.21
id:0.63 blosum:0.55 compass:0.67 pearson:0.90
Scaled scores:
dali:0.69 daliz:0.35 gdtts:0.39 tmscore:0.25 rmsd:0.64 AHM:0.54 LBcontacta:0.35 LBcontactb:0.45 LHM:0.22
id:0.02 blosum:0.07 compass:0.02 pearson:0.20

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:103.20)
Query          1 ---pDYPV-ldailELYV----drdtgADAIVAA-GYDRELVVKTLRMVDTAE-YKRRQY     50
d1hlva1        1 mgpkRRQLtfreksRIIQeveenpdlrKGEIARRfNIPPSTLSTILKNKRAILaSERKYG     60

Query         51 Ppgtkisakgfgkdrrlpitnrwregh     77
d1hlva1       61 V---------------------astcr     66


hit structure      alignment
FAST alignment (Normalized score: 3.77 Raw score:268.90)
Query          1 -------PDYPVLDAILELYVDR--DTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQY     50
d1hlva1        1 MGPKRRQLTFREKSRIIQEVEE-NPDLRKGEIARRFNIPPSTLSTILKNKR---------     50

Query         51 PPGTKISAKGFGKDRRLPITNRWREGH----------------     77
d1hlva1       51 ---------------------------AILASERKYGVASTCR     66


hit structure      alignment
TMalign alignment (TM-score: 0.39 Raw score:30.33)
Query          1 -------PDYPVLDAILELYVDRD-TGADAIVAAGYDR-ELVVKTLRMVDTA--------     43
d1hlva1        1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTIL-KNK-RAILASERK     58

Query         44 --------EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1hlva1       59 YGVASTCR----------------------------------     66


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.04)
DALI match       .  ...      ...   ....************
Query          8 AILELYVDRDTGADA---IVAAGYDRELVVKTLR     38
d1hlva1       15 RIIQEV-EENPDLRKGEIARRFNIPPSTLSTILK     47



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28: d1mgta1 O6-​alkylguanine-​DNA alkyltransferase (svm: 0.903)

SCOP Superfamily: Methylated DNA-​protein cysteine methyltransferase,​ C-​terminal domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 131
Modified z-scores:
dali:0.83 daliz:0.82 gdtts:0.84 tmscore:0.84 rmsd:0.37 AHM:0.32 LBcontacta:0.67 LBcontactb:0.72 LHM:0.15
id:0.60 blosum:0.62 compass:0.55 pearson:0.95
Scaled scores:
dali:0.65 daliz:0.33 gdtts:0.45 tmscore:0.31 rmsd:0.67 AHM:0.67 LBcontacta:0.26 LBcontactb:0.33 LHM:0.39
id:0.00 blosum:0.09 compass:0.23 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 1.6 Raw score:108.90)
Query          1 ---PDYPVLDAILE-lyvdRDTGADAIVAA-GYDRELVVKTLRM----------------     39
d1mgta1        1 vtpFEKKVYEWLTKnvkrgSVITYGDLAKAlNTSPRAVGGAMKRnpypivvpchrvvahd     60

Query         40 ---vDTAEYKRrqyppgtkisakgFGKDRrlpitnrwregh     77
d1mgta1       61 gigyYSSGIEE----------kkfLLEIE----------gv     81


hit structure      alignment
FAST alignment (Normalized score: 3.66 Raw score:288.80)
Query          1 PDYPVLDAILELYVDR------DTGADAIVA-AGYDRELVVKTLRMVDT-----------     42
d1mgta1        1 -VTPFEKKVYEWLTK-NVKRGSVITYGDLAKALNTSPRAVGGAMK----RNPYPIVVPCH     54

Query         43 -------------AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------     77
d1mgta1       55 RVVAHDGIGYYSSGIEEKK-----------------------------FLLEIEGV     81


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.44)
Query          1 PDYPVLDAILELYVDRD----TG-ADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYPPGT     54
d1mgta1        1 -VTPFEKKVYEWLTKNVKRGSVITYGDLAKALNTSPRAVGGAMKRN-PYP--I-------     49

Query         55 KISAKGFGKDR-RL------------PITNR--W---------REGH     77
d1mgta1       50 ------VV--PC-HRVVAHDGIGYYS--SGIEEKKFLLEIEGV----     81


hit structure      alignment
HHsearch alignment (Probability: 0.00 E-value:0.80)
DALI match                 
Query         48 RQYPPGTKIS     57
d1mgta1       14 KNVKRGSVIT     23



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29: d2bbya_ DNA-​binding domain from rap30 (svm: 0.897)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.52  Contact: 142
Modified z-scores:
dali:0.73 daliz:0.72 gdtts:0.84 tmscore:0.83 rmsd:0.31 AHM:0.26 LBcontacta:0.60 LBcontactb:0.62 LHM:0.17
id:0.91 blosum:0.79 compass:0.70 pearson:0.95
Scaled scores:
dali:0.59 daliz:0.29 gdtts:0.54 tmscore:0.37 rmsd:0.70 AHM:0.68 LBcontacta:0.26 LBcontactb:0.32 LHM:0.35
id:0.09 blosum:0.13 compass:0.21 pearson:0.31

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:92.40)
Query          1 ----PDYPVLDAILEL-yvdRDTGADAIVAAgYDRElVVKTLRMVDTaeykrrqyppgtk     55
d2bbya_        1 raraDKQHVLDMLFSAfekhQYYNLKDLVDI-TKQP-VVYLKEILKE-igvqnvkgihkn     57

Query         56 isakGFGKdrrlpitnrwregh     77
d2bbya_       58 twelKPEY----------rhyq     69


hit structure      alignment
FAST alignment (Normalized score: 4.31 Raw score:314.30)
Query          1 PDYPVLDAILELYVD-----RDTGADAIVA-AGYDRELVVKTLRMVD-------------     41
d2bbya_        1 RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKE--IGVQNVKGIHKNT     58

Query         42 --TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----     77
d2bbya_       59 WELKPEY-------------------------------RHYQ     69


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.71)
Query          1 PDYPVLDAILELYVDR-D--T--G-ADAIVA-AGYDRELVVKTLRMVDT-----------     42
d2bbya_        1 RARADKQHVLDML-FSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTW     59

Query         43 --AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d2bbya_       60 ELKPE-YR-H----Y----Q-----------------     69


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.16)
DALI match                        
Query         30 RELVVKTLRMVDTAEYK     46
d2bbya_       40 KEILKEIGVQNVKGIHK     56



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30: d1pb6a1 Hypothetical transcriptional regulator YcdC (svm: 0.904)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.26  Contact: 159
Modified z-scores:
dali:0.85 daliz:0.81 gdtts:0.79 tmscore:0.82 rmsd:0.63 AHM:0.74 LBcontacta:0.73 LBcontactb:0.65 LHM:0.26
id:0.89 blosum:0.23 compass:0.41 pearson:0.85
Scaled scores:
dali:0.65 daliz:0.33 gdtts:0.39 tmscore:0.28 rmsd:0.55 AHM:0.45 LBcontacta:0.29 LBcontactb:0.26 LHM:0.27
id:0.06 blosum:0.01 compass:0.17 pearson:0.14

hit structure      alignment
DALI alignment (Z-score: 1.9 Raw score:131.20)
Query          1 pDYPVLDAILELYVDRD-------tGADAI------vaaGYDR--ELVVKTLRMVDTAEY     45
d1pb6a1        1 aVSAKKKAILSAALDTFsqfgfhgtRLEQIaelagvsktNLLYyfPSKEALYIAVLRQIL     60

Query         46 KRRQY--PPGTkisakgfgkdrrlpitnrwregh     77
d1pb6a1       61 DIWLAplKAFR----------------------e     72


hit structure      alignment
FAST alignment (Normalized score: 3.05 Raw score:227.00)
Query          1 PDYPVLDAILELYVDRD---------TGADAIVA-AGYD----------RELVVKTLRMV     40
d1pb6a1        1 AVSAKKKAILSAALD--TFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQ     58

Query         41 DTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-----     77
d1pb6a1       59 ILDIWLAPL----------------------------KAFRE     72


hit structure      alignment
TMalign alignment (TM-score: 0.26 Raw score:20.01)
Query          1 PDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAE-YKRRQYP--------     51
d1pb6a1        1 ---------------------------AVSAKKKAILSAALDTFSQFGFHGTRLEQIAEL     33

Query         52 --------------PGTKISAKGF--GKDR--RL----------------PITNRWREGH     77
d1pb6a1       34 AGVSKTNLLYYFPS-------KEALY---IAV-LRQILDIWLAPLKAFRE----------     72


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.10)
DALI match                               
Query         20 ADAIVAAGYDRELVVKTLRMVDTA     43
d1pb6a1       14 LDTFSQFGFHGTRLEQIAELAGVS     37



hit structures. 
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31: d1j5ya1 Putative transcriptional regulator TM1602,​ N-​terminal domain (svm: 1.541)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.34  Contact: 162
Modified z-scores:
dali:0.73 daliz:0.66 gdtts:0.76 tmscore:0.77 rmsd:0.43 AHM:0.31 LBcontacta:0.75 LBcontactb:0.73 LHM:0.16
id:0.72 blosum:0.70 compass:0.70 pearson:0.95
Scaled scores:
dali:0.56 daliz:0.23 gdtts:0.40 tmscore:0.27 rmsd:0.66 AHM:0.65 LBcontacta:0.32 LBcontactb:0.36 LHM:0.35
id:0.02 blosum:0.12 compass:0.22 pearson:0.25

hit structure      alignment
DALI alignment (Z-score: 1.2 Raw score:91.00)
Query          1 ---PDYPVLDAILELyVDRD---TGADAIVAAgYDRElvVKTLRMVDT-AEYKrrqyppg     53
d1j5ya1        1 mktVRQERLKSIVRI-LERSkepVSGAQLAEE-LSVS-rQVIVQDIAYlRSLG-ynivat     56

Query         54 tkisaKGFGkdrrlpitnrwregh     77
d1j5ya1       57 prgyvLAGG---------------     65


hit structure      alignment
FAST alignment (Normalized score: 4.73 Raw score:334.90)
Query          1 P----DYPVLDAILELYV--DRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG     53
d1j5ya1        1 -MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRS-----------     48

Query         54 TKISAKGFGKDRRLPITNRWREGH-----------------     77
d1j5ya1       49 ------------------------LGYNIVATPRGYVLAGG     65


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:34.12)
Query          1 PDY-PVLDAILELYVDRD--T---G-ADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYPP     52
d1j5ya1        1 -MKTV-RQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLG--------     50

Query         53 GTKISAKGFGKDRRLPITNRWREGH--------     77
d1j5ya1       51 -------------YNI----V-ATPRGYVLAGG     65


hit structure      alignment
HHsearch alignment (Probability: 0.10 E-value:0.02)
DALI match       *********......  ******* . ....  ..........
Query          4 PVLDAILELYVDRDT--GADAIVA-AGYDRELVVKTLRMVDTA     43
d1j5ya1        7 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSL     49



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32: d1rp3a1 Sigma factor sigma-​28 (FliA) (svm: 0.895)

SCOP Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.44  Contact: 109
Modified z-scores:
dali:0.78 daliz:0.78 gdtts:0.75 tmscore:0.75 rmsd:0.57 AHM:0.61 LBcontacta:0.71 LBcontactb:0.81 LHM:0.24
id:0.80 blosum:0.68 compass:0.66 pearson:0.91
Scaled scores:
dali:0.66 daliz:0.37 gdtts:0.36 tmscore:0.24 rmsd:0.51 AHM:0.42 LBcontacta:0.31 LBcontactb:0.41 LHM:0.32
id:0.05 blosum:0.10 compass:0.05 pearson:0.19

hit structure      alignment
DALI alignment (Z-score: 1.6 Raw score:121.40)
Query          1 pdypvlDAILELYvDRDT-----------gADAIVAA-GYDRELVVKTLRMVDTAEYKRR     48
d1rp3a1        1 -gsrqvREKERRI-KEVVeklkeklgreptDEEVAKElGISTEELFKTLDKINFSYILSL     58

Query         49 QY--PPGTkisakgfgkdrrlpitnrwregh     77
d1rp3a1       59 EEvfRDFA------------rdyselipsst     77


hit structure      alignment
FAST alignment (Normalized score: 3.87 Raw score:297.80)
Query          1 P----DYPVLDAILELYVD------RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQ     49
d1rp3a1        1 -GSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSL-     58

Query         50 YPPGTKISAKGFGKDRRLPITNRWREGH-------------------     77
d1rp3a1       59 ----------------------------EEVFRDFARDYSELIPSST     77


hit structure      alignment
TMalign alignment (TM-score: 0.36 Raw score:27.57)
Query          1 ---PDYPVL-DAILELYVDRDT----------G-ADAIVAAGYDR-ELVVKTLRMVDTAE     44
d1rp3a1        1 GSR--Q--VRE-KERRI-KEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSY     54

Query         45 YKRR-QY----------------PPGTKISAKGFGKDRRLPITNRWREGH     77
d1rp3a1       55 ILSLEEVFRDFARDYSELIPSST---------------------------     77


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.08)
DALI match        ******* ******************
Query         19 GADAIVAA-GYDRELVVKTLRMVDTAE     44
d1rp3a1       28 TDEEVAKELGISTEELFKTLDKINFSY     54



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33: d1or7a1 SigmaE factor (RpoE) (svm: 1.037)

SCOP Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.44  Contact: 198
Modified z-scores:
dali:0.93 daliz:0.94 gdtts:0.88 tmscore:0.89 rmsd:0.29 AHM:0.41 LBcontacta:0.87 LBcontactb:0.88 LHM:0.44
id:0.90 blosum:0.51 compass:0.55 pearson:0.93
Scaled scores:
dali:0.71 daliz:0.52 gdtts:0.52 tmscore:0.41 rmsd:0.72 AHM:0.60 LBcontacta:0.43 LBcontactb:0.48 LHM:-0.11
id:0.06 blosum:0.07 compass:0.21 pearson:0.24

hit structure      alignment
FAST alignment (Normalized score: 5.43 Raw score:392.70)
Query          1 PD-------------------YPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMV     40
d1or7a1        1 --NLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRA     58

Query         41 DT-AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-     77
d1or7a1       59 REAIDNKVQ-----------------------------P     68


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.64)
Query          1 ------------------PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVKTLRMV-     40
d1or7a1        1 NLMLSEELRQIVFRTIES-LPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRI-FRA     58

Query         41 DTA--EYKR-RQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1or7a1       59 -REAI--DNK-VQP--------------------------     68


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.07)
DALI match       ******************. ****************.
Query          8 AILELYVDRDTGADAIVAA-GYDRELVVKTLRMVDTA     43
d1or7a1       25 MAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREA     61



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34: d1dpua_ C-​terminal domain of RPA32 (svm: 0.994)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.49  Contact: 106
Modified z-scores:
dali:0.67 daliz:0.67 gdtts:0.67 tmscore:0.67 rmsd:0.40 AHM:0.46 LBcontacta:0.67 LBcontactb:0.52 LHM:0.21
id:0.62 blosum:0.60 compass:0.60 pearson:0.67
Scaled scores:
dali:0.61 daliz:0.28 gdtts:0.39 tmscore:0.24 rmsd:0.67 AHM:0.56 LBcontacta:0.32 LBcontactb:0.28 LHM:0.24
id:0.00 blosum:0.06 compass:0.06 pearson:0.08

hit structure      alignment
DALI alignment (Z-score: 0.5 Raw score:88.30)
Query          1 --pDYPVLDAILELyVDRD---------tGADAIVaagydreLVVKTLRMVDTAeykrrq     49
d1dpua_        1 angLTVAQNQVLNL-IKACprpeglnfqdLKNQLK------hMSVSSIKQAVDF------     47

Query         50 yppgtkisakgfgkDRRLpitnrwregh     77
d1dpua_       48 ----lsneghiystVDDD--hfkstdae     69


hit structure      alignment
FAST alignment (Normalized score: 4.72 Raw score:344.00)
Query          1 P---DYPVLDAILELYVDR------DTGADAIVA--AGYDRELVVKTLRMVDTAEYKRRQ     49
d1dpua_        1 -ANGLTVAQNQVLNLIK--ACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSN-------     50

Query         50 YPPGTKISAKGFGKDRRLPITNRWREGH-------------------     77
d1dpua_       51 ----------------------------EGHIYSTVDDDHFKSTDAE     69


hit structure      alignment
TMalign alignment (TM-score: 0.45 Raw score:34.54)
Query          1 ---PDYPVLDAILELYVDR----DTGADAIVAA-G-YDRELVVKTLRMVDTAEYKR----     47
d1dpua_        1 ANGLTV-AQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEG--HIYST     57

Query         48 -------RQYPPGTKISAKGFG-KDRRLPITNRWREGH     77
d1dpua_       58 VDDDHFK-----------STDAE---------------     69


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.05)
DALI match       ........      ......     .   .......
Query          5 VLDAILELYVDRDTGADAIVAA--GYDRELVVKTLR     38
d1dpua_       11 VLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVD     46



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35: d1d5ya2 Rob transcription factor,​ N-​terminal domain (svm: 0.901)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 174
Modified z-scores:
dali:0.86 daliz:0.86 gdtts:0.91 tmscore:0.92 rmsd:0.28 AHM:0.36 LBcontacta:0.73 LBcontactb:0.74 LHM:0.21
id:0.66 blosum:0.24 compass:0.58 pearson:0.93
Scaled scores:
dali:0.56 daliz:0.31 gdtts:0.54 tmscore:0.39 rmsd:0.72 AHM:0.57 LBcontacta:0.25 LBcontactb:0.31 LHM:0.27
id:0.00 blosum:-0.01 compass:0.14 pearson:0.17

hit structure      alignment
DALI alignment (Z-score: 1.3 Raw score:95.30)
Query          1 pdyPVLDAILELYVDRDTGADAIVAAGYD--RELVV--------kTLRMVDTAEYkrrqy     50
d1d5ya2        1 ---RRLSKSAVALRLTARPILDIALQYRFdsQQTFTrafkkqfaqTPALYRRSPE-----     52

Query         51 ppgtkisakgfgkdrrlpitnrwregh     77
d1d5ya2       53 --------------wsafgirpplrlg     65


hit structure      alignment
FAST alignment (Normalized score: 2.82 Raw score:199.60)
Query          1 PDYPVLDAILELYVDRDTGADAIVA-AGY-DRELVVKTLRMVDTAEYKRRQYPPGTKISA     58
d1d5ya2        1 ---RRLSKSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQF-----------------     40

Query         59 KGFGKDRRLPITNRWREGH-------------------------     77
d1d5ya2       41 -------------------AQTPALYRRSPEWSAFGIRPPLRLG     65


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:28.39)
Query          1 PDYPVLDAILELYVDRDTGADAI-VAAGYD-R--ELVVK-TL----RMV-DTAEYKRRQY     50
d1d5ya2        1 ---RRLSKSAVALRLTARPILDIAL-QYRFDSQQTF-TRAFKKQFAQTPALYRR--SP--     51

Query         51 PPGTKISAKGFG------------KDRRLPITNRWREGH     77
d1d5ya2       52 ----------EWSAFGIRPPLRLG---------------     65


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.06)
DALI match       *********************
Query          6 LDAILELYVDRDTGADAIVAA     26
d1d5ya2        3 LSKSAVALRLTARPILDIALQ     23



hit structures. 
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36: d1hsta_ Histone H5,​ globular domain (svm: 0.907)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 189
Modified z-scores:
dali:0.80 daliz:0.73 gdtts:0.87 tmscore:0.89 rmsd:0.31 AHM:0.37 LBcontacta:0.61 LBcontactb:0.46 LHM:0.20
id:0.47 blosum:0.34 compass:0.54 pearson:0.86
Scaled scores:
dali:0.55 daliz:0.25 gdtts:0.47 tmscore:0.37 rmsd:0.68 AHM:0.62 LBcontacta:0.22 LBcontactb:0.19 LHM:0.36
id:-0.02 blosum:0.03 compass:0.12 pearson:0.13

hit structure      alignment
DALI alignment (Z-score: 1.3 Raw score:122.50)
Query          1 pdyPVLDAILELYVDRD---------TGADAIVAAGYDRELVVKTLRMVDTA-EYKRrqy     50
d1hsta_        1 -shPTYSEMIAAAIRAEksrggssrqSIQKYIKSHYKVGHNADLQIKLSIRRlLAAG---     56

Query         51 ppgtkisakgfgkdRRLP----itnrwregh     77
d1hsta_       57 -------------vLKQTkgvgasgsfrlak     74


hit structure      alignment
FAST alignment (Normalized score: 2.77 Raw score:208.90)
Query          1 P----DYPVLDAILELYVDR------DTGADAIVAAGY-----------DRELVVKTLRM     39
d1hsta_        1 -SHPTYSEMIAAAIR-----AEKSRGGSSRQSIQK---YIKSHYKVGHNADLQIKLSIRR     51

Query         40 VDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------------     77
d1hsta_       52 LLA-----------------------------------AGVLKQTKGVGASGSFRLAK     74


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:29.35)
Query          1 PDYPVL-DAILELYVDR-------D---TGADAIVAAGYDRELVVKTLRMVDTAE-YKRR     48
d1hsta_        1 -S-HPTYSEMIAAA-IRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSI-RRL-LA-     54

Query         49 QYPPGTKISAKGFGKDRRL------------PITNRWREGH     77
d1hsta_       55 -A-G-------VLK--QTKGVGASGSFRLAK----------     74


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.31)
DALI match                    ........
Query          5 VLDAILELYVDRDTGADAIVA     25
d1hsta_        9 IAAAIRAEKSRGGSSRQSIQK     29



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37: d1ufma_ COP9 signalosome complex subunit 4,​ GSN4 (svm: 0.729)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.40  Contact: 165
Modified z-scores:
dali:0.67 daliz:0.61 gdtts:0.83 tmscore:0.83 rmsd:0.30 AHM:0.30 LBcontacta:0.64 LBcontactb:0.49 LHM:0.20
id:0.32 blosum:0.10 compass:0.31 pearson:0.28
Scaled scores:
dali:0.56 daliz:0.19 gdtts:0.47 tmscore:0.35 rmsd:0.71 AHM:0.64 LBcontacta:0.25 LBcontactb:0.24 LHM:0.28
id:-0.04 blosum:-0.05 compass:-0.04 pearson:-0.07

hit structure      alignment
DALI alignment (Z-score: 0.4 Raw score:106.70)
Query          1 ---------PDYPvLDAILELyVDRD----------tGADAIVaagydrelVVKTLRMVD     41
d1ufma_        1 gssgssggsSILD-RAVIEHN-LLSAsklynnitfeeLGALLE-------iPAAKAEKIA     51

Query         42 TA-EYKRrqyppgtkisakgfgkdRRLP-itnRWRE-----------gh     77
d1ufma_       52 SQmITEG----------------rMNGFidqiDGIVhfetreasgpssg     84


hit structure      alignment
FAST alignment (Normalized score: 3.63 Raw score:292.00)
Query          1 P-------------DYPVLDAILELYVD--RDTGADAIVA-AGYDRELVVKTLRMVDTAE     44
d1ufma_        1 -GSSGSSGGSSILDRAVIEHNLLS-ASKLYNNITFEELGALLEIPAAKAEKIASQMIT--     56

Query         45 YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------------------------     77
d1ufma_       57 ---------------------------------EGRMNGFIDQIDGIVHFETREASGPSS     83

Query         78 -     78
d1ufma_       84 G     84


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:31.73)
Query          1 ------------PDYPVLDAILELYVD-R-DTGADAIVAAGYDR-ELVVKTLRM-VDTAE     44
d1ufma_        1 GSSGSSGGSSILDRAVIEHNLLSA-SKLYNNITFEELGALLEIPAAKAEKIASQMI-TEG     58

Query         45 --YKR------------RQYPPGTKISAKGFGKDR----RLPITNRWREGH     77
d1ufma_       59 RM--NGFIDQIDGIVHF----------ETR-EASGPSSG------------     84


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.38)
DALI match                        
Query          2 DYPVLDAILELYVDRDT     18
d1ufma_       43 PAAKAEKIASQMITEGR     59



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38: d1p6ra_ Penicillinase repressor BlaI (svm: 0.910)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.32  Contact: 171
Modified z-scores:
dali:0.74 daliz:0.69 gdtts:0.85 tmscore:0.87 rmsd:0.33 AHM:0.37 LBcontacta:0.70 LBcontactb:0.50 LHM:0.25
id:0.62 blosum:0.46 compass:0.54 pearson:0.87
Scaled scores:
dali:0.55 daliz:0.24 gdtts:0.49 tmscore:0.37 rmsd:0.67 AHM:0.57 LBcontacta:0.29 LBcontactb:0.24 LHM:0.17
id:0.01 blosum:0.06 compass:0.20 pearson:0.18

hit structure      alignment
DALI alignment (Z-score: 0.8 Raw score:98.60)
Query          1 -----pdYPVLDAILELyVDRDT------GADAIVAAgYDRElvVKTLRMVDTA-EYKR-     47
d1p6ra_        1 mkkipqiSDAELEVMKV-IWKHSsintneVIKELSKT-STWS--PKTIQTMLLRlIKKGa     56

Query         48 -rqyppgtkisaKGFGkdrrlpitnrwregh     77
d1p6ra_       57 lnhhkegrvfvyTPNI-----desdyievks     82


hit structure      alignment
FAST alignment (Normalized score: 3.84 Raw score:304.80)
Query          1 P------DYPVLDAILELYVD-RDTGADAIVA-----AGYDRELVVKTLRMVDTAEYKRR     48
d1p6ra_        1 -MKKIPQISDAELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIK------     53

Query         49 QYPPGTKISAKGFGKDRRLPITNRWREGH-----------------------------     77
d1p6ra_       54 -----------------------------KGALNHHKEGRVFVYTPNIDESDYIEVKS     82


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.47)
Query          1 ------PDYPVLDAILELYVDRD--T----GADAIVAAGYDR-ELVVKTLRMVDTAEYKR     47
d1p6ra_        1 MKKIPQ-ISDAELEVMKVI-WKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKG--A     56

Query         48 RQYPPGTKISAKGFGKDRRLPITN-RWRE----------------GH     77
d1p6ra_       57 -------------L----NHH--KEGRVFVYTPNIDESDYIEVKS--     82


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.21)
DALI match                         
Query          1 PDYPVLDAILELYVDRDT     18
d1p6ra_       39 WSPKTIQTMLLRLIKKGA     56



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39: d1ucra_ Dissimilatory sulfite reductase DsvD (svm: 0.906)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.49  Contact: 160
Modified z-scores:
dali:0.83 daliz:0.80 gdtts:0.85 tmscore:0.87 rmsd:0.42 AHM:0.43 LBcontacta:0.69 LBcontactb:0.61 LHM:0.32
id:0.74 blosum:0.48 compass:0.66 pearson:0.88
Scaled scores:
dali:0.62 daliz:0.31 gdtts:0.47 tmscore:0.36 rmsd:0.67 AHM:0.60 LBcontacta:0.27 LBcontactb:0.27 LHM:0.16
id:0.02 blosum:0.07 compass:0.11 pearson:0.18

hit structure      alignment
DALI alignment (Z-score: 1.5 Raw score:111.10)
Query          1 pDYPVLDAILEL-----yvdrDTGADAIVAAG--yDRELVVKTLRMVDTAEykrrqyppg     53
d1ucra_        1 -MEEAKQKVVDFlnsksgsksKFYFNDFTDLFpdmKQREVKKILTALVNDEvleywssgs     59

Query         54 tkisakGFGKDRRLpitnrwregh     77
d1ucra_       60 ttmyglKGAGKQAA---------a     74


hit structure      alignment
FAST alignment (Normalized score: 3.65 Raw score:275.60)
Query          1 PDYPVLDAILELYVD-------RDTGADAIVA--AGYDRELVVKTLRMVDTAEYKRRQYP     51
d1ucra_        1 -MEEAKQKVVDFL--NSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVN---------     48

Query         52 PGTKISAKGFGKDRRLPITNRWREGH--------------------------     77
d1ucra_       49 --------------------------DEVLEYWSSGSTTMYGLKGAGKQAAA     74


hit structure      alignment
TMalign alignment (TM-score: 0.39 Raw score:30.40)
Query          1 PDYPVLDAILELYVD---R---DTGADAIVAA-GYD-RELVVKTLRMVDTAEYK------     46
d1ucra_        1 -MEEAKQKVVDF-LNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDE-VLEYWSS     57

Query         47 ------RRQYPPGTKISAKGFGKDRRL-----PITNRWREGH     77
d1ucra_       58 GSTTMY------------GLK---GAGKQAAA----------     74


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.50)
DALI match                  
Query          8 AILELYVDRDT     18
d1ucra_       41 KILTALVNDEV     51



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40: d1sd4a_ Penicillinase repressor BlaI (svm: 0.911)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.43  Contact: 148
Modified z-scores:
dali:0.69 daliz:0.71 gdtts:0.81 tmscore:0.79 rmsd:0.37 AHM:0.41 LBcontacta:0.54 LBcontactb:0.58 LHM:0.27
id:0.87 blosum:0.56 compass:0.50 pearson:0.79
Scaled scores:
dali:0.59 daliz:0.27 gdtts:0.42 tmscore:0.29 rmsd:0.63 AHM:0.54 LBcontacta:0.26 LBcontactb:0.33 LHM:0.15
id:0.08 blosum:0.07 compass:0.16 pearson:0.16

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:109.90)
Query          1 -pdyPVLDAILELYVDRD------tGADAIVAaGYDRElvVKTLRMVDTA-EYKRrqypp     52
d1sd4a_        1 qveiSMAEWDVMNIIWDKksvsaneIVVEIQK-YKEVS--DKTIRTLITRlYKKE-----     52

Query         53 gtkisakgFGKD------------------------------------------------     64
d1sd4a_       53 ------iiKRYKseniyfyssnikeddikmktaktflnklyggdmkslvlnfakneelnn    106

Query         65 ---rrlpitnrwregh     77
d1sd4a_      107 keieelrdilndiskk    122


hit structure      alignment
FAST alignment (Normalized score: 3.18 Raw score:308.20)
Query          1 P---DYPVLDAILELYVD--RDTGADAIVA-----AGYDRELVVKTLRMVDTAEYKRRQY     50
d1sd4a_        1 -QVEISMAEWDVMNIIW-DKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYK--------     50

Query         51 PPGTKISAKGFGKDRRLPITNRWREGH---------------------------------     77
d1sd4a_       51 ---------------------------KEIIKRYKSENIYFYSSNIKEDDIKMKTAKTFL     83

Query         78 ---------------------------------------     78
d1sd4a_       84 NKLYGGDMKSLVLNFAKNEELNNKEIEELRDILNDISKK    122


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.96)
Query          1 ----PDYPVLDAILELYVDR--DTGADAIVAA-G----YDRELVVKTLRMVDTAEYKR--     47
d1sd4a_        1 QVEI-SM-AEWDVMNII-WDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKE--IIK     55

Query         48 -----------RQYPPGTKISAKGFG----------------------------------     62
d1sd4a_       56 RYKSENIYFYS-----------SNIKEDDIKMKTAKTFLNKLYGGDMKSLVLNFAKNEEL    104

Query         63 ------------------KDRRLPITNRWREGH     77
d1sd4a_      105 NNKEIEELRDILNDISKK---------------    122


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.15)
DALI match                                                         
Query          4 PVLDAILELYVDR--DTGADAIVA-----AGYDRELVVKTLRMVDTAEYK     46
d1sd4a_       73 DIKMKTAKTFLNKLYGGDMKSLVLNFAKNEELNNKEIEELRDILNDISKK    122



hit structures. 
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41: d1gdta1 gamma,​delta resolvase (C-​terminal domain) (svm: 1.647)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.63  Contact: 164
Modified z-scores:
dali:0.95 daliz:0.98 gdtts:0.95 tmscore:0.96 rmsd:0.20 AHM:0.23 LBcontacta:0.93 LBcontactb:0.93 LHM:0.18
id:0.99 blosum:0.97 compass:0.74 pearson:0.97
Scaled scores:
dali:0.72 daliz:0.60 gdtts:0.76 tmscore:0.56 rmsd:0.76 AHM:0.64 LBcontacta:0.51 LBcontactb:0.63 LHM:0.24
id:0.22 blosum:0.31 compass:0.19 pearson:0.37

hit structure      alignment
FAST alignment (Normalized score: 4.60 Raw score:264.60)
Query          1 PDYP------VLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPG     53
d1gdta1        1 ----GRKRKIDRDAVLNMW-QQGLGASHISKTMNIARSTVYKVINE--------------     41

Query         54 TKISAKGFGKDRRLPITNRWREGH--     77
d1gdta1       42 ------------------------SN     43


hit structure      alignment
TMalign alignment (TM-score: 0.39 Raw score:30.18)
Query          1 --PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVKTLRMVDTAEYKRRQYPPGTKIS     57
d1gdta1        1 GRKRKIDRDAVLNMW-QQGLGASHISKTMNIARSTVYKVI-NE-SN--------------     43

Query         58 AKGFGKDRRLPITNRWREGH     77
d1gdta1       44 --------------------     44


hit structure      alignment
HHsearch alignment (Probability: 0.15 E-value:0.00)
DALI match       ******* ***********. ************
Query          7 DAILELYVDRDTGADAIVAA-GYDRELVVKTLR     38
d1gdta1        9 DAVLNMW-QQGLGASHISKTMNIARSTVYKVIN     40



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42: d1bjaa_ Transcription factor MotA,​ activation domain (svm: 0.905)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 145
Modified z-scores:
dali:0.80 daliz:0.87 gdtts:0.88 tmscore:0.86 rmsd:0.20 AHM:0.19 LBcontacta:0.70 LBcontactb:0.66 LHM:0.34
id:0.46 blosum:0.47 compass:0.65 pearson:0.74
Scaled scores:
dali:0.73 daliz:0.49 gdtts:0.62 tmscore:0.47 rmsd:0.76 AHM:0.74 LBcontacta:0.37 LBcontactb:0.39 LHM:0.14
id:-0.02 blosum:0.03 compass:0.02 pearson:0.11

hit structure      alignment
DALI alignment (Z-score: 1.3 Raw score:114.20)
Query          1 --------pdypvlDAILELYVDRD---------tGADAIvaAGYDRELVVKTLRMVDTA     43
d1bjaa_        1 skvtyiikasndvlNEKTATILITIakkdfitaaeVREVH--PDLGNAVVNSNIGVLIKK     58

Query         44 E---------ykrrqyppgtKISAkgfgkdrrlpitnrwregh     77
d1bjaa_       59 GlveksgdgliitgeaqdiiSNAA------tlyaqenapellk     95


hit structure      alignment
FAST alignment (Normalized score: 3.99 Raw score:341.60)
Query          1 P-------------DYPVLDAILELYVD-RDTGADAIVA--AGYDRELVVKTLRMVDTAE     44
d1bjaa_        1 -SKVTYIIKASNDVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIK--     57

Query         45 YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------------------------     77
d1bjaa_       58 ---------------------------------KGLVEKSGDGLIITGEAQDIISNAATL     84

Query         78 -----------     78
d1bjaa_       85 YAQENAPELLK     95


hit structure      alignment
TMalign alignment (TM-score: 0.45 Raw score:34.49)
Query          1 --------------PDYPVLDAILELYVDR-D-TGADAIVAA-G-YDRELVVKTLRMVDT     42
d1bjaa_        1 SKVTYIIKASNDVL-NE-KTATILITI-AKKDFITAAEVREVHPDLGNAVVNSNIGVLIK     57

Query         43 AEYKR--------RQYPPGTKISAKGFGK-DR--------------------RLPITNRW     73
d1bjaa_       58 KG--LVEKSGDGL-----------IITGEA-QDIISNAATLYAQENAPELLK--------     95

Query         74 REGH     77
d1bjaa_       96 ----     96


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.50)
DALI match                  
Query          9 ILELYVDRDTG     19
d1bjaa_       56 IKKGLVEKSGD     66



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43: d1lvaa1 C-​terminal fragment of elongation factor SelB (svm: 0.723)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.56  Contact: 126
Modified z-scores:
dali:0.58 daliz:0.43 gdtts:0.77 tmscore:0.80 rmsd:0.51 AHM:0.55 LBcontacta:0.47 LBcontactb:0.39 LHM:0.18
id:0.61 blosum:0.50 compass:0.65 pearson:0.80
Scaled scores:
dali:0.49 daliz:0.10 gdtts:0.39 tmscore:0.28 rmsd:0.65 AHM:0.55 LBcontacta:0.16 LBcontactb:0.14 LHM:0.32
id:-0.00 blosum:0.07 compass:0.01 pearson:0.13

hit structure      alignment
DALI alignment (Z-score: 0.1 Raw score:69.80)
Query          1 pdYPVLDAILELyVDRDT-------GADAIVaagydreLVVKTLRMVDTAEYKRrqyppg     53
d1lvaa1        1 --GSPEKILAQI-IQEHRegldwqeAATRAS------lSLEETRKLLQSMAAAG------     45

Query         54 tkisakgfgkdrRLPItNRWR---egh     77
d1lvaa1       46 ----------qvTLLR-VENDlyaist     61


hit structure      alignment
FAST alignment (Normalized score: 4.48 Raw score:306.90)
Query          1 PDY-PVLDAILELYVD---RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1lvaa1        1 ---GSPEKILAQIIQ-EHREGLDWQEAATRASLSLEETRKLLQSMAA-------------     43

Query         56 ISAKGFGKDRRLPITNRWREGH------------------     77
d1lvaa1       44 ----------------------AGQVTLLRVENDLYAIST     61


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:34.06)
Query          1 PDYPVLDAILELYVDRD---TGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYPPGTKI     56
d1lvaa1        1 --GSPEKILAQII-QEHREGLDWQEAATRASLSLEETRKLLQSMAAAG------------     45

Query         57 SAKGFGKDRRL--PITNRW---REG-----H     77
d1lvaa1       46 ----Q----VTLL-----RVEN-DLYAIST-     61


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.49)
DALI match        .......... ...........    .  .......
Query          2 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLR     38
d1lvaa1        3 PEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQ     39



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44: d2foka2 Restriction endonuclease FokI,​ N-​terminal (recognition) domain (svm: 0.712)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.48  Contact: 209
Modified z-scores:
dali:0.76 daliz:0.79 gdtts:0.91 tmscore:0.91 rmsd:0.30 AHM:0.34 LBcontacta:0.55 LBcontactb:0.53 LHM:0.47
id:0.92 blosum:0.75 compass:0.68 pearson:0.91
Scaled scores:
dali:0.59 daliz:0.31 gdtts:0.57 tmscore:0.48 rmsd:0.68 AHM:0.58 LBcontacta:0.23 LBcontactb:0.27 LHM:0.01
id:0.10 blosum:0.14 compass:0.06 pearson:0.21

hit structure      alignment
DALI alignment (Z-score: 0.9 Raw score:129.80)
Query          1 -------------pDYPVLDAILELYV-DRDTGADAIVAAGY------------------     28
d2foka2        1 gsaiekeilieaisSYPPAIRILTLLEdGQHLTKFDLGKNLGfsgesgftslpegilldt     60

Query         29 -------------------DRELVVKTLRMVDTAE--------ykrrqyppgtkisakgF     61
d2foka2       61 lanampkdkgeirnnwegsSDKYARMIGGWLDKLGlvkqgkkefiiptnkefishafkiT    120

Query         62 GKD--rrlpitnrwregh     77
d2foka2      121 GEGlkvlrrakgstkftr    138


hit structure      alignment
FAST alignment (Normalized score: 2.68 Raw score:276.00)
Query          1 PD---------------YPVLDAILELYV-DRDTGADAIVAAGY----------------     28
d2foka2        1 --GSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGK---NLGFSGESGFTSLPEG     55

Query         29 ------------------------DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD     64
d2foka2       56 ILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDK----------------------     93

Query         65 RRLPITNRWREGH---------------------------------------------     77
d2foka2       94 -------------LGLVKQGKKEFIIPTNKEFISHAFKITGEGLKVLRRAKGSTKFTR    138


hit structure      alignment
TMalign alignment (TM-score: 0.33 Raw score:25.72)
Query          1 PDYPVLDAILELYVDRDTG-----------------------------------------     19
d2foka2        1 GSAIEKEILIEAIS-SYPPAIRILTLLEDGQHLTKFDLGKNLGFSGESGFTSLPEGILLD     59

Query         20 ----------------------------ADAIVAAGYDRELVVKTLR--MVDT-------     42
d2foka2       60 TLANAMPKDKGEIRNNWEGSSDKYARMI--------------GGWLDKLGLVKQGKKEFI    105

Query         43 ------------AEYKR-R---QYPP----GTKISAKGFGKDRRLPITNRWREGH     77
d2foka2      106 IPTNKEFISHAFKITGEGLKVL---RRAKGSTKFTR-------------------    138


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.50)
DALI match                  
Query         35 KTLRMVDTAEY     45
d2foka2       21 RILTLLEDGQH     31



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45: d1pdnc_ Paired protein (prd) (svm: 0.843)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.51  Contact: 72
Modified z-scores:
dali:0.43 daliz:0.45 gdtts:0.61 tmscore:0.50 rmsd:0.34 AHM:0.43 LBcontacta:0.38 LBcontactb:0.37 LHM:0.30
id:0.34 blosum:0.54 compass:0.55 pearson:0.44
Scaled scores:
dali:0.70 daliz:0.21 gdtts:0.50 tmscore:0.20 rmsd:0.68 AHM:0.53 LBcontacta:0.25 LBcontactb:0.24 LHM:0.14
id:-0.02 blosum:0.04 compass:0.06 pearson:0.06

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:54.90)
Query          1 pdypvlDAILELyvdrdTGADaivaagydrelvvktLRMVDTAEYKRRQYP----pgtki     56
d1pdnc_        1 --qgrvNQLGGV-----FING------------rplPNNIRLKIVEMAADGirpcvisrq     41

Query         57 sakgfgkdRRLP------iTNRW-------------------------------------     73
d1pdnc_       42 lrvshgcvSKILnryqetgSIRPgviggskpriatpeienrieeykrsspgmfsweirek    101

Query         74 ------------------regh     77
d1pdnc_      102 liregvcdrstapsvsaisrlv    123


hit structure      alignment
FAST alignment (Normalized score: 3.90 Raw score:379.40)
Query          1 ----------------PDYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTA     43
d1pdnc_        1 QGRVNQLGGVFINGRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQE-     58

Query         44 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------------------     77
d1pdnc_       59 ----------------------------------TGSIRPGVIGGSKPRIATPEIENRIE     84

Query         78 ---------------------------------------     78
d1pdnc_       85 EYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV    123


hit structure      alignment
TMalign alignment (TM-score: 0.47 Raw score:35.87)
Query          1 ----------------PDYPVLDAILELYVDRDTGADAIVAA-GYDRELVVKTLRMVDTA     43
d1pdnc_        1 QGRVNQLGGVFINGRPLPNNIRLKIVEMAA-DGIRPCVISRQLRVSHGCVSKILNRYQET     59

Query         44 EYK---------------------------------------------------------     46
d1pdnc_       60 G-SIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSA    118

Query         47 -----RRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1pdnc_      119 ISRLV-------------------------------    123


hit structure      alignment
HHsearch alignment (Probability: 0.04 E-value:0.21)
DALI match                                                                  
Query          2 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKG     60
d1pdnc_       18 PNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIAT     76



hit structures. 
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46: d1u78a2 Transposase tc3a1-​65 (svm: 1.664)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 196
Modified z-scores:
dali:0.94 daliz:0.96 gdtts:0.93 tmscore:0.95 rmsd:0.23 AHM:0.41 LBcontacta:0.85 LBcontactb:0.80 LHM:0.27
id:0.51 blosum:0.50 compass:0.68 pearson:0.94
Scaled scores:
dali:0.68 daliz:0.54 gdtts:0.66 tmscore:0.51 rmsd:0.74 AHM:0.48 LBcontacta:0.37 LBcontactb:0.37 LHM:0.08
id:-0.01 blosum:0.07 compass:0.06 pearson:0.25

hit structure      alignment
FAST alignment (Normalized score: 4.95 Raw score:306.90)
Query          1 ------PDYPVLDAILELYVDRDTGADAIVAA----GYDRELVVKTLRMVDTAEYKRRQY     50
d1u78a2        1 APRRKALSVRDERNVIRAASNSCKTARDIRN-ELQLSASKRTILNVIKRS----------     49

Query         51 PPGTKISAKGFGKDRRLPITNRWREGH-     77
d1u78a2       50 ---------------------------G     50


hit structure      alignment
TMalign alignment (TM-score: 0.40 Raw score:30.55)
Query          1 ------PDYPVLDAILELYVDRD-TGADAIVAA-GYDRELVVKTLRM-VDTAEYKRRQYP     51
d1u78a2        1 APRRKALSVRDERNVIRAA-SNSCKTARDIRNELQLSAS-KRTILNVIK--RS--G----     50

Query         52 PGTKISAKGFGKDRRLPITNRWREGH     77
d1u78a2       51 --------------------------     51


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.17)
DALI match       ***************** ..............   
Query          9 ILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA     43
d1u78a2       15 VIRAASNSCKTARDIRNELQLSASKRTILNVIKRS     49



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47: d1u5tb2 Vacuolar protein sorting-​associated protein VPS36 (svm: 0.899)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.43  Contact: 136
Modified z-scores:
dali:0.72 daliz:0.66 gdtts:0.80 tmscore:0.82 rmsd:0.40 AHM:0.50 LBcontacta:0.57 LBcontactb:0.52 LHM:0.13
id:0.75 blosum:0.45 compass:0.66 pearson:0.82
Scaled scores:
dali:0.54 daliz:0.22 gdtts:0.41 tmscore:0.30 rmsd:0.65 AHM:0.53 LBcontacta:0.21 LBcontactb:0.23 LHM:0.47
id:0.03 blosum:0.07 compass:0.06 pearson:0.13

hit structure      alignment
DALI alignment (Z-score: 0.7 Raw score:87.50)
Query          1 -pDYPVLDAILELYvDRDT------GADAIVAAG--YDRElvVKTLRMVDTAeykrrqyp     51
d1u5tb2        1 ekFDVVKEKLVDLI-GDNPgsdllrLTQILSSNNskSNWT--LGILMEVLQN--------     49

Query         52 pgtkisakGFGKD--rrlpitnrwregh     77
d1u5tb2       50 --cvdegdLLIDKqlsgiyyyknsywps     75


hit structure      alignment
FAST alignment (Normalized score: 4.35 Raw score:330.90)
Query          1 P--DYPVLDAILELYVD-RDTGADAIVA--------AGYDRELVVKTLRMVDTAEYKRRQ     49
d1u5tb2        1 -EKFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVD-------     52

Query         50 YPPGTKISAKGFGKDRRLPITNRWREGH-----------------------     77
d1u5tb2       53 ----------------------------EGDLLIDKQLSGIYYYKNSYWPS     75


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.94)
Query          1 PD---YPVLDAILELYVD-RD-TGADAIVAA-G-------YDRELVVKTLRMVDTAEYK-     46
d1u5tb2        1 -EKFDV-VKEKLVDLI-GDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEG-DL     56

Query         47 ------------RRQYPPGTKISAKGFGKD-RRLPITNRWREGH     77
d1u5tb2       57 LIDKQLSGIYYY------------KNSYWPS-------------     75


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.54)
DALI match                    
Query          5 VLDAILELYVDRD     17
d1u5tb2       42 ILMEVLQNCVDEG     54



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48: d2foka3 Restriction endonuclease FokI,​ N-​terminal (recognition) domain (svm: 0.896)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.45  Contact: 169
Modified z-scores:
dali:0.73 daliz:0.71 gdtts:0.82 tmscore:0.84 rmsd:0.32 AHM:0.43 LBcontacta:0.62 LBcontactb:0.45 LHM:0.31
id:0.92 blosum:0.85 compass:0.66 pearson:0.84
Scaled scores:
dali:0.57 daliz:0.28 gdtts:0.49 tmscore:0.39 rmsd:0.70 AHM:0.57 LBcontacta:0.26 LBcontactb:0.21 LHM:0.14
id:0.10 blosum:0.17 compass:0.03 pearson:0.15

hit structure      alignment
DALI alignment (Z-score: 0.8 Raw score:102.60)
Query          1 ------------------PDYPVLDAILELyVDRDT------GADAIVAAGYDRElvVKT     36
d2foka3        1 vpkrvywemlatnltdkeYVRTRRALILEI-LIKAGslkieqIQDNLKKLGFDEV--IET     57

Query         37 LRMVDTAeykrrqyppgtkisakgfgkdrRLPI-----------tnrwregh     77
d2foka3       58 IENDIKG--------------lintgifiEIKGrfyqlkdhilqfvipnrlv     95


hit structure      alignment
FAST alignment (Normalized score: 3.89 Raw score:332.70)
Query          1 P-------------------DYPVLDAILELYVD-RDTGADAIVA------AGYDRELVV     34
d2foka3        1 -VPKRVYWEMLATNLTDKEYVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIE     59

Query         35 KTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-----------------     77
d2foka3       60 NDIKGLIN-----------------------------------TGIFIEIKGRFYQLKDH     84

Query         78 -----------     78
d2foka3       85 ILQFVIPNRLV     95


hit structure      alignment
TMalign alignment (TM-score: 0.39 Raw score:30.39)
Query          1 ------------------PDYPVLDAILELYVDRD------TGADAIVAAGYDRELVV-K     35
d2foka3        1 VPKRVYWEMLATNLTDKEYVRTRRALILEI-LIKAGSLKIEQIQDNLKKLGFDEV--IET     57

Query         36 TLRM-VDTA--EYKRRQY-PPGTKISAKGFGKDRRLPITNRWR-----------------     74
d2foka3       58 I-ENDI--KGL---I--NT--G------IF---IEIK--G-RFYQLKDHILQFVIPNRLV     95

Query         75 EGH     77
d2foka3       96 ---     96


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.57)
DALI match                                  
Query         14 VDRDTGADAIVAAGYDRELVVKTLRMV     40
d2foka3        1 VPKRVYWEMLATNLTDKEYVRTRRALI     27



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49: d1tqia1 Rio2 serine protein kinase N-​terminal domain (svm: 0.906)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.47  Contact: 166
Modified z-scores:
dali:0.64 daliz:0.60 gdtts:0.75 tmscore:0.72 rmsd:0.34 AHM:0.32 LBcontacta:0.51 LBcontactb:0.42 LHM:0.27
id:0.75 blosum:0.53 compass:0.66 pearson:0.86
Scaled scores:
dali:0.53 daliz:0.21 gdtts:0.41 tmscore:0.25 rmsd:0.65 AHM:0.59 LBcontacta:0.20 LBcontactb:0.15 LHM:0.15
id:0.04 blosum:0.07 compass:0.03 pearson:0.15

hit structure      alignment
DALI alignment (Z-score: 0.5 Raw score:85.60)
Query          1 --------pdYPVLDAILELyVDRD------TGADAIVAAgydreLVVKTLRMVDTAEYK     46
d1tqia1        1 mniaelygkmGKHSWRIMDA-IFKNlwdyeyVPLQLISSH--ariGEEKARNILKYLSDL     57

Query         47 R-rqyppgtkisakGFGK-drrlpitnrwregh     77
d1tqia1       58 RvvqnrqkdyegstFTFIglslyslhrlvrsgk     90


hit structure      alignment
FAST alignment (Normalized score: 3.67 Raw score:305.70)
Query          1 P---------DYPVLDAILELYVD-----RDTGADAIVA-AGYDRELVVKTLRMVDTAEY     45
d1tqia1        1 -MNIAELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSD---     56

Query         46 KRRQYPPGTKISAKGFGKDRRLPITNRWREGH----------------------------     77
d1tqia1       57 --------------------------------LRVVQNRQKDYEGSTFTFIGLSLYSLHR     84

Query         78 ------     78
d1tqia1       85 LVRSGK     90


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.25)
Query          1 ---------PDYPVLDAILELYVDR--D-----TGADAIVAA-GYDRELVVKTLRMVDTA     43
d1tqia1        1 MNIAELYGK-MGKHSWRIMDAI--FKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDL     57

Query         44 EYKR------------RQYPPGTKISAKGFGK-DR-------------RLPITNRWREGH     77
d1tqia1       58 R--VVQNRQKDYEGST------------FTFIG-LSLYSLHRLVRSGK------------     90


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.07)
DALI match        ..........     .........    .  ................          . 
Query          2 DYPVLDAILELYVDRDTGADAIVAA--GYDRELVVKTLRMVDTAEYKRRQYPP--GTKIS     57
d1tqia1       14 SWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQNRQKDYEGSTFT     73



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50: d1rp3a2 Sigma factor sigma-​28 (FliA) (svm: 1.099)

SCOP Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.55  Contact: 51
Modified z-scores:
dali:0.37 daliz:0.35 gdtts:0.40 tmscore:0.33 rmsd:0.40 AHM:0.38 LBcontacta:0.39 LBcontactb:0.48 LHM:0.32
id:0.58 blosum:0.67 compass:0.61 pearson:0.58
Scaled scores:
dali:0.59 daliz:0.11 gdtts:0.30 tmscore:0.07 rmsd:0.56 AHM:0.49 LBcontacta:0.24 LBcontactb:0.33 LHM:0.10
id:0.06 blosum:0.09 compass:0.18 pearson:0.18

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:48.80)
Query          1 pdypvldailelyvdrdtgadaivaagydrelvVKTLRMVDTAE----YKRRqyppgtki     56
d1rp3a2        1 -----------nveeevikreltekvkeavsklPEREKLVIQLIfyeeLPAK-----eva     44

Query         57 sakGFGKDRR----lpiTNRW--regh     77
d1rp3a2       45 kilETSVSRVsqlkakaLERLremlsn     71


hit structure      alignment
FAST alignment (Normalized score: 5.44 Raw score:402.30)
Query          1 PD----------------------YPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTL     37
d1rp3a2        1 --NVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLK     58

Query         38 RMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-     77
d1rp3a2       59 AKALERLREMLS----------------------------N     71


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:31.80)
Query          1 ---------------------PDYPVLDAILELYVDRDTGADAIVAA-GYDRELVVKTLR     38
d1rp3a2        1 NVEEEVIKRELTEKVKEAVSK-LPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKA     59

Query         39 M-VDTAEYKR-RQYP-PGTKISAKGFGKDRRLPITNRWREGH     77
d1rp3a2       60 KAL-ERL-REM--LSN--------------------------     71


hit structure      alignment
HHsearch alignment (Probability: 0.07 E-value:0.02)
DALI match                                            
Query          8 AILELYVDRDTGADAIVAA-GYDRELVVKTLRMVDTA     43
d1rp3a2       28 LVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALER     64



hit structures. 
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51: d1hw1a1 Fatty acid responsive transcription factor FadR,​ N-​terminal domain (svm: 0.896)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.43  Contact: 155
Modified z-scores:
dali:0.66 daliz:0.64 gdtts:0.82 tmscore:0.79 rmsd:0.29 AHM:0.36 LBcontacta:0.58 LBcontactb:0.52 LHM:0.13
id:0.82 blosum:0.76 compass:0.79 pearson:0.94
Scaled scores:
dali:0.49 daliz:0.24 gdtts:0.55 tmscore:0.38 rmsd:0.68 AHM:0.55 LBcontacta:0.24 LBcontactb:0.26 LHM:0.44
id:0.07 blosum:0.13 compass:0.29 pearson:0.30

hit structure      alignment
FAST alignment (Normalized score: 3.58 Raw score:270.60)
Query          1 P----DYPVLDAILELYVDR--------DTGADAIVA-AGYDRELVVKTLRMVDTAEYKR     47
d1hw1a1        1 -AQSPAGFAEEYIIESIWN-NRFPPGTILPAERELSELIGVTRTTLREVLQRLAR-----     53

Query         48 RQYPPGTKISAKGFGKDRRLPITNRWREGH---------------------     77
d1hw1a1       54 ------------------------------DGWLTIQHGKPTKVNNFWETS     74


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.47)
Query          1 -PD--YPVL-DAILELYVD----R-----DTGADAIVAA-GYDRELVVKTLRMVDTAE--     44
d1hw1a1        1 AQSPAG-FAEEYIIES--IWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWL     57

Query         45 ----------YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1hw1a1       58 TIQHGKPTKV--------------NNFWE--TS----------     74


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.03)
DALI match        **************                 .*****************          
Query          1 PDYPVLDAILELYVDRDTGADAIV--------AAGYDRELVVKTLRMVDTAEYKRRQYPP     52
d1hw1a1        4 PAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK     63

DALI match             
Query         53 GTKISA     58
d1hw1a1       64 PTKVNN     69



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52: d1ft9a1 CO-​sensing protein CooA,​ C-​terminal domain (svm: 0.910)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 128
Modified z-scores:
dali:0.61 daliz:0.63 gdtts:0.75 tmscore:0.73 rmsd:0.31 AHM:0.28 LBcontacta:0.50 LBcontactb:0.54 LHM:0.28
id:0.61 blosum:0.53 compass:0.67 pearson:0.82
Scaled scores:
dali:0.62 daliz:0.27 gdtts:0.54 tmscore:0.34 rmsd:0.72 AHM:0.65 LBcontacta:0.28 LBcontactb:0.36 LHM:0.15
id:0.03 blosum:0.07 compass:0.13 pearson:0.23

hit structure      alignment
DALI alignment (Z-score: 0.5 Raw score:82.20)
Query          1 PDYPVLDAILE-----------lyvDRDTGADAIVAA-gYDRElvvKTLRMVDtaeykrr     48
d1ft9a1        1 DIKQRIAGFFIdhanttgrqtgvivSVDFTVEEIANLigSSRQttsTALNSLI----keg     56

Query         49 qyppgtkisaKGFGkdrrlpitnrwregh     77
d1ft9a1       57 yisrqgrghyTIPN-------lvrlkaaa     78


hit structure      alignment
FAST alignment (Normalized score: 3.49 Raw score:270.80)
Query          1 PDYP-VLDAILELYVD--------------RDTGADAIVA-AGYDRELVVKTLRMVDTAE     44
d1ft9a1        1 ----DIKQRIAGFFIDHANTTGRQTGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIK--     54

Query         45 YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------------------------     77
d1ft9a1       55 ---------------------------------EGYISRQGRGHYTIPNLVRLKAAA     78


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.72)
Query          1 PDYPVLDAILELYVD-R-------------D-TGADAIVAA-GYDRELVVKTLRMVDTAE     44
d1ft9a1        1 --D-IKQRIAGF-FIDHANTTGRQTGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEG     56

Query         45 YKR----------RQYPPGTKISAKGFGK-------DRRLPITNRWREGH     77
d1ft9a1       57 --YISRQGRGHYT------------IPNLVRLKAAA--------------     78


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.11)
DALI match        ****   ******* 
Query         27 GYDRELVVKTLRMVDT     42
d1ft9a1       39 GSSRQTTSTALNSLIK     54



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53: d1tc3c_ Transposase tc3a1-​65 (svm: 1.664)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.59  Contact: 169
Modified z-scores:
dali:0.95 daliz:0.97 gdtts:0.94 tmscore:0.96 rmsd:0.18 AHM:0.29 LBcontacta:0.95 LBcontactb:0.97 LHM:0.20
id:0.52 blosum:0.41 compass:0.67 pearson:0.91
Scaled scores:
dali:0.71 daliz:0.61 gdtts:0.70 tmscore:0.57 rmsd:0.78 AHM:0.58 LBcontacta:0.56 LBcontactb:0.68 LHM:0.20
id:-0.01 blosum:0.04 compass:0.05 pearson:0.19

hit structure      alignment
FAST alignment (Normalized score: 4.89 Raw score:306.40)
Query          1 -----PDYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGT     54
d1tc3c_        1 PRGSALSDTERAQLDVM-KLLNVSLHEMSRKISRSRHCIRVYLK----------------     43

Query         55 KISAKGFGKDRRLPITNRWREGH--------     77
d1tc3c_       44 -----------------------DPVSYGTS     51


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.52)
Query          1 -----PDYPVLDAILELYVDRDTGADAIVAAGYDR-ELVVKTLRMV------DTAEYKRR     48
d1tc3c_        1 PRGSALSDTERAQLDVMKL-LNVSLHEMSRKISRSRHCIRVYLKDPVSYGTS--------     51

Query         49 QYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1tc3c_       52 -----------------------------     52


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.31)
DALI match                   
Query         34 VKTLRMVDTAEY     45
d1tc3c_       25 HEMSRKISRSRH     36



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54: d1hkqa_ Replication protein A,​ repA (svm: 0.728)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.43  Contact: 169
Modified z-scores:
dali:0.73 daliz:0.76 gdtts:0.84 tmscore:0.83 rmsd:0.26 AHM:0.33 LBcontacta:0.62 LBcontactb:0.56 LHM:0.24
id:0.91 blosum:0.63 compass:0.46 pearson:0.75
Scaled scores:
dali:0.70 daliz:0.34 gdtts:0.52 tmscore:0.42 rmsd:0.76 AHM:0.63 LBcontacta:0.31 LBcontactb:0.34 LHM:0.25
id:0.09 blosum:0.09 compass:0.12 pearson:0.13

hit structure      alignment
DALI alignment (Z-score: 1.0 Raw score:114.40)
Query          1 ------pdypvldailelYVDRD-----------------TGADAIVAA-GYDRELVVKT     36
d1hkqa_        1 qsnkliesshtltlnekrLVLCAaslidsrkplpkdgyltIRADTFAEVfGIDVKHAYAA     60

Query         37 LRMVDT-AEYKrrQYPPgtkisakgfgkdRRLPitnrWREGH------------------     77
d1hkqa_       61 LDDAATkLFNR--DIRR-yvkgkvvermrWVFH---vKYREGqgcvelgfsptiiphltm    114

Query         78 -----------     78
d1hkqa_      115 lhkeftsyqlk    125


hit structure      alignment
FAST alignment (Normalized score: 1.93 Raw score:189.10)
Query          1 P--------------DYPVLDAILELYVD-------------RDTGADAIVA-AGYDREL     32
d1hkqa_        1 -QSNKLIESSHTLTLNEKRLVLCAAS---LIDSRKPLPKDGYLTIRADTFAEVFGIDVKH     56

Query         33 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------------     77
d1hkqa_       57 AYAALDDAAT-----------------------------------KLFNRDIRRYVKGKV     81

Query         78 --------------------------------------------     78
d1hkqa_       82 VERMRWVFHVKYREGQGCVELGFSPTIIPHLTMLHKEFTSYQLK    125


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.97)
Query          1 ------------PDYPVLDAILELYVDRD-----------------TGADAIVAA-GYDR     30
d1hkqa_        1 QSNKLIESSHTL-----TL-NEKRLVLCAASLIDSRKPLPKDGYLTIRADTFAEVFGIDV     54

Query         31 -ELVVKTLRMVDTA-EYKRRQYPPG---------TKISAKGFGKDRRLPITNRWRE--GH     77
d1hkqa_       55 KH-AYAALDDAATKLF-NR--DIRRYVKGKVVER--------MR-WVFH--VKYREGQGC     99

Query         78 --------------------------     78
d1hkqa_      100 VELGFSPTIIPHLTMLHKEFTSYQLK    125


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.50)
DALI match                     
Query          3 YPVLDAILELYVDR     16
d1hkqa_       58 YAALDDAATKLFNR     71



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55: d1smyf1 Sigma70 (svm: 0.906)

SCOP Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.43  Contact: 158
Modified z-scores:
dali:0.75 daliz:0.79 gdtts:0.81 tmscore:0.81 rmsd:0.31 AHM:0.52 LBcontacta:0.66 LBcontactb:0.71 LHM:0.24
id:0.94 blosum:0.96 compass:0.82 pearson:0.96
Scaled scores:
dali:0.55 daliz:0.35 gdtts:0.50 tmscore:0.35 rmsd:0.64 AHM:0.32 LBcontacta:0.26 LBcontactb:0.32 LHM:0.19
id:0.13 blosum:0.26 compass:0.36 pearson:0.38

hit structure      alignment
FAST alignment (Normalized score: 3.67 Raw score:251.30)
Query          1 P------DYPVLDAILELYVD--------RDTGADAIVA---AGYDRELVVKTLRMVDTA     43
d1smyf1        1 -IRIPVHMVETINKLSRTA--RQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIA---     54

Query         44 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-------     77
d1smyf1       55 ----------------------------------QEPVSLE     61


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:28.42)
Query          1 -----PDYPVLDAILE-LY-VDR-----DTGADAIVAA-G-YDR-ELVVKTLRMV-DTAE     44
d1smyf1        1 IRIPVHMVETINKLSRTARQ-LQQELGREPTYEEIAEAMGPGWDAKRVEETL-KIA--QE     56

Query         45 YKRRQ--YPPGTKISAKGFGKDRRLPITNRWREGH     77
d1smyf1       57 PV--SLE----------------------------     61


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.09)
DALI match             **********.   *************
Query         10 LELYVDRDTGADAIVAA---GYDRELVVKTLRM     39
d1smyf1       21 LQQELGREPTYEEIAEAMGPGWDAKRVEETLKI     53



hit structures. 
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56: d1lnwa_ MexR repressor (svm: 0.901)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.32  Contact: 151
Modified z-scores:
dali:0.61 daliz:0.64 gdtts:0.74 tmscore:0.68 rmsd:0.33 AHM:0.29 LBcontacta:0.57 LBcontactb:0.55 LHM:0.26
id:0.85 blosum:0.83 compass:0.73 pearson:0.87
Scaled scores:
dali:0.56 daliz:0.27 gdtts:0.42 tmscore:0.27 rmsd:0.65 AHM:0.63 LBcontacta:0.31 LBcontactb:0.32 LHM:0.21
id:0.07 blosum:0.15 compass:0.28 pearson:0.27

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:94.90)
Query          1 --------------------------------pdYPVLDAILELyVDRD--TGADAIVAA     26
d1lnwa_        1 nypvnpdlmpalmavfqhvrtriqseldcqrldlTPPDVHVLKL-IDEQrgLNLQDLGRQ     59

Query         27 gYDRElvVKTLRMVDT-AEYK----rrqyppgtkisakGFGK------------------     63
d1lnwa_       60 -MCRD-kALITRKIRElEGRNlvrrernpsdqrsfqlfLTDEglaihqhaeaimsrvhde    117

Query         64 ----------drrlpitnrwregh     77
d1lnwa_      118 lfapltpveqatlvhlldqclaaq    141


hit structure      alignment
FAST alignment (Normalized score: 2.12 Raw score:221.20)
Query          1 ---------------------------------PDYPVLDAILELYVDRDTGADAIVA--     25
d1lnwa_        1 NYPVNPDLMPALMAVFQHVRTRIQSELDCQRLDLTPPDVHVLKLIDE-----------QR     49

Query         26 --------------------------------------------AGYDRELVVKTLRMVD     41
d1lnwa_       50 GLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEA    109

Query         42 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-----------------------     77
d1lnwa_      110 IMSRVHDEL---------------------------FAPLTPVEQATLVHLLDQCLAAQ    141


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:32.79)
Query          1 ---------------------------------PDYPVLDAILELYVDR-D-TGADAIVA     25
d1lnwa_        1 NYPVNPDLMPALMAVFQHVRTRIQSELDCQRLD-LTPPDVHVLKLI-DEQRGLNLQDLGR     58

Query         26 AGYD-RELVVKTLRMVDTAEYK---------------RRQYPPGTKISAKGFGK------     63
d1lnwa_       59 QMCRDKALITRKIRELEGRN-LVRRERNPSDQRSFQL------------FLTDEGLAIHQ    105

Query         64 ------------------------------------DRRLPITNRWREGH     77
d1lnwa_      106 HAEAIMSRVHDELFAPLTPVEQATLVHLLDQCLAAQ--------------    141


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.10)
DALI match       ......... ....*********  ....  .............         
Query          4 PVLDAILELYVDRDTGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1lnwa_       37 PDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQ     89



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57: d1hq1a_ Signal sequence binding protein Ffh (svm: 0.866)

SCOP Superfamily: Signal peptide-​binding domain  |  SCOP Fold: Signal peptide-​binding domain  |  SCOP Class: All alpha proteins

Consensus: 0.54  Contact: 42
Modified z-scores:
dali:0.40 daliz:0.34 gdtts:0.41 tmscore:0.39 rmsd:0.53 AHM:0.51 LBcontacta:0.37 LBcontactb:0.54 LHM:0.17
id:0.76 blosum:0.58 compass:0.32 pearson:0.46
Scaled scores:
dali:0.59 daliz:0.10 gdtts:0.31 tmscore:0.12 rmsd:0.61 AHM:0.53 LBcontacta:0.21 LBcontactb:0.33 LHM:0.39
id:0.06 blosum:0.05 compass:0.01 pearson:0.02

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:56.60)
Query          1 pdypvlDAILELyvdrdtgadaivaagydrelvvktlrmVDTAEYK-RRQY--PPGTKis     57
d1hq1a_        1 --gfdlNDFLEQ---lrqddkvlvrmeaiinsmtmkeraKPEIIKGsRKRRiaAGSGM--     53

Query         58 akgfGKDRRlpitnrwREGH---     77
d1hq1a_       54 qvqdVNRLLkqfddmqRMMKkmk     76


hit structure      alignment
FAST alignment (Normalized score: 4.03 Raw score:308.70)
Query          1 ---------------PDYPVLDAILELYVDRDT---------------GADAIVA-AGYD     29
d1hq1a_        1 GFDLNDFLEQLRQDDKVLVRMEAIINS------MTMKERAKPEIIKGSRKRRIAAGSGMQ     54

Query         30 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--     77
d1hq1a_       55 VQDVNRLLKQFDDMQRMMKK----------------------------MK     76


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:34.10)
Query          1 ---------------PDYPVLDAILELYVDR-D------T---GADAIVAA-GYDRELVV     34
d1hq1a_        1 GFDLNDFLEQLRQDDKVLVRMEAIINSM-TMKERAKPEIIKGSRKRRIAAGSGMQVQDVN     59

Query         35 KTLRMVDTAEYKRR-QYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1hq1a_       60 RLLKQFDDMQRMMKKMK---------------------------     76


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.26)
DALI match                                      
Query         29 DRELVVKTLRMVDTAEYKRRQYPPGTKISAK     59
d1hq1a_       14 DDKVLVRMEAIINSMTMKERAKPEIIKGSRK     44



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58: d1gvda_ c-​Myb,​ DNA-​binding domain (svm: 0.896)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.54  Contact: 49
Modified z-scores:
dali:0.48 daliz:0.38 gdtts:0.59 tmscore:0.51 rmsd:0.44 AHM:0.55 LBcontacta:0.45 LBcontactb:0.40 LHM:0.25
id:0.91 blosum:0.69 compass:0.44 pearson:0.64
Scaled scores:
dali:0.57 daliz:0.04 gdtts:0.40 tmscore:0.14 rmsd:0.60 AHM:0.46 LBcontacta:0.20 LBcontactb:0.16 LHM:0.18
id:0.13 blosum:0.09 compass:0.09 pearson:0.07

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:34.40)
Query          1 pdypvldailelyvdRDTGAdaivaagydrelvvkTLRMVDT-AEYKRrqyppgtkiSAK     59
d1gvda_        1 -----------likgPWTKE------------edqRLIKLVQkYGPKR-wsviakhlKGR     36

Query         60 GF-gkdRRLPitnrwregh     77
d1gvda_       37 IGkqcrERWH---nhlnpe     52


hit structure      alignment
FAST alignment (Normalized score: 3.62 Raw score:229.10)
Query          1 -----PDYPVLDAILELYVDRDT----GADAIVA--AGYDRELVVKTLRMVDTAEYKRRQ     49
d1gvda_        1 LIKGPWTKEEDQRLIKLVQK---YGPKRWSVIAKHLKGRIGKQCRERWH-----------     46

Query         50 YPPGTKISAKGFGKDRRLPITNRWREGH------     77
d1gvda_       47 ----------------------------NHLNPE     52


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:31.89)
Query          1 -----PDYPVLDAILELYVDRDT---GADAIVAAGY-DR-ELVVKTLRM--VDTAEYKRR     48
d1gvda_        1 LIKGPWTKEEDQRLIKLV-QK-YGPKRWSVIAKHLKGRIGKQCRERWHNHLN--PE----     52

Query         49 QYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1gvda_       53 -----------------------------     53


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.12)
DALI match                   ........***** 
Query         23 IVAAGYDRELVVKTLRMVDTAEYKRR     48
d1gvda_        1 LIKGPWTKEEDQRLIKLVQKYGPKRW     26



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59: d1fnna1 CDC6,​ C-​terminal domain (svm: 0.905)

SCOP Superfamily: "​Winged helix"​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.29  Contact: 165
Modified z-scores:
dali:0.65 daliz:0.58 gdtts:0.78 tmscore:0.80 rmsd:0.40 AHM:0.43 LBcontacta:0.56 LBcontactb:0.61 LHM:0.22
id:0.87 blosum:0.62 compass:0.59 pearson:0.71
Scaled scores:
dali:0.59 daliz:0.21 gdtts:0.46 tmscore:0.36 rmsd:0.69 AHM:0.60 LBcontacta:0.24 LBcontactb:0.30 LHM:0.34
id:0.07 blosum:0.11 compass:0.05 pearson:0.06

hit structure      alignment
DALI alignment (Z-score: 0.5 Raw score:95.20)
Query          1 ------pdYPVLDAILELYVDRD----------------TGADAIVAAGYDrelVVKTlR     38
d1fnna1        1 iseevligLPLHEKLFLLAIVRSlkishtpyitfgdaeeSYKIVCEEYGER---PRVH-S     56

Query         39 MVDTaeykrrqyppgTKISakGFGK-DRRL--------------pitnrwregh     77
d1fnna1       57 QLWS-----ylndlrEKGI--VETRqNTTLisigtepldtleavitklikeelr    103


hit structure      alignment
FAST alignment (Normalized score: 2.36 Raw score:209.90)
Query          1 P-----------DYPVLDAILELYVD----RDTGADAIVAA------------GYDRELV     33
d1fnna1        1 -ISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEE-SYKIVCEEYGERPRVHSQL     58

Query         34 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----------------     77
d1fnna1       59 WSYLNDLRE-----------------------------------KGIVETRQNTTLISIG     83

Query         78 --------------------     78
d1fnna1       84 TEPLDTLEAVITKLIKEELR    103


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.56)
Query          1 --------PDYPVLDAILELYVDR-D-------TGADA-IVA--A---------GYDREL     32
d1fnna1        1 ISEEVLIGLPL-HEKLFLLAI-VRSLKISHTPYITFGDAE-ESYKIVCEEYGERPRVHSQ     57

Query         33 VVKTLRMVDTAEY--------------KRRQYPPGTK-ISAKG-------------FGKD     64
d1fnna1       58 LWSYLNDLREKGIVETRQNTTLISIGT---------EP-LDTLEAVITKLIKEELR----    103

Query         65 RRLPITNRWREGH     77
d1fnna1      104 -------------    104


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.79)
DALI match       *******.  .... ....
Query         23 IVAAGYDRELVVKTLRMVD     41
d1fnna1       45 CEEYGERPRVHSQLWSYLN     63



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60: d1kqpa_ NH3-​dependent NAD+-​synthetase (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.18  Contact: 39
Modified z-scores:
dali:0.39 daliz:0.38 gdtts:0.51 tmscore:0.44 rmsd:0.38 AHM:0.38 LBcontacta:0.43 LBcontactb:0.31 LHM:0.32
id:0.69 blosum:0.68 compass:0.33 pearson:0.36
Scaled scores:
dali:0.69 daliz:0.17 gdtts:0.47 tmscore:0.22 rmsd:0.67 AHM:0.60 LBcontacta:0.30 LBcontactb:0.10 LHM:0.28
id:0.09 blosum:0.08 compass:-0.00 pearson:0.02

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:55.40)
Query          1 ------------------------------------------------------------      1
d1kqpa_        1 smqekimrelhvkpsidpkqeiedrvnflkqyvkktgakgfvlgisggqdstlagrlaql     60

Query          1 --------pdypvLDAI-------------------------------------------      9
d1kqpa_       61 avesireeggdaqFIAVrlphgtqqdeddaqlalkfikpdkswkfdikstvsafsdqyqq    120

Query         10 ---------lelyvdrdtGADAIVAAGYdrelvvkTLRM---------------------     39
d1kqpa_      121 etgdqltdfnkgnvkartRMIAQYAIGG-qegllvLGTDhaaeavtgfftkygdggadll    179

Query         40 --vdtaEYKRRQY--PPGTKIsakgFGKDRRL----------------------------     67
d1kqpa_      180 pltgltKRQGRTLlkELGAPE---rLYLKEPTadlldekpqqsdetelgisydeiddyle    236

Query         68 -------------------------pitnrwregh     77
d1kqpa_      237 gkevsakvsealekrysmtehkrqvpasmfddwwk    271


hit structure      alignment
FAST alignment (Normalized score: 1.55 Raw score:223.30)
Query          1 P---------------------DYPVLDAILELYVDRDTGADAIVAAGY-----------     28
d1kqpa_        1 -SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAK---------GFVLGISGGQD     50

Query         29 ---DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------     77
d1kqpa_       51 STLAGRLAQLAVESIRE-----------------------------------EGGDAQFI     75

Query         78 ------------------------------------------------------------     78
d1kqpa_       76 AVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVK    135

Query         78 ------------------------------------------------------------     78
d1kqpa_      136 ARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKE    195

Query         78 ------------------------------------------------------------     78
d1kqpa_      196 LGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMT    255

Query         78 ----------------     78
d1kqpa_      256 EHKRQVPASMFDDWWK    271


hit structure      alignment
TMalign alignment (TM-score: 0.35 Raw score:26.86)
Query          1 ----------------------PDY-PVL-DAILELYVDRDTGADAIVA------AG-YD     29
d1kqpa_        1 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQY-VKK-TGAKG-F-V-LGISGGQD-STLA     54

Query         30 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR-----------------------     66
d1kqpa_       55 GRLAQLAVESIREEG----------------G----DAQFIAVRLPHGTQQDEDDAQLAL     94

Query         67 ---LPITNRWREGH----------------------------------------------     77
d1kqpa_       95 KFI--------KPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAI    146

Query         78 ------------------------------------------------------------     78
d1kqpa_      147 GGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKE    206

Query         78 ------------------------------------------------------------     78
d1kqpa_      207 PTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMF    266

Query         78 -----     78
d1kqpa_      267 DDWWK    271


hit structure      alignment
HHsearch alignment (Probability: 0.94 E-value:0.00)
DALI match                                                            
Query          2 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGT     54
d1kqpa_      227 SYDEIDDYLEGK-------------EVSAKVSEALEKRYSMTEHKR-QVPASM    265



hit structures. 
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61: d1mswd_ T7 RNA polymerase (svm: 0.897)

SCOP Superfamily: DNA/​RNA polymerases  |  SCOP Fold: DNA/​RNA polymerases  |  SCOP Class: Multi-​domain proteins (alpha and beta)

Consensus: 0.27  Contact: 168
Modified z-scores:
dali:0.66 daliz:0.68 gdtts:0.72 tmscore:0.72 rmsd:0.40 AHM:0.39 LBcontacta:0.61 LBcontactb:0.50 LHM:0.55
id:0.86 blosum:0.59 compass:0.41 pearson:0.72
Scaled scores:
dali:0.66 daliz:0.31 gdtts:0.47 tmscore:0.37 rmsd:0.71 AHM:0.62 LBcontacta:0.30 LBcontactb:0.25 LHM:-0.02
id:0.06 blosum:0.08 compass:0.09 pearson:0.08

hit structure      alignment
DALI alignment (Z-score: 0.9 Raw score:132.90)
Query          1 ------------------------------------------------------------      1
d1mswd_        1 ntiniakndfsdielaaipfntladhygerlareqlalehesyemgearfrkmferqlka     60

Query          1 ------------------------------------------------pDYPVLDAILEL     12
d1mswd_       61 gevadnaaakplittllpkmiarindwfeevkakrgkrptafqflqeikPEAVAYITIKT    120

Query         13 YVDRD---------tGADAIVAAG------------------------------------     27
d1mswd_      121 TLACLtsadnttvqaVASAIGRAIedearfgrirdleakhfkknveeqlnkrvghvykka    180

Query         28 ------------------------------YDRELVVKTLR--MVDT----------AEY     45
d1mswd_      181 fmqvveadmlskgllggeawsswhkedsihVGVRCIEMLIEstGMVSlhrqsetielAPE    240

Query         46 KRRQY--PPGT-------------------------------------------------     54
d1mswd_      241 YAEAIatRAGAlagispmfqpcvvppkpwtgitgggywangrrplalvrthskkalmrye    300

Query         55 ------------------------------------------------------------     55
d1mswd_      301 dvympevykainiaqntawkinkkvlavanvitkwkhcpvedipaiereelpmktawkra    360

Query         55 ------------------------------------------------------------     55
d1mswd_      361 aaavyrkdkarksrrislefmleqankfanhkaiwfpynmdwrgrvyavsmfnpqgndmt    420

Query         55 ------------------------------------------------------------     55
d1mswd_      421 kglltlakgkpigkegyywlkihgancagvdkvpfperikfieenhenimacaksplent    480

Query         55 ------------------------------------------------------------     55
d1mswd_      481 wwaeqdspfcflafcfeyagvqhhglsyncslplafdgscsgiqhfsamlrdevggravn    540

Query         55 ------------------------------------------------------------     55
d1mswd_      541 llpsetvqdiygivakkvneilqadaingtdnevvtvtdentgeisekvklgtkalagqw    600

Query         55 ------------------------------------------------------------     55
d1mswd_      601 laygvtrsvtkrsvmtlaygskefgfrqqvledtiqpaidsgkglmftqpnqaagymakl    660

Query         55 ------------------------------------------------------------     55
d1mswd_      661 iwesvsvtvvaaveamnwlksaakllaaevkdkktgeilrkrcavhwvtpdgfpvwqeyk    720

Query         55 ------------------------------------------------------------     55
d1mswd_      721 kpiqtrlnlmflgqfrlqptintnkdseidahkqesgiapnfvhsqdgshlrktvvwahe    780

Query         55 ------------------------------------------------------------     55
d1mswd_      781 kygiesfalihdsfgtipadaanlfkavretmvdtyescdvladfydqfadqlhesqldk    840

Query         55 kisakgfgkdrrlpitnrwregh     77
d1mswd_      841 mpalpakgnlnlrdilesdfafa    863


hit structure      alignment
FAST alignment (Normalized score: 0.97 Raw score:249.20)
Query          1 ------------------------------------------------------------      1
d1mswd_        1 NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKA     60

Query          1 ------------------------------------------------PDYPVLDAILEL     12
d1mswd_       61 GEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT    120

Query         13 YVDRDT------------GADAIVAAGY--------------------------------     28
d1mswd_      121 TLA---CLTSADNTTVQAVASAIGR---AIEDEARFGRIRDLEAKHFKKNVEEQLNKRVG    174

Query         29 ---------------------------------DRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1mswd_      175 HVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIE-------------    221

Query         56 ISAKGFGKDRRLPITNRWREGH--------------------------------------     77
d1mswd_      222 ----------------------STGMVSLHRQSETIELAPEYAEAIATRAGALAGISPMF    259

Query         78 ------------------------------------------------------------     78
d1mswd_      260 QPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAW    319

Query         78 ------------------------------------------------------------     78
d1mswd_      320 KINKKVLAVANVITKWKHCPVEDIPAIEREELPMKTAWKRAAAAVYRKDKARKSRRISLE    379

Query         78 ------------------------------------------------------------     78
d1mswd_      380 FMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYW    439

Query         78 ------------------------------------------------------------     78
d1mswd_      440 LKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYA    499

Query         78 ------------------------------------------------------------     78
d1mswd_      500 GVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVN    559

Query         78 ------------------------------------------------------------     78
d1mswd_      560 EILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAY    619

Query         78 ------------------------------------------------------------     78
d1mswd_      620 GSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWL    679

Query         78 ------------------------------------------------------------     78
d1mswd_      680 KSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQP    739

Query         78 ------------------------------------------------------------     78
d1mswd_      740 TINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPA    799

Query         78 ------------------------------------------------------------     78
d1mswd_      800 DAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESD    859

Query         78 ----     78
d1mswd_      860 FAFA    863


hit structure      alignment
TMalign alignment (TM-score: 0.33 Raw score:25.21)
Query          1 ------------------------------------------------------------      1
d1mswd_        1 NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKA     60

Query          1 ------------------------------------------------------------      1
d1mswd_       61 GEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT    120

Query          1 ---------------------------------------PDYPVLDAILELYVDR-DT--     18
d1mswd_      121 TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAK------------HFKKNVEEQ    168

Query         19 -GADAI-VAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWR--     74
d1mswd_      169 L----NK---RVGHVYKKAFMQVVEADMLS-KG----------------LLGGEAWSSWH    204

Query         75 ------------------------------------------------------------     75
d1mswd_      205 KEDSIHVGVRCIEMLIESTGMVSLHRQSETIELAPEYAEAIATRAGALAGISPMFQPCVV    264

Query         75 ------------------------------------------------------------     75
d1mswd_      265 PPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKK    324

Query         75 ------------------------------------------------------------     75
d1mswd_      325 VLAVANVITKWKHCPVEDIPAIEREELPMKTAWKRAAAAVYRKDKARKSRRISLEFMLEQ    384

Query         75 ------------------------------------------------------------     75
d1mswd_      385 ANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHG    444

Query         75 ------------------------------------------------------------     75
d1mswd_      445 ANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHH    504

Query         75 ------------------------------------------------------------     75
d1mswd_      505 GLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQA    564

Query         75 ------------------------------------------------------------     75
d1mswd_      565 DAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEF    624

Query         75 ------------------------------------------------------------     75
d1mswd_      625 GFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAK    684

Query         75 ---------------------------------------------EG-------------     76
d1mswd_      685 LLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTN    744

Query         77 ------------------------------------------------------------     77
d1mswd_      745 KDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANL    804

Query         77 -----------------------------------------------------------H     77
d1mswd_      805 FKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA-    863


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.12)
DALI match                                                                   
Query          3 YPVLDAILELYVDRD-----------------------------TGADAIVAAGYDRELV     33
d1mswd_      551 YGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVT    610

DALI match           
Query         34 VKTL     37
d1mswd_      611 KRSV    614



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62: d1u5ta1 Vacuolar sorting protein SNF8 (svm: 0.703)

SCOP Superfamily: ​(​Winged helix​(​ DNA-​binding domain  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.21  Contact: 205
Modified z-scores:
dali:0.69 daliz:0.61 gdtts:0.79 tmscore:0.83 rmsd:0.53 AHM:0.51 LBcontacta:0.44 LBcontactb:0.42 LHM:0.29
id:0.45 blosum:0.12 compass:0.24 pearson:0.55
Scaled scores:
dali:0.58 daliz:0.20 gdtts:0.39 tmscore:0.32 rmsd:0.63 AHM:0.55 LBcontacta:0.14 LBcontactb:0.14 LHM:0.18
id:-0.02 blosum:-0.01 compass:0.03 pearson:0.03

hit structure      alignment
DALI alignment (Z-score: 0.4 Raw score:97.10)
Query          1 --------------------------pdyPVLDAILE--lyVDRDT---------GADAi     23
d1u5ta1        1 vnktilekqsvelrdqlmvfqerlvefakKHNSELQAspefRSKFMhmcssigidPLSL-     59

Query         24 vaagyDRELVvKTLRMVDTA-EYKRRQY------------PPGT-----kisaKGFG-kd     64
d1u5ta1       60 ---fdRDKHL-FTVNDFYYEvCLKVIEIcrqtkdmnggviSFQElekvhfrklNVGLddl    115

Query         65 RRLP--ITNR---------------wregh     77
d1u5ta1      116 EKSIdmLKSLecfeifqirgkkflrsvpne    145


hit structure      alignment
FAST alignment (Normalized score: 1.23 Raw score:129.60)
Query          1 P-------------------------------DYPVLDAILELYVDRDT---GADAIVAA     26
d1u5ta1        1 -VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQA-----------SPEFRSKFMH-     47

Query         27 GY-----------------DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPI     69
d1u5ta1       48 --MCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQ-------------------     86

Query         70 TNRWREGH----------------------------------------------------     77
d1u5ta1       87 --------TKDMNGGVISFQELEKVHFRKLNVGLDDLEKSIDMLKSLECFEIFQIRGKKF    138

Query         78 -------     78
d1u5ta1      139 LRSVPNE    145


hit structure      alignment
TMalign alignment (TM-score: 0.36 Raw score:27.66)
Query          1 ------------------------------------PDYPVLDA-ILE-L-----YVDRD     17
d1u5ta1        1 VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFR-SKFMHMCSSIGI-----     54

Query         18 TGADAIVA---AGYDRELVVKTLRMVDTA-EYKRR--QY--P---PGTK-----------     55
d1u5ta1       55 DPLS-LFDRDK---HLFTVNDFYYEVCLKVIEI-CRQTKDMNGGVISFQELEKVHFRKLN    109

Query         56 ------ISAKG--FG-------KDR--------R------LPITNRWREGH     77
d1u5ta1      110 VGLDDL----EKSIDMLKSLECFEIFQIRGKKFLRSVPNE-----------    145


hit structure      alignment
HHsearch alignment (Probability: 0.00 E-value:0.56)
DALI match                      
Query         30 RELVVKTLRMVDTAE     44
d1u5ta1       98 QELEKVHFRKLNVGL    112



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63: d6paxa2 Pax-​6 (svm: 1.285)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.55  Contact: 61
Modified z-scores:
dali:0.34 daliz:0.28 gdtts:0.41 tmscore:0.39 rmsd:0.60 AHM:0.56 LBcontacta:0.31 LBcontactb:0.38 LHM:0.20
id:0.48 blosum:0.48 compass:0.55 pearson:0.60
Scaled scores:
dali:0.54 daliz:0.00 gdtts:0.34 tmscore:0.12 rmsd:0.56 AHM:0.50 LBcontacta:0.15 LBcontactb:0.21 LHM:0.25
id:0.01 blosum:0.01 compass:0.10 pearson:0.14

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:33.50)
Query          1 pdypvldAILElyvdrdtgadaivaagydrelvvktlrmVDTA-----------eykRRQ     49
d6paxa2        1 -----ggSKPR-----------------------vatpeVVSKiaqykqecpsifawEIR     32

Query         50 Y---ppgtkiSAKGFGKD--RRLP-itNRWRegh     77
d6paxa2       33 DrllsegvctNDNIPSVSsiNRVLrnlASEK-qq     65


hit structure      alignment
FAST alignment (Normalized score: 5.00 Raw score:353.50)
Query          1 P--------DYPVLDAILELYVDR-DTGADAIVAA------------GYDRELVVKTLRM     39
d6paxa2        1 -GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRD-RLLSEGVCTNDNIPSVSSINRVLRN     58

Query         40 VDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-     77
d6paxa2       59 LASEKQ--------------------------------Q     65


hit structure      alignment
TMalign alignment (TM-score: 0.45 Raw score:34.44)
Query          1 -------PDYPVLDAILELYVDRD--TGADAIVAA-G---------YD-RELVVKTLRMV     40
d6paxa2        1 GGSKPRVATPEVVSKIAQYK-QECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNL     59

Query         41 DTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d6paxa2       60 ASEKQQ-------------------------------     65


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.05)
DALI match       ...      
Query         41 DTAEYKRRQ     49
d6paxa2       15 KIAQYKQEC     23



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64: d1e3oc1 Oct-​1 POU Homeodomain (svm: 0.763)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.56  Contact: 57
Modified z-scores:
dali:0.38 daliz:0.32 gdtts:0.47 tmscore:0.41 rmsd:0.47 AHM:0.37 LBcontacta:0.33 LBcontactb:0.35 LHM:0.20
id:0.50 blosum:0.51 compass:0.44 pearson:0.36
Scaled scores:
dali:0.57 daliz:0.06 gdtts:0.35 tmscore:0.13 rmsd:0.61 AHM:0.58 LBcontacta:0.18 LBcontactb:0.17 LHM:0.27
id:0.02 blosum:-0.01 compass:-0.03 pearson:-0.03

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:35.60)
Query          1 pdypvldailelyvDRDTgadaivaagydrelvvkTLRMVDTAEY-KRRQYppgtkisak     59
d1e3oc1        1 ----------krtsIETN-----------irvaleKSFMENQKPTsEDITL----iaeql     35

Query         60 gFGKDRR---lpitNRWR-egh     77
d1e3oc1       36 nMEKEVIrvwfsnrRQKEkrin     57


hit structure      alignment
FAST alignment (Normalized score: 4.08 Raw score:270.40)
Query          1 ----PDYPVLDAILELYVD---RDTGADAIVA----AGYDRELVVKTLRMVDTAEYKRRQ     49
d1e3oc1        1 KRTSIETNIRVALEKSF--MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKE-----     53

Query         50 YPPGTKISAKGFGKDRRLPITNRWREGH----     77
d1e3oc1       54 ----------------------------KRIN     57


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.54)
Query          1 ----PDYPVLDAILELYVDRDT-GA-DAIVAA--GY-D-RELVVKTLRMVDTA-EYKRRQ     49
d1e3oc1        1 KRTSIETNIRVALEKSF-MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR--IN     57

Query         50 YPPGTKISAKGFGKDRRLPITNRWREGH     77
d1e3oc1       58 ----------------------------     58


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.57)
DALI match                             
Query          2 DYPVLDAILELYVDRDTGADAI     23
d1e3oc1       21 QKPTSEDITLIAEQLNMEKEVI     42



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65: d1ru8a_ Putative N-​type ATP pyrophosphatase PF0828 (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.14  Contact: 23
Modified z-scores:
dali:0.36 daliz:0.31 gdtts:0.41 tmscore:0.37 rmsd:0.41 AHM:0.45 LBcontacta:0.31 LBcontactb:0.38 LHM:0.38
id:0.25 blosum:0.22 compass:0.31 pearson:0.35
Scaled scores:
dali:0.74 daliz:0.09 gdtts:0.46 tmscore:0.15 rmsd:0.72 AHM:0.65 LBcontacta:0.21 LBcontactb:0.34 LHM:0.23
id:-0.06 blosum:-0.09 compass:0.00 pearson:0.02

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:95.80)
Query          1 pDYPVldAILE-------------------------------------------------     11
d1ru8a_        1 gLADV--AVLYsggkdsnyalywaiknrfsvkflvtmvseneesymytinanltdlqara     58

Query         12 ---------lyvdrdtgadAIVAAG-----------------------ydrelvvkTLRM     39
d1ru8a_       59 lgiplvkgftqgekekeveDLKRVLsglkiqgivagaskyqrkriekvakelglevYTPA    118

Query         40 ----vdtAEYKRRQYPpgtkisakgfGKDR------------------------------     65
d1ru8a_      119 wgrdakeYMRELLNLG---------fKIMVvgvsaygldeswlgrildesaleelitlne    169

Query         66 ---rlPITNRW-------------------------------------------regh     77
d1ru8a_      170 kykvhVAGEGGefetfvldmplfkykivvdkakkvwepctssgkliieeahleskleh    227


hit structure      alignment
FAST alignment (Normalized score: 0.86 Raw score:113.70)
Query          1 ----------PDYPVLDAILELYVDRDTGADAIVAAGY----------------------     28
d1ru8a_        1 GLADVAVLYSGGKDSNYALYWAI-KNRFS---------VKFLVTMVSENEESYMYTINAN     50

Query         29 -DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----------     77
d1ru8a_       51 LTDLQARA------------------------------------------LGIPLVKGFT     68

Query         78 ------------------------------------------------------------     78
d1ru8a_       69 QGEKEKEVEDLKRVLSGLKIQGIVAGASKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMR    128

Query         78 ------------------------------------------------------------     78
d1ru8a_      129 ELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLD    188

Query         78 ---------------------------------------     78
d1ru8a_      189 MPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESKLEH    227


hit structure      alignment
TMalign alignment (TM-score: 0.35 Raw score:27.13)
Query          1 -PDYPVLDAILEL---YV------------------DR----------------------     16
d1ru8a_        1 GLA-DV-AV-LYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYTINANLTDLQAR     57

Query         17 -------------------------------------DT--GADAIVAAG----YDRELV     33
d1ru8a_       58 ALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGASKYQRKRIEKVAKELGLE--VY    115

Query         34 VKTLRMV-D-TAEYKRRQ-YPPGTKISAKGFGKDR-------------------------     65
d1ru8a_      116 T-PAWGRDAKEYMRELLNLGFK---------IMVVGVSAYGLDESWLGRILDESALEELI    165

Query         66 ---------RLP------------------------------------------------     68
d1ru8a_      166 TLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESKL    225

Query         69 --ITNRWREGH     77
d1ru8a_      226 EH---------    227


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.25)
DALI match                 
Query         20 ADAIVAAGYD     29
d1ru8a_      127 MRELLNLGFK    136



hit structures. 
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66: d1jgta1 beta-​Lactam synthetase (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.00  Contact: 51
Modified z-scores:
dali:0.42 daliz:0.39 gdtts:0.43 tmscore:0.41 rmsd:0.54 AHM:0.58 LBcontacta:0.46 LBcontactb:0.45 LHM:0.45
id:0.69 blosum:0.52 compass:0.41 pearson:0.31
Scaled scores:
dali:0.69 daliz:0.17 gdtts:0.35 tmscore:0.15 rmsd:0.65 AHM:0.57 LBcontacta:0.28 LBcontactb:0.31 LHM:0.14
id:0.07 blosum:0.04 compass:-0.06 pearson:-0.07

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:72.00)
Query          1 -----------------------------pdypvldailelyvdrdtGADAIVA-AGYDR     30
d1jgta1        1 pglsrrilpegeavaavraalekavaqrvtpgdtplvvlsggidssgVAACAHRaAGELD     60

Query         31 E-----------------------------------------------------------     31
d1jgta1       61 Tvsmgtdtsnefrearavvdhlrtrhreitipttellaqlpyavwasesvdpdiieyllp    120

Query         32 -----------lvvktlrmVDTAE--------------yKRRQ--YPPGT--KISA----     58
d1jgta1      121 ltalyraldgperriltgyGADIPlggmhredrlpaldtVLAHdmATFDGlnEMSPvlst    180

Query         59 ----------kgfgkdRRLP-----------itNRWR-----------------------     74
d1jgta1      181 laghwtthpywdrevlDLLVsleaglkrrhgrdKWVLraamadalpaetvnrpklssfsr    240

Query         75 -----------------------------------------------egh     77
d1jgta1      241 llldhgvaedrvheakrqvvrelfdltvgggrhpsevdtddvvrsvadrt    290


hit structure      alignment
FAST alignment (Normalized score: 1.12 Raw score:168.00)
Query          1 P-------------DYPVLDAILELYVDRDTGADAIVAAGY----------------DRE     31
d1jgta1        1 -PGLSRRILPEGEAVAAVRAALEKAVAQ-------------RVTPGDTPLVVLSGGIDSS     46

Query         32 LVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------     77
d1jgta1       47 GVAACAHRA-------------------------------------AGELDTVSMGTDTS     69

Query         78 ------------------------------------------------------------     78
d1jgta1       70 NEFREARAVVDHLRTRHREITIPTTELLAQLPYAVWASESVDPDIIEYLLPLTALYRALD    129

Query         78 ------------------------------------------------------------     78
d1jgta1      130 GPERRILTGYGADIPLGGMHREDRLPALDTVLAHDMATFDGLNEMSPVLSTLAGHWTTHP    189

Query         78 ------------------------------------------------------------     78
d1jgta1      190 YWDREVLDLLVSLEAGLKRRHGRDKWVLRAAMADALPAETVNRPKLSSFSRLLLDHGVAE    249

Query         78 -----------------------------------------     78
d1jgta1      250 DRVHEAKRQVVRELFDLTVGGGRHPSEVDTDDVVRSVADRT    290


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:29.15)
Query          1 ---------------------------------PDYPVLDAILELY---VDR--------     16
d1jgta1        1 PGLSRRILPEGEAVAAVRAALEKAVAQRVTPGD---TP-LV--VLSGGI-DSSGVAACAH     53

Query         17 ---------DT-------GADAIVAAG----YDRELVVKTLRMVDT--AEYKRRQY--PP     52
d1jgta1       54 RAAGELDTV-SMGTDTSNEFREARAVVDHLRTRH-RE--I-TI--PTTELLAQLPYAVWA    106

Query         53 GTK---ISAKGFGKDR-R------------------------------------------     66
d1jgta1      107 SESVDP-----DIIEYLLPLTALYRALDGPERRILTGYGADIPLGGMHREDRLPALDTVL    161

Query         67 ------------------------------------------------------------     67
d1jgta1      162 AHDMATFDGLNEMSPVLSTLAGHWTTHPYWDREVLDLLVSLEAGLKRRHGRDKWVLRAAM    221

Query         67 --------------LPI-T-----------------------------------------     70
d1jgta1      222 ADALPAETVNRPKLSSFSRLLLDHGVAEDRVHEAKRQVVRELFDLTVGGGRHPSEVDTDD    281

Query         71 ---------NRWREGH     77
d1jgta1      282 VVRSVADRT-------    290


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.20)
DALI match                                               
Query          4 PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA     43
d1jgta1       19 AALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRAAGE     58



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67: d1q15a1 beta-​Lactam synthetase (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.00  Contact: 74
Modified z-scores:
dali:0.41 daliz:0.36 gdtts:0.49 tmscore:0.44 rmsd:0.38 AHM:0.28 LBcontacta:0.37 LBcontactb:0.42 LHM:0.49
id:0.54 blosum:0.41 compass:0.47 pearson:0.47
Scaled scores:
dali:0.64 daliz:0.10 gdtts:0.41 tmscore:0.18 rmsd:0.70 AHM:0.72 LBcontacta:0.17 LBcontactb:0.24 LHM:0.10
id:0.04 blosum:0.03 compass:-0.00 pearson:0.06

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:63.20)
Query          1 ----------pdypvldailelYVDRD-----------------------tGADAIvAAG     27
d1q15a1        1 pasnqllalprepllalidrylNAPLEdlaprfdtvgiplsggldsslvtaLASRH-FKK     59

Query         28 YD----------------------------------------------------------     29
d1q15a1       60 LNtysigtelsnefefsqqvadalgthhqmkilsetevingiiesiyyneifdglsaeiq    119

Query         30 --------relvvktlrmvdtAEYKR-------------------rQYPP----------     52
d1q15a1      120 sglfnvyrqaqgqvscmltgyGSDLLfggilkpgaqydnpnqllaeQVYRtrwtgefath    179

Query         53 -----gtkisakgFGKDRR----------------lpiTNRW---REGH-----------     77
d1q15a1      180 gascygidirhpfWSHSLIslchalhpdykifdnevknILREyadSLQLlpkdivwrsvn    239

Query         78 ------------------------------------------------     78
d1q15a1      240 qafanvlgstvdnyqtksrftyrvyqaflrgrlsitdvtpsqlkdlik    287


hit structure      alignment
FAST alignment (Normalized score: 1.71 Raw score:254.20)
Query          1 P-----------------------------------------------------------      1
d1q15a1        1 -PASNQLLALPREPLLALIDRYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRHFKK     59

Query          2 ----------------------------------DYPVLDAILELYVDRDT-GADAIVAA     26
d1q15a1       60 LNTYSIGTELSNEFEFSQQVADALGTHHQMKILSETEVINGIIESIYYNEIFDGLSAEI-    118

Query         27 GY----------------------------------------------------------     28
d1q15a1      119 --QSGLFNVYRQAQGQVSCMLTGYGSDLLFGGILKPGAQYDNPNQLLAEQVYRTRWTGEF    176

Query         29 ------------------------------------------------------------     29
d1q15a1      177 ATHGASCYGIDIRHPFWSHSLISLCHALHPDYKIFDNEVKNILREYADSLQLLPKDIVWR    236

Query         29 -------------------DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPI     69
d1q15a1      237 SVNQAFANVLGSTVDNYQTKSRFTYRVYQAFLR---------------------------    269

Query         70 TNRWREGH------------------     77
d1q15a1      270 --------GRLSITDVTPSQLKDLIK    287


hit structure      alignment
TMalign alignment (TM-score: 0.39 Raw score:29.72)
Query          1 ----------------------------------PDYPVLDAILELYVD-RDT-------     18
d1q15a1        1 PASNQLLALPREPLLALIDRYLNAPLEDLAPRFD--TV--GI-P-LSGGLDSSLVTALAS     54

Query         19 -----------------GADAIVAA-G---YDRELVVKTLRMVDT--AEYKRRQY-P---     51
d1q15a1       55 RHFKKLNTYSIGTELSNEFEFSQQVADALGTHH-QM-K--I--LSETEVINGIIESIYYN    108

Query         52 -P----------------------------------------------------------     52
d1q15a1      109 EIFDGLSAEIQSGLFNVYRQAQGQVSCMLTGYGSDLLFGGILKPGAQYDNPNQLLAEQVY    168

Query         53 -----GTKI------------S-A------------------------------------     58
d1q15a1      169 RTRWTGEFATHGASCYGIDIRHPFWSHSLISLCHALHPDYKIFDNEVKNILREYADSLQL    228

Query         59 ---------KGFGKDRRLPI-T--------------------------------------     70
d1q15a1      229 LPKDIVWRS------VNQAFANVLGSTVDNYQTKSRFTYRVYQAFLRGRLSITDVTPSQL    282

Query         71 -----NRWREGH     77
d1q15a1      283 KDLIK-------    287


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.10)
DALI match                                               
Query          4 PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA     43
d1q15a1       20 RYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRHFKK     59



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68: d1ni5a1 Putative cell cycle protein MesJ,​ N-​terminal domain (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.00  Contact: 0
Modified z-scores:
dali:0.37 daliz:0.36 gdtts:0.44 tmscore:0.39 rmsd:0.35 AHM:0.36 LBcontacta:0.36 LBcontactb:0.31 LHM:0.47
id:0.42 blosum:0.60 compass:0.35 pearson:0.40
Scaled scores:
dali:0.72 daliz:0.21 gdtts:0.47 tmscore:0.18 rmsd:0.68 AHM:0.67 LBcontacta:0.26 LBcontactb:0.13 LHM:0.24
id:0.01 blosum:0.03 compass:0.01 pearson:0.04

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:81.70)
Query          1 -----------pDYPVldAILE--------------------------------------     11
d1ni5a1        1 smtltlnrqlltSRQI--LVAFsggldstvllhqlvqwrtenpgvalraihvhhglsana     58

Query         12 --------------------------------lyvdrdtGADAIVAAG------------     27
d1ni5a1       59 dawvthcenvcqqwqvplvvervqlaqeglgieaqarqaRYQAFARTLlpgevlvtaqhl    118

Query         28 ---------------------------yDRELvvKTLRmvDTAEYKRRQY----pPGTKI     56
d1ni5a1      119 ddqcetfllalkrgsgpaglsamaevseFAGT--RLIR--PLLARTRGELvqwarQYDLR    174

Query         57 SAK--------------------------------gfgkdrrlpitnrwregh     77
d1ni5a1      175 WIEdesnqddsydrnflrlrvvpllqqrwphfaeatarsaalcaeqeslldel    227


hit structure      alignment
FAST alignment (Normalized score: 0.91 Raw score:120.20)
Query          1 PDYPVLDAILELYVDRDT------------------------------------------     18
d1ni5a1        1 ------------------SMTLTLNRQLLTSRQILVAFSGGLDSTVLLHQLVQWRTENPG     42

Query         19 ------------------------------------------------------------     19
d1ni5a1       43 VALRAIHVHHGLSANADAWVTHCENVCQQWQVPLVVERVQLAQEGLGIEAQARQARYQAF    102

Query         19 ------------------------------------------------------------     19
d1ni5a1      103 ARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSEFAGTRLIRPLLARTRG    162

Query         19 --------------------------------GADAIVAAG-YDRELVVKTLRMVDTAEY     45
d1ni5a1      163 ELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQR-WPHFAEATARSAALCAEQE    221

Query         46 KRRQYPPGTKISAKGFGKDRRLPITNRWREGH---     77
d1ni5a1      222 SLL-----------------------------DEL    227


hit structure      alignment
TMalign alignment (TM-score: 0.35 Raw score:26.92)
Query          1 PDYPVLDAILELYVDRD-TGADAIV----AAGYDRELVVKTLRMVDTAEYKRRQYPPGTK     55
d1ni5a1        1 --S-MTLTLNRQL-LTSRQILVA-FSGGL----DSTVLLHQLVQWRTEN-----------     40

Query         56 ISAKGFGKDRRLPITNRWREG----------------------------H----------     77
d1ni5a1       41 ----------PGV----ALRAIHVHHGLSANADAWVTHCENVCQQWQVPLVVERVQLAQE     86

Query         78 ------------------------------------------------------------     78
d1ni5a1       87 GLGIEAQARQARYQAFARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSE    146

Query         78 ------------------------------------------------------------     78
d1ni5a1      147 FAGTRLIRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHF    206

Query         78 ---------------------     78
d1ni5a1      207 AEATARSAALCAEQESLLDEL    227


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.23)
DALI match                                                  
Query         25 AAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRL     67
d1ni5a1       57 NADAWVTHCENVCQQWQVPLVVERVQLAQEGLGIEAQARQARY     99



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69: d1ct9a1 Asparagine synthetase B,​ C-​terminal domain (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.00  Contact: 52
Modified z-scores:
dali:0.40 daliz:0.38 gdtts:0.44 tmscore:0.43 rmsd:0.47 AHM:0.42 LBcontacta:0.42 LBcontactb:0.47 LHM:0.49
id:0.33 blosum:0.44 compass:0.40 pearson:0.41
Scaled scores:
dali:0.65 daliz:0.15 gdtts:0.38 tmscore:0.19 rmsd:0.67 AHM:0.63 LBcontacta:0.27 LBcontactb:0.40 LHM:0.07
id:-0.01 blosum:0.00 compass:0.02 pearson:0.04

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:49.30)
Query          1 -------pdypvldailelyVDRD-----------------------tGADA--ivaaGY     28
d1ct9a1        1 rdwfdydavkdnvtdknelrQALEdsvkshlmsdvpygvllsggldssIISAitkkyaLH     60

Query         29 DRE---------------------------------------------------------     31
d1ct9a1       61 SFAvglpgspdlkaaqevanhlgtvhheihftvqegldairdviyhietydvttirastp    120

Query         32 -------------------------lvvktlrmvdtaeykRRQY--PPGT----------     54
d1ct9a1      121 mylmsrkikamgikmvlsgegsdevfggylyfhkapnakeLHEEtvRKLLalhmydcara    180

Query         55 ---------------kiSAKG-fGKDRR--LPITNR------------------------     72
d1ct9a1      181 nkamsawgvearvpfldKKFLdvAMRINpqDKMCKMekhilrecfeaylpasvawrqkeq    240

Query         73 ------------------------------------------------------------     73
d1ct9a1      241 fsdgvgyswidtlkevaaqqvsdqqletarfrfpyntptskeaylyreifeelfplpsaa    300

Query         73 wregh     77
d1ct9a1      301 ecvpg    305


hit structure      alignment
FAST alignment (Normalized score: 1.00 Raw score:153.20)
Query          1 PDYPVLDAILELYVDRD---TGADAIVAAGY-----------------------------     28
d1ct9a1        1 -----------------RDWFDYDAVK----DNVTDKNELRQALEDSVKSHLMSDVPYGV     39

Query         29 ------------------------------------------------------------     29
d1ct9a1       40 LLSGGLDSSIISAITKKYALHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDA     99

Query         29 ----------------------------------------------------------DR     30
d1ct9a1      100 IRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAK    159

Query         31 ELVVKTLRMVDTAE-YKRRQYPPGTKISA---------------KGFGKDRRLPITNRWR     74
d1ct9a1      160 ELHEETVRKLLALHMYDCA----------RANKAMSAWGVEARVPFLDKK----------    199

Query         75 EGH---------------------------------------------------------     77
d1ct9a1      200 ---FLDVAMRINPQDKMCKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEV    256

Query         78 -------------------------------------------------     78
d1ct9a1      257 AAQQVSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPG    305


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:28.86)
Query          1 -----------------------------------PDYPVLDAILEL-------------     12
d1ct9a1        1 RDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDV-PYGV--LL--SGGLDSSIISAITK     55

Query         13 -------YV----DRDTGADAIVAAGY---D-RELVVKTLRMVDTAEYKRRQY--PPGTK     55
d1ct9a1       56 KYALHSFAVGLPG--SPDLKAAQEVANHLGTV-HHE--I-HFTVQEGLDAIRDVIYHIET    109

Query         56 ---ISAK--GFG------------------------------------------------     62
d1ct9a1      110 YDV--TTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHEETVR    167

Query         63 ------------------------------------------------------------     63
d1ct9a1      168 KLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCKMEKHILRECFEA    227

Query         63 --------------------KDRRL--PI-------------------------------     69
d1ct9a1      228 YLPASVAWRQKEQFSDGVGY---SWIDTLKEVAAQQVSDQQLETARFRFPYNTPTSKEAY    284

Query         70 ---------------------TNRWREGH     77
d1ct9a1      285 LYREIFEELFPLPSAAECVPG--------    305


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.15)
DALI match                                                  
Query          3 YPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEY     45
d1ct9a1       20 RQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYALHSF     62



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70: d1k92a1 Argininosuccinate synthetase,​ N-​terminal domain (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.00  Contact: 20
Modified z-scores:
dali:0.32 daliz:0.30 gdtts:0.31 tmscore:0.32 rmsd:0.35 AHM:0.30 LBcontacta:0.26 LBcontactb:0.29 LHM:0.63
id:0.33 blosum:0.66 compass:0.57 pearson:0.26
Scaled scores:
dali:0.60 daliz:0.00 gdtts:0.40 tmscore:0.04 rmsd:0.59 AHM:0.57 LBcontacta:0.14 LBcontactb:0.15 LHM:0.09
id:-0.01 blosum:0.00 compass:-0.06 pearson:-0.11

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:47.30)
Query          1 --------pdYPVL------dailelYVDR--dtgadaIVAA------------------     26
d1k92a1        1 ttilkhlpvgQRIGiafsggldtsaaLLWMrqkgavpyAYTAnlgqpdeedydaiprram     60

Query         27 ---------------------------------------------------------gyd     29
d1k92a1       61 eygaenarlidcrkqlvaegiaaiqcgafhnttggltyfnttplgravtgtmlvaamked    120

Query         30 relvvkTLRM---------vdtaeykrrqyppgtkisakgFGKDRRLP-----------i     69
d1k92a1      121 gvniwgDGSTykgndierfyryglltnaelqiykpwldtdFIDELGGRhemsefmiacgf    180

Query         70 tnrwregh     77
d1k92a1      181 dykmsvek    188


hit structure      alignment
FAST alignment (Normalized score: 1.15 Raw score:138.30)
Query          1 ------------------PDYPVLDAILELYVDRDTGADAIVAAGY--------------     28
d1k92a1        1 TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQ-KGAV---------PYAYTANLGQPDEE     50

Query         29 ----DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-------     77
d1k92a1       51 DYDAIPRRAME------------------------------------------YGAENAR     68

Query         78 ------------------------------------------------------------     78
d1k92a1       69 LIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDG    128

Query         78 ------------------------------------------------------------     78
d1k92a1      129 STYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACGFDYKMSVEK    188


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:28.22)
Query          1 ------------PDYPVLDA----------------------ILELYVDRD-TGADAIVA     25
d1k92a1        1 TTILKHLPVGQRIG--IAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYD-AIPR     57

Query         26 AGY------DRELVVKTLRMVDTA-EYKRRQY----P----------PGTK--ISAKGF-     61
d1k92a1       58 RAMEYGAENA--RL--ID--CRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPL-----GR    106

Query         62 ------------------------------------------------------------     62
d1k92a1      107 AVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELG    166

Query         62 ----------------------GKDRRLPITNRWREGH     77
d1k92a1      167 GRHEMSEFMIACGFDYKMSVEK----------------    188


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.29)
DALI match                                 
Query          1 PDYPVLDAILEL-YVDRDTGADAIVA     25
d1k92a1      148 AELQIYKPWLDTDFIDELGGRHEMSE    173



hit structures. 
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71: d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domain (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.00  Contact: 29
Modified z-scores:
dali:0.33 daliz:0.30 gdtts:0.34 tmscore:0.33 rmsd:0.33 AHM:0.26 LBcontacta:0.26 LBcontactb:0.30 LHM:0.54
id:0.42 blosum:0.79 compass:0.68 pearson:0.42
Scaled scores:
dali:0.71 daliz:0.00 gdtts:0.46 tmscore:0.07 rmsd:0.64 AHM:0.67 LBcontacta:0.14 LBcontactb:0.15 LHM:0.10
id:0.06 blosum:0.13 compass:0.16 pearson:0.15

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:49.00)
Query          1 pdypvLDAI----lelYVDRD--------------------------tgadaivaAGYD-     29
d1vl2a1        1 -kekvVLAYsggldtsVILKWlcekgfdviayvanvgqkddfvaikekalktgasKVYVe     59

Query         30 -------------------------------------------relvvktlrmvdTAEYK     46
d1vl2a1       60 dlrrefvtdyiftallgnamyegryllgtaiarpliakrqveiaekegaqyvahgATGKG    119

Query         47 -------------rrqyppgtkisakgFGKDRR---lpitnrwregh     77
d1vl2a1      120 ndqvrfeltyaalnpnlkvispwkdpeFLAKFKtdlinyamekgipi    166


hit structure      alignment
FAST alignment (Normalized score: 1.34 Raw score:151.00)
Query          1 PDYPVLDAILELYVDRD-------------------------------------------     17
d1vl2a1        1 -----------------KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVA     43

Query         18 -----------------------TGADAIVAAG----------YDRELVVKTLRMVDTAE     44
d1vl2a1       44 IKEKALKTGASKVYVEDLRREFVTDYIFTAL--LGNAMYEGRYLLGTAIARPLIAKRQVE    101

Query         45 YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------------------------     77
d1vl2a1      102 IAEK-----------------------------EGAQYVAHGATGKGNDQVRFELTYAAL    132

Query         78 ----------------------------------     78
d1vl2a1      133 NPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI    166


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:29.05)
Query          1 ---PDYPVLDA----------------------ILELYVDRDTGADAIVAAGY-----DR     30
d1vl2a1        1 KEKVV--LAYSGGLDTSVILKWLCEKGFDVIAYVA--NVGQKDDFVAIKEKALKTGASKV     56

Query         31 ELVVKTLRMVDTA-EYKRRQYP----P-G---T-KIS-AKGF------------------     61
d1vl2a1       57 -YV--E-D-LRREFVTDYIFTALLGNAMYEGRYLLGTA--IARPLIAKRQVEIAEKEGAQ    109

Query         62 ---------------------------------------------------------GKD     64
d1vl2a1      110 YVAHGATGKGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI---    166

Query         65 RRLPITNRWREGH     77
d1vl2a1      167 -------------    167


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.59)
DALI match                
Query         17 DTGADAIVA     25
d1vl2a1      149 AKFKTDLIN    157



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72: d1sura_ Phosphoadenylyl sulphate (PAPS) reductase (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.23  Contact: 0
Modified z-scores:
dali:0.32 daliz:0.29 gdtts:0.34 tmscore:0.32 rmsd:0.53 AHM:0.56 LBcontacta:0.31 LBcontactb:0.40 LHM:0.36
id:0.32 blosum:0.61 compass:0.54 pearson:0.42
Scaled scores:
dali:0.76 daliz:0.00 gdtts:0.43 tmscore:0.05 rmsd:0.64 AHM:0.59 LBcontacta:0.26 LBcontactb:0.46 LHM:0.36
id:-0.02 blosum:-0.03 compass:0.06 pearson:0.11

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:32.20)
Query          1 ----------------pdypvldailelyvdrdTGADAIVaAGYDrelvvktlRMVD---     41
d1sura_        1 skldlnalnelpkvdrilalaetnaelekldaeGRVAWAL-DNLP-----geyVLSSsfg     54

Query         42 ------------------TAEYkrRQYP--------------------------------     51
d1sura_       55 iqaavslhlvnqirpdipVILT--DTGYlfpetyrfideltdklklnlkvyratesaawq    112

Query         52 ---------------------------------------------pgTKISAK-------     59
d1sura_      113 earygklweqgvegiekyndinkvepmnralkelnaqtwfaglrreqSGSRANlpvlaiq    172

Query         60 -------------------------gfgkdrrlpitnrwregh     77
d1sura_      173 rgvfkvlpiidwdnrtiyqylqkhglkyhplwdegylsvgdth    215


hit structure      alignment
FAST alignment (Normalized score: 1.01 Raw score:129.50)
Query          1 P-----------------------------------------------------DYPVLD      7
d1sura_        1 -SKLDLNALNELPKVDRILALAETNAELEKLDAEGRVAWALDNLPGEYVLSSSFGIQAAV     59

Query          8 AILELYVDRDTGADAIVAAGY----------------DRELVVKTLRMVDTAEYKRRQYP     51
d1sura_       60 SLHLVNQIR------------PDIPVILTDTGYLFPETYRFIDELTDK------------     95

Query         52 PGTKISAKGFGKDRRLPITNRWREGH----------------------------------     77
d1sura_       96 --------------------------LKLNLKVYRATESAAWQEARYGKLWEQGVEGIEK    129

Query         78 ------------------------------------------------------------     78
d1sura_      130 YNDINKVEPMNRALKELNAQTWFAGLRREQSGSRANLPVLAIQRGVFKVLPIIDWDNRTI    189

Query         78 --------------------------     78
d1sura_      190 YQYLQKHGLKYHPLWDEGYLSVGDTH    215


hit structure      alignment
TMalign alignment (TM-score: 0.28 Raw score:21.88)
Query          1 ----------------------------------------------------PDYPVLDA      8
d1sura_        1 SKLDLNALNELPKVDRILALAETNAELEKLDAEGRVAWALDNLPGEYVLSSSFGIQAAVS     60

Query          9 ILE-LYV--D--RDTGADAIVAA--GY--DRELVVKTLRMVD------------------     41
d1sura_       61 -LHL-VNQIRPDIPV---ILTDTGYLFPETYRFIDELTDKLKLNLKVYRATESAAWQEAR    115

Query         42 ------------------------------------------------------------     42
d1sura_      116 YGKLWEQGVEGIEKYNDINKVEPMNRALKELNAQTWFAGLRREQSGSRANLPVLAIQRGV    175

Query         42 ----------------------------------------TAEYKRRQYPPGTKISAKGF     61
d1sura_      176 FKVLPIIDWDNRTIYQYLQKHGLKYHPLWDEGYLSVGDTH--------------------    215

Query         62 GKDRRLPITNRWREGH     77
d1sura_      216 ----------------    216


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.28)
DALI match                               
Query          7 DAILELYVDRDTGADAIVAAGYDR     30
d1sura_      187 RTIYQYLQKHGLKYHPLWDEGYLS    210



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73: d1gpma1 GMP synthetase,​ central domain (hh: 0.944)

SCOP Superfamily: Adenine nucleotide alpha hydrolases-​like  |  SCOP Fold: Adenine nucleotide alpha hydrolase-​like  |  SCOP Class: Alpha and beta proteins (a/​b)

Consensus: 0.01  Contact: 1
Modified z-scores:
dali:0.31 daliz:0.29 gdtts:0.32 tmscore:0.32 rmsd:0.52 AHM:0.51 LBcontacta:0.29 LBcontactb:0.30 LHM:0.49
id:0.42 blosum:0.69 compass:0.45 pearson:0.27
Scaled scores:
dali:0.65 daliz:0.00 gdtts:0.39 tmscore:0.04 rmsd:0.54 AHM:0.48 LBcontacta:0.18 LBcontactb:0.14 LHM:0.11
id:0.05 blosum:0.05 compass:-0.04 pearson:-0.08

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:27.90)
Query          1 -------------------------pdypvldailelyvdrdTGADAIV-----------     24
d1gpma1        1 wtpakiiddavarireqvgddkvilglsggvdssvtamllhrAIGKNLTcvfvdngllrl     60

Query         25 -------------aaGYDRE----------------------------------------     31
d1gpma1       61 neaeqvldmfgdhfgLNIVHvpaedrflsalagendpeakrkiigrvfvevfdeealkle    120

Query         32 --lvvktlrmvdtaeykrrqyppgtkiSAKGfGKDRR-------lPITN-rwregh     77
d1gpma1      121 dvkwlaqgtiypdviesaakmglveplKELF-KDEVRkiglelglPYDMlyrhpfp    175


hit structure      alignment
FAST alignment (Normalized score: 0.96 Raw score:111.40)
Query          1 PDYPVLDAILELYVDRDTGADAIVAAG---------------------------------     27
d1gpma1        1 ---------------------------WTPAKIIDDAVARIREQVGDDKVILGLSGGVDS     33

Query         28 ------------------------------------------------------------     28
d1gpma1       34 SVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAG     93

Query         28 -YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH---------     77
d1gpma1       94 ENDPEAKRKIIGRVFVEVFDEEAL---------------------------KLEDVKWLA    126

Query         78 -------------------------------------------------     78
d1gpma1      127 QGTIYPDVIESAAKMGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPFP    175


hit structure      alignment
TMalign alignment (TM-score: 0.29 Raw score:22.20)
Query          1 ------------------------------------------------------------      1
d1gpma1        1 WTPAKIIDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL     60

Query          1 -----------------------PDYPVLDAILELYVDRDTGADAIVAAGY---DRELVV     34
d1gpma1       61 NEAEQVLDMFGDHFGLNIVHVPA----------------EDRFLSALAGENDPEAKRKII    104

Query         35 KTLRMVDTA-EYKRRQY-------------------------------------------     50
d1gpma1      105 GRVFVEVFDEEA-LKLEDVKWLAQGTIYPDVIESAAKMGLVEPLKELFKDEVRKIGLELG    163

Query         51 -----------PPGTKISAKGFGKDRRLPITNRWREGH     77
d1gpma1      164 LPYDMLYRHPF--------------------------P    175


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.53)
DALI match                                   
Query         27 GYDRELVVKTLRMVDTAEYKRRQYPPGT     54
d1gpma1      149 ELFKDEVRKIGLELGLPYDML-YRHPFP    175



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74: d1mija_ Homeo-​prospero domain of Prospero protein (svm: 0.558)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.61  Contact: 263
Modified z-scores:
dali:0.93 daliz:0.90 gdtts:0.95 tmscore:0.96 rmsd:0.34 AHM:0.36 LBcontacta:0.80 LBcontactb:0.77 LHM:0.19
id:0.73 blosum:0.16 compass:0.50 pearson:0.70
Scaled scores:
dali:0.67 daliz:0.39 gdtts:0.51 tmscore:0.48 rmsd:0.76 AHM:0.67 LBcontacta:0.28 LBcontactb:0.27 LHM:0.36
id:0.01 blosum:0.03 compass:0.00 pearson:0.04

hit structure      alignment
DALI alignment (Z-score: 3.0 Raw score:204.30)
Query          1 ---PDYPVLDAILELyVDRD--tGADAIVAAG-------yDRELVVKTLRMVDTA-EYKR     47
d1mija_        1 sstLTPMHLRKAKLM-FFWVrypSSAVLKMYFpdikfnknNTAQLVKWFSNFREFyYIQM     59

Query         48 RQY--------PPGT------------kISAKG-fGKDRR--------------------     66
d1mija_       60 EKYarqavtesELYRvlnlhynrnnhieVPQNFrfVVESTlreffraiqggkdteqswkk    119

Query         67 lPITN---------rwregh     77
d1mija_      120 sIYKIisrmddpvpeyfksp    139


hit structure      alignment
FAST alignment (Normalized score: 2.90 Raw score:299.90)
Query          1 ---PDYPVLDAILELYVD----RDTGADAIVAAGY----------DRELVVKTLRMVDTA     43
d1mija_        1 SSTLTPMHLRKAKLM---FFWVRYPSSAVLKM---YFPDIKFNKNNTAQLVKWFSNFREF     54

Query         44 EYKRRQYPPG----------------------TKISAKGFGKDRRLPITNRWREGH----     77
d1mija_       55 YYIQME----KYARQAVTESELYRVLNLHYNRNNHI--------------------EVPQ     90

Query         78 -------------------------------------------------     78
d1mija_       91 NFRFVVESTLREFFRAIQGGKDTEQSWKKSIYKIISRMDDPVPEYFKSP    139


hit structure      alignment
TMalign alignment (TM-score: 0.55 Raw score:42.63)
Query          1 ---PDYPVLDAILELYVDRD-TGA-DAIVAAG--Y-----DRELVVKTLRMVDTA-EYKR     47
d1mija_        1 SSTLTPMHLRKAKLM-FFWVRYPSSAVLKMYFPDIKFNKNNTAQLVKWFSNFREFYYI-Q     58

Query         48 R-QY-------PP--GT-K---------ISA--KGFGKDRR--LP-------------IT     70
d1mija_       59 MEKYARQAVTESELYRVLNLHYNRNNHIEVPQNFRFVVESTLREFFRAIQGGKDTEQSWK    118

Query         71 N--RW-----------------REGH     77
d1mija_      119 KSI-YKIISRMDDPVPEYFKSP----    139


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.27)
DALI match             
Query         66 RLPITN     71
d1mija_       20 RYPSSA     25



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75: d2ezha_ Transposase (svm: -0.699)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 176
Modified z-scores:
dali:0.84 daliz:0.80 gdtts:0.85 tmscore:0.87 rmsd:0.36 AHM:0.39 LBcontacta:0.68 LBcontactb:0.44 LHM:0.20
id:0.76 blosum:0.67 compass:0.65 pearson:0.94
Scaled scores:
dali:0.61 daliz:0.29 gdtts:0.46 tmscore:0.33 rmsd:0.72 AHM:0.64 LBcontacta:0.25 LBcontactb:0.14 LHM:0.32
id:0.02 blosum:0.12 compass:0.13 pearson:0.23

hit structure      alignment
DALI alignment (Z-score: 1.7 Raw score:122.90)
Query          1 --PDYPVLDAILELYV---DRDT--GADAIVAAG----ydrELVVKTLRMVDTAEYkrrq     49
d2ezha_        1 seFDEDAWQFLIADYLrpeKPAFrkCYERLELAArehgwsiPSRATAFRRIQQLDE----     56

Query         50 yppgtkisakGFGKDrrlpitnrwregh     77
d2ezha_       57 ------amvvACREG-------------     65


hit structure      alignment
FAST alignment (Normalized score: 3.19 Raw score:225.50)
Query          1 --PDYPVLDAILELY-VDRDTGADAIVAAG-------------YDRELVVKTLRMVDTAE     44
d2ezha_        1 SEFDEDAWQFLIADYLRPEKPAFRKCYE--RLELAAREHGWSIPSRATAFRRIQQLD---     55

Query         45 YKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----------     77
d2ezha_       56 ---------------------------------EAMVVACREG     65


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:33.03)
Query          1 --PDYPVLDAILELYVD-RDTGADAIVAAGY---------DRELVVKTLRMVDTAEYKRR     48
d2ezha_        1 SEFDEDAWQFLIADYLRPEKPAFRKCYERLELAAREHGWSIPS-RATAFRRIQQLDE--A     57

Query         49 QYPPGTKISAKGFGKDRR----LPITNRWREGH     77
d2ezha_       58 ------------MV--VACREG-----------     65


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.35)
DALI match                       
Query         37 LRMVDTAEYKRRQYPP     52
d2ezha_       28 ERLELAAREHGWSIPS     43



hit structures. 
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76: d1wdka1 Fatty oxidation complex alpha subunit,​ C-​terminal domain (svm: -1.348)

SCOP Superfamily: 6-​phosphogluconate dehydrogenase C-​terminal domain-​like  |  SCOP Fold: 6-​phosphogluconate dehydrogenase C-​terminal domain-​like  |  SCOP Class: All alpha proteins

Consensus: 0.35  Contact: 163
Modified z-scores:
dali:0.84 daliz:0.80 gdtts:0.85 tmscore:0.88 rmsd:0.35 AHM:0.37 LBcontacta:0.84 LBcontactb:0.93 LHM:0.14
id:0.64 blosum:0.31 compass:0.16 pearson:0.69
Scaled scores:
dali:0.68 daliz:0.30 gdtts:0.45 tmscore:0.35 rmsd:0.73 AHM:0.66 LBcontacta:0.32 LBcontactb:0.47 LHM:0.46
id:-0.01 blosum:0.04 compass:0.07 pearson:0.06

hit structure      alignment
DALI alignment (Z-score: 1.2 Raw score:144.80)
Query          1 ---pdypvldailelYVDR-------dtGADAIVAAGYDRelVVKTLR-MVDT-AEYKRR     48
d1wdka1        1 pgflvnrvlfpyfggFAKLvsagvdfvrIDKVMEKFGWPM-gPAYLMDvVGIDtGHHGRD     59

Query         49 QY-PPGTKIsakgfGKDRR---lpiTNRW-------REGH--------------------     77
d1wdka1       60 VMaEGFPDR---mkDDRRSaidalyEAKRlgqkngkGFYAyekklvdssvlevlkpivye    116

Query         78 --     78
d1wdka1      117 qr    118


hit structure      alignment
FAST alignment (Normalized score: 1.37 Raw score:131.00)
Query          1 PDYPVLDAILELYVDRD-------------TGADAIVAAGYDRELVVKTLRMVDTAEYKR     47
d1wdka1        1 -----------------PGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEK--------     35

Query         48 RQYPPGTKISAKGFGKDRRLPITNRWREGH------------------------------     77
d1wdka1       36 ------------------------------FGWPMGPAYLMDVVGIDTGHHGRDVMAEGF     65

Query         78 -----------------------------------------------------     78
d1wdka1       66 PDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEKKLVDSSVLEVLKPIVYEQR    118


hit structure      alignment
TMalign alignment (TM-score: 0.47 Raw score:36.34)
Query          1 ---PDYPVLDAILELYVDR--D------T--GADAIVAAGYDRELV--VKTLR-MVDTA-     43
d1wdka1        1 PGF-LVN-RVLFPY-FGGFAKLVSAGVDFVRIDKVMEKFGWPM--GPAY-LMDVVGIDTG     54

Query         44 EYKRRQY-PPG--TKISAKGFGKDR---RLPI--TN------RWREG---H---------     77
d1wdka1       55 H-HGRDVM-AEGFPDRM---KDDRRSAIDALYEAKRLGQKNGKGFYAYEKKLVDSSVLEV    109

Query         78 ---------     78
d1wdka1      110 LKPIVYEQR    118


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.05)
DALI match                          
Query         20 ADAIVAAGYDRELVVKTLR     38
d1wdka1       16 FAKLVSAGVDFVRIDKVME     34



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77: d1t4ga1 DNA repair protein Rad51,​ N-​terminal domain (svm: -1.092)

SCOP Superfamily: Rad51 N-​terminal domain-​like  |  SCOP Fold: SAM domain-​like  |  SCOP Class: All alpha proteins

Consensus: 0.52  Contact: 102
Modified z-scores:
dali:0.60 daliz:0.56 gdtts:0.67 tmscore:0.66 rmsd:0.48 AHM:0.38 LBcontacta:0.65 LBcontactb:0.67 LHM:0.20
id:0.70 blosum:0.42 compass:0.51 pearson:0.54
Scaled scores:
dali:0.61 daliz:0.13 gdtts:0.42 tmscore:0.21 rmsd:0.62 AHM:0.63 LBcontacta:0.28 LBcontactb:0.33 LHM:0.29
id:0.04 blosum:0.05 compass:0.09 pearson:0.08

hit structure      alignment
DALI alignment (Z-score: 0.0 Raw score:70.80)
Query          1 pdypvldaiLELY-VDRDtgadaivaagydrelvvkTLRMVDTAeyKRRQyppgtkisak     59
d1t4ga1        1 ---------LTDLpGVGP------staeklveagyiDFMKIATA--TVGE-----ltdie     38

Query         60 gFGKDRR--lpitnrWREGH--     77
d1t4ga1       39 gISEKAAakmimgarDLCDLgf     60


hit structure      alignment
FAST alignment (Normalized score: 3.49 Raw score:237.10)
Query          1 P-------DYPVLDAILELYVDR----------DTGADAIVA-AGYDRELVVKTLRMVDT     42
d1t4ga1        1 -LTDLPGVGPSTAEKLVE-----AGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARD     54

Query         43 AEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-----     77
d1t4ga1       55 L----------------------------------CDLGF     60


hit structure      alignment
TMalign alignment (TM-score: 0.43 Raw score:32.93)
Query          1 ------PDYPVLD-AI--LEL--YVD-RDTGADAIVAAG-YDRELVVKTLRMVDTAEYKR     47
d1t4ga1        1 LTDLPGVGPSTAEKLVEAGYIDFMKIA-TATVGELTDIEGISEKAAAKMIMGARDLCD--     57

Query         48 RQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1t4ga1       58 --------------------L--GF-----     60


hit structure      alignment
HHsearch alignment (Probability: 0.05 E-value:0.04)
DALI match                                   
Query         17 DTGADAIVAA-GYDRELVVKTLRMVDTA     43
d1t4ga1       28 TATVGELTDIEGISEKAAAKMIMGARDL     55



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78: d1c20a_ DNA-​binding domain from the dead ringer protein (svm: -1.201)

SCOP Superfamily: ARID-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.51  Contact: 146
Modified z-scores:
dali:0.82 daliz:0.81 gdtts:0.87 tmscore:0.89 rmsd:0.33 AHM:0.34 LBcontacta:0.71 LBcontactb:0.75 LHM:0.14
id:0.89 blosum:0.45 compass:0.60 pearson:0.85
Scaled scores:
dali:0.63 daliz:0.29 gdtts:0.47 tmscore:0.38 rmsd:0.72 AHM:0.66 LBcontacta:0.28 LBcontactb:0.32 LHM:0.46
id:0.06 blosum:0.06 compass:0.08 pearson:0.12

hit structure      alignment
DALI alignment (Z-score: 0.9 Raw score:132.00)
Query          1 ------------------------------------------------pdYPVLDAILEL     12
d1c20a_        1 gwsfeeqfkqvrqlyeinddpkrkeflddlfsfmqkrgtpinrlpimaksVLDLYELYNL     60

Query         13 yVDRD---------tGADAIVAAGYD----rELVVKTLRMVDTAeykrrqyppgtkisak     59
d1c20a_       61 -VIARgglvdvinkkLWQEIIKGLHLpssitSAAFTLRTQYMKY------------lypy    107

Query         60 gFGKD-RRLPI--TNRWregh     77
d1c20a_      108 eCEKKnLSTPAelQAAIdgnr    128


hit structure      alignment
FAST alignment (Normalized score: 2.08 Raw score:206.60)
Query          1 PDYP----------------------------------------------------VLDA      8
d1c20a_        1 ----GWSFEEQFKQVRQLYEINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYE     56

Query          9 ILELYVDRDT-----------GADAIVAAGYDR---------ELVVKTLRMVD-TAEYKR     47
d1c20a_       57 LYNLVIA---RGGLVDVINKKLWQEIIK-----GLHLPSSITSAAFTLRTQYMKYLYPYE    108

Query         48 RQYPPGTKISAKGFGKDR----RLPITNRWREGH-----------     77
d1c20a_      109 C-----------------EKKNLSTP--------AELQAAIDGNR    128


hit structure      alignment
TMalign alignment (TM-score: 0.44 Raw score:33.80)
Query          1 ------------------------------------------PDY-----PVLD-AILEL     12
d1c20a_        1 GWSFEEQFKQVRQLYEINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNL     60

Query         13 YVDRD-----T----GADAIVAAGYD---R-ELVVKTLRMVDTA-EYKRRQYPPGTKISA     58
d1c20a_       61 V-IARGGLVDVINKKLWQEIIKGLHLPSSITSAAFTLRTQYMKYLY--P--Y--------    107

Query         59 KGF--GKDRRLPI-TNR-WR-EGH     77
d1c20a_      108 -ECEKKN-LSTPAELQAAIDG-NR    128


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.12)
DALI match                                                    
Query         15 DRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK     59
d1c20a_        6 EQFKQVRQLYEINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKS     50



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79: d2ezla_ Ibeta subdomain of the mu end DNA-​binding domain of phage mu transposase (svm: -0.841)

SCOP Superfamily: Homeodomain-​like  |  SCOP Fold: DNA/​RNA-​binding 3-​helical bundle  |  SCOP Class: All alpha proteins

Consensus: 0.39  Contact: 167
Modified z-scores:
dali:0.85 daliz:0.90 gdtts:0.91 tmscore:0.90 rmsd:0.24 AHM:0.23 LBcontacta:0.84 LBcontactb:0.85 LHM:0.24
id:0.34 blosum:0.24 compass:0.64 pearson:0.83
Scaled scores:
dali:0.63 daliz:0.44 gdtts:0.60 tmscore:0.46 rmsd:0.75 AHM:0.70 LBcontacta:0.40 LBcontactb:0.46 LHM:0.24
id:-0.06 blosum:-0.03 compass:0.03 pearson:0.15

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:126.70)
Query          1 -----------------------------pDYPVLDAILELYVDRD-------tGADAIV     24
d2ezla_        1 miarptleahdydrealwskwdnasdsqrrLAEKWLPAVQAADEMLnqgistktAFATVA     60

Query         25 AAgYDRElVVKTLRMVDTAEYKRrqyppgtkisakgfgkdrrlpitnrwregh     77
d2ezla_       61 GH-YQVS-ASTLRDKYYQVQKFA------------kpdwaaalvdgrgasrrn     99


hit structure      alignment
FAST alignment (Normalized score: 2.53 Raw score:220.80)
Query          1 P----------------------------------DYPVLDAILELYVDRDTGADAIVA-     25
d2ezla_        1 -MIARPTLEAHDYDREALWSKWDNASDSQRRLAEKWLPAVQAADEML-NQGISTKTAFAT     58

Query         26 ----AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----     77
d2ezla_       59 VAGHYQVSASTLRDKYYQVQK-----------------------------------FAKP     83

Query         78 ----------------     78
d2ezla_       84 DWAAALVDGRGASRRN     99


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:28.23)
Query          1 -------------------------------P--DYPVLDAILELYVDRDTGADAIVAAG     27
d2ezla_        1 MIARPTLEAHDYDREALWSKWDNASDSQRRLAEKWLPAVQAADEML-NQGISTKTAFATV     59

Query         28 Y-----DRELVVK-TLRMV-DTAEYK-------------------RRQYPPGTKISAKGF     61
d2ezla_       60 AGHYQVSASTLRDKY--YQV-QK--FAKPDWAAALVDGRGASRRN---------------     99

Query         62 GKDRRLPITNRWREGH     77
d2ezla_      100 ----------------    100


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.47)
DALI match                  
Query         20 ADAIVAAGYDR     30
d2ezla_       42 ADEMLNQGIST     52



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80: d1ikpa3 Exotoxin A,​ middle domain (svm: -0.854)

SCOP Superfamily: Exotoxin A,​ middle domain  |  SCOP Fold: Toxins'​ membrane translocation domains  |  SCOP Class: Membrane and cell surface proteins and peptides

Consensus: 0.44  Contact: 143
Modified z-scores:
dali:0.79 daliz:0.84 gdtts:0.78 tmscore:0.79 rmsd:0.35 AHM:0.42 LBcontacta:0.83 LBcontactb:0.73 LHM:0.24
id:0.79 blosum:0.77 compass:0.65 pearson:0.83
Scaled scores:
dali:0.65 daliz:0.41 gdtts:0.46 tmscore:0.36 rmsd:0.69 AHM:0.57 LBcontacta:0.38 LBcontactb:0.38 LHM:0.31
id:0.02 blosum:0.11 compass:0.02 pearson:0.14

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:131.40)
Query          1 -----------------------------------pDYPVLDAILELyVDRDT---GADA     22
d1ikpa3        1 eggslaaltahqachlpletftrhrqprgaeqleqcGYPVQRLVALY-LAARLswnQVDQ     59

Query         23 IVAAG-------------------yDRELVVKTLRMVDTAEYKRRQ----------yppg     53
d1ikpa3       60 VIRNAlaspgsggdlgeaireqpeqARLALTLAAAESERFVRQGTGndeagaanadvvsl    119

Query         54 tkisakgfgkdrrlpitnrwregh     77
d1ikpa3      120 tcpvaagecagpadsgdallerny    143


hit structure      alignment
FAST alignment (Normalized score: 2.79 Raw score:292.40)
Query          1 ----------------------------------PDYPVLDAILELYVDRDT----GADA     22
d1ikpa3        1 EGGSLAALTAHQACHLPLETFTRHRQPRGAEQLEQCGYPVQRLVALYLAAR-LSWNQVDQ     59

Query         23 IVAAG------------------YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD     64
d1ikpa3       60 VI---RNALASPGSGGDLGEAIREQPEQARLALTLAAAESERFVRQG-------------    103

Query         65 RRLPITNRWREGH----------------------------------------     77
d1ikpa3      104 -------------TGNDEAGAANADVVSLTCPVAAGECAGPADSGDALLERNY    143


hit structure      alignment
TMalign alignment (TM-score: 0.49 Raw score:37.50)
Query          1 -------------P---------------------DYPVLDAILELYVDRDT-------G     19
d1ikpa3        1 EGGSLAALTAHQACHLPLETFTRHRQPRGAEQLEQCGYPVQRLVALYLAARLSWNQVDQV     60

Query         20 A--D------A--IVAA-GYDRELVVKTLRMVDTA-EYKRR-QY-PP--GTKISAKGFGK     63
d1ikpa3       61 IRNALASPGSGGDLGEAIREQPEQARLALTLAAAESER-FVRQGT-GND-------EAGA    111

Query         64 --------------------------------DRRLPITNRWREGH     77
d1ikpa3      112 ANADVVSLTCPVAAGECAGPADSGDALLERNY--------------    143


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.35)
DALI match                                                     
Query          3 YPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRR     48
d1ikpa3       54 WNQVDQVIRNALASPGSGGDLGEAIREQPEQARLALTLAAAESERF     99



hit structures. 
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81: d1kb4b_ Vitamin D3 receptor,​ VDR,​ DNA-​binding domain (svm: -1.282)

SCOP Superfamily: Glucocorticoid receptor-​like (DNA-​binding domain)  |  SCOP Fold: Glucocorticoid receptor-​like (DNA-​binding domain)  |  SCOP Class: Small proteins

Consensus: 0.38  Contact: 137
Modified z-scores:
dali:0.84 daliz:0.83 gdtts:0.86 tmscore:0.91 rmsd:0.43 AHM:0.49 LBcontacta:0.72 LBcontactb:0.65 LHM:0.19
id:0.51 blosum:0.15 compass:0.16 pearson:0.70
Scaled scores:
dali:0.64 daliz:0.31 gdtts:0.43 tmscore:0.34 rmsd:0.66 AHM:0.55 LBcontacta:0.30 LBcontactb:0.24 LHM:0.37
id:-0.01 blosum:-0.01 compass:0.02 pearson:0.04

hit structure      alignment
DALI alignment (Z-score: 1.0 Raw score:108.30)
Query          1 ------------------PDYPVLDAILELYVdRDTGA---------------daiVAAG     27
d1kb4b_        1 ricgvcgdratgfhfnamTCEGCKGFFRRSMK-RKALFtcpfngdcritkdnrrhcQACR     59

Query         28 ---YDRELVvkTLRMVDtAEYKRRQY--PPGTkisakgfgkdrrlpitnrwregh     77
d1kb4b_       60 lkrCVDIGM--MKEFIL-TDEEVQRKreMILK------------rkeeealkdsl     99


hit structure      alignment
FAST alignment (Normalized score: 1.93 Raw score:168.30)
Query          1 P------------------DYPVLDAILELYVDRDTGADAIVAAGYD-------------     29
d1kb4b_        1 -RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKA-----------LFTCPFNGDCRIT     48

Query         30 ----RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------     77
d1kb4b_       49 KDNRRHCQACRLKRCVD-----------------------------------IGMMKEFI     73

Query         78 --------------------------     78
d1kb4b_       74 LTDEEVQRKREMILKRKEEEALKDSL     99


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:29.64)
Query          1 ------------------PDYPVLDAILELYVDRDTGADAIV---A-------------A     26
d1kb4b_        1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK-RKAL--FTCPFNGDCRITKDNRRHCQA     57

Query         27 GY--D-RELVVKTLRMVDTAE-YKRRQYPP---------------GTKISAKGFGKDRRL     67
d1kb4b_       58 CRLKRCVDI-GMMKEFI--LTDEEVQRKREMILKRKEEEALKDSL---------------     99

Query         68 PITNRWREGH     77
d1kb4b_      100 ----------    100


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.42)
DALI match                                   
Query         21 DAIVAAGYDRELVVKTLRMVDTAEYKRR     48
d1kb4b_       61 KRCVDIGMMKEFILTDEEVQRKREMILK     88



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82: d1f14a1 Short chain L-​3-​hydroxyacyl CoA dehydrogenase (svm: -0.973)

SCOP Superfamily: 6-​phosphogluconate dehydrogenase C-​terminal domain-​like  |  SCOP Fold: 6-​phosphogluconate dehydrogenase C-​terminal domain-​like  |  SCOP Class: All alpha proteins

Consensus: 0.21  Contact: 214
Modified z-scores:
dali:0.84 daliz:0.74 gdtts:0.91 tmscore:0.94 rmsd:0.39 AHM:0.39 LBcontacta:0.77 LBcontactb:0.88 LHM:0.10
id:0.85 blosum:0.46 compass:0.05 pearson:0.56
Scaled scores:
dali:0.61 daliz:0.22 gdtts:0.44 tmscore:0.38 rmsd:0.72 AHM:0.68 LBcontacta:0.24 LBcontactb:0.33 LHM:0.62
id:0.02 blosum:0.08 compass:-0.03 pearson:-0.02

hit structure      alignment
DALI alignment (Z-score: 1.3 Raw score:123.80)
Query          1 ---pdyPVLDAILELyVDRD----TGADAIVAAGY----drelVVKTLR-MVDTA-EYKR     47
d1f14a1        1 gfivnrLLVPYLMEA-IRLYergdASKEDIDTAMKlgagypmgPFELLDyVGLDTtKFIV     59

Query         48 RQY--PPGTKIsakgfgkdrrlPITNR------WREGH--     77
d1f14a1       60 DGWheMDAENPlhqpspslnklVAENKfgkktgEGFYKyk     99


hit structure      alignment
FAST alignment (Normalized score: 1.73 Raw score:151.00)
Query          1 PDYPV-LDAILELYVDRDTGADAIVA----------------------------------     25
d1f14a1        1 -----GFIVNRLLVPY----------LMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFE     45

Query         26 --AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------     77
d1f14a1       46 LLDYVGLDTTKFIVDGWHE-----------------------------------MDAENP     70

Query         78 -----------------------------     78
d1f14a1       71 LHQPSPSLNKLVAENKFGKKTGEGFYKYK     99


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:35.43)
Query          1 --PDY-PVLDAILELYVDRD------T--GADAIVAAGYDRELV-VKTLR-MVDTA-EYK     46
d1f14a1        1 GF-IVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFE-LLDYVGLDTTK-F     57

Query         47 RRQY-PP-GTKISAKGFGKDR--RLPI--TN-----RWR-EGH-     77
d1f14a1       58 IVDGWHEMDAENP-LHQP-SPSLNKLVAENKFGKKTGEGFYKYK     99


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.12)
DALI match                          
Query         22 AIVAAGY-DRELVVKTLRM     39
d1f14a1       17 RLYERGDASKEDIDTAMKL     35



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83: d1u9la_ Transcription elongation protein NusA (svm: -1.425)

SCOP Superfamily: Rad51 N-​terminal domain-​like  |  SCOP Fold: SAM domain-​like  |  SCOP Class: All alpha proteins

Consensus: 0.50  Contact: 103
Modified z-scores:
dali:0.75 daliz:0.75 gdtts:0.80 tmscore:0.77 rmsd:0.33 AHM:0.41 LBcontacta:0.70 LBcontactb:0.58 LHM:0.18
id:0.73 blosum:0.48 compass:0.31 pearson:0.61
Scaled scores:
dali:0.68 daliz:0.36 gdtts:0.56 tmscore:0.35 rmsd:0.75 AHM:0.66 LBcontacta:0.35 LBcontactb:0.26 LHM:0.37
id:0.04 blosum:0.05 compass:0.04 pearson:0.06

hit structure      alignment
DALI alignment (Z-score: 0.8 Raw score:94.50)
Query          1 pdYPVLDAILELYVDRdtgadaivaagydrelvvkTLRMVDTA-EYKRRQyppgtkisak     59
d1u9la_        1 --AHAAIDTFTKYLDI-----dedfatvlveegfsTLEELAYVpMKELLE--------ie     45

Query         60 gfGKDRRL----pitnrwREGH-     77
d1u9la_       46 glDEPTVEalreraknalATIAq     68


hit structure      alignment
FAST alignment (Normalized score: 3.45 Raw score:249.70)
Query          1 P--------------DYPVLDAILELYVDR----------DTGADAIVAA-GYDRELVVK     35
d1u9la_        1 -AHAAIDTFTKYLDIDEDFATVLVE-----EGFSTLEELAYVPMKELLEIEGLDEPTVEA     54

Query         36 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-     77
d1u9la_       55 LRERAKNALATIA-----------------------------Q     68


hit structure      alignment
TMalign alignment (TM-score: 0.42 Raw score:32.68)
Query          1 -------------PDYPVLD--AI--LELYVDRD---TGADAIVAAG-YDRELVVKTLRM     39
d1u9la_        1 AHAAIDTFTKYLDIDEDF-ATVLVEE-GFSTLEELAYVPMKELLEIEGLDEPTVEALRER     58

Query         40 VDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH     77
d1u9la_       59 AKNALATIAQ----------------------------     68


hit structure      alignment
HHsearch alignment (Probability: 0.10 E-value:0.01)
DALI match                                                     
Query          4 PVLDAILELYVDRDTGADAIVA----------AGYDRELVVKTLRM     39
d1u9la_       13 DIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRER     58