T0491

Targets
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T0491

primosomal replication protein N from Bordetella pertussis

Target type: Server only

Target sequence:

>T0491 Primosomal replication protein, Bordetella pertussis, 115 residues
MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIAGSMGRDPLVGLEHHHHHH

Structure:
Method: X-ray, res=2.0Å, R/Rfree=0.25/0.24
Determined by: NESG
PDB ID: 3dm4

3dm4 cartoon
Cartoon diagram of 491: 3dm4

PyMOL of 3dm4

Domains:  PyMOL of domains

Single domain protein. Despite claimed 2Å, it looks like a poorly refined structure with R factor exceeding Rfree.

Structure classification:

OB fold.

CASP category:

Comparative modeling:easy.

Closest templates:

1v1q, 1txy.

Target sequence - PDB file inconsistencies:

T0491    3dm4.pdb    T0491.pdb    PyMOL    PyMOL of domains    

T0491    1 MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIAGSMGRDPLVGLEHHHHHH 115
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~~~~~~~
3dm4A    1 MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIAG----------------- 98

Residue change log: change 1, 16, 70, MSE to MET;

Single domain protein: target 1-98 ; pdb 1-98

Sequence classification:

OB-fold nucleic acid binding domain (tRNA_anti) in Pfam.

Server predictions:

T0491:pdb 1-98:seq 1-98:CM_easy;   alignment

distribution of first scores
First models for T0491: Gaussian kernel density estimation for GDT-TS scores of the first server models, plotted at various bandwidths (=standard deviations). The GDT-TS scores are shown as a spectrum along the horizontal axis: each bar represents first server model. The bars are colored green, gray and black for top 10, bottom 25% and the rest of servers. The family of curves with varying bandwidth is shown. Bandwidth varies from 0.3 to 8.2 GDT-TS % units with a step of 0.1, which corresponds to the color ramp from magenta through blue to cyan. Thicker curves: red, yellow-framed brown and black, correspond to bandwidths 1, 2 and 4 respectively.

click on a score in the table below to display the model in PyMOL

# GROUP ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ ↓ GROUP #
T0491 T0491 T0491 T0491
First score First Z-score Best score Best Z-score
1 keasar−server 87.50 81.21 81.49 1.24 1.31 0.27 87.50 81.97 88.36 1.41 1.39 1.16 keasar−server 1
2 YASARA 86.73 77.38 86.20 1.14 0.83 0.88 86.99 77.38 86.20 1.29 0.45 0.71 YASARA 2
3 circle 86.48 76.28 82.04 1.10 0.69 0.34 86.48 81.21 84.14 1.17 1.23 0.27 circle 3
4 3DShot2 86.22 80.78 86.88 1.07 1.25 0.97 86.22 80.78 86.88 1.11 1.14 0.85 3DShot2 4
5 mGenTHREADER 85.46 81.04 79.18 0.97 1.29 -0.03 85.46 81.04 79.18 0.93 1.20 -0.77 mGenTHREADER 5
6 SAM−T02−server 84.95 80.19 80.14 0.90 1.18 0.09 84.95 80.53 81.61 0.81 1.09 -0.26 SAM−T02−server 6
7 LEE−SERVER 84.95 79.34 82.51 0.90 1.07 0.40 89.54 81.55 90.55 1.89 1.30 1.62 LEE−SERVER 7
8 SAM−T08−server 84.69 78.06 89.68 0.87 0.91 1.33 84.69 80.44 89.68 0.75 1.07 1.44 SAM−T08−server 8
9 BioSerf 84.69 74.15 90.26 0.87 0.42 1.40 84.69 74.15 90.26 0.75 -0.20 1.56 BioSerf 9
10 PSI 84.44 77.98 82.09 0.83 0.90 0.35 84.44 77.98 84.22 0.69 0.57 0.29 PSI 10
11 HHpred5 83.93 78.83 83.89 0.77 1.01 0.58 83.93 78.83 83.89 0.57 0.75 0.22 HHpred5 11
12 MUFOLD−Server 83.67 77.21 81.84 0.73 0.80 0.31 85.20 81.12 81.84 0.87 1.21 -0.21 MUFOLD−Server 12
13 COMA 82.91 78.15 81.72 0.63 0.92 0.30 82.91 78.15 83.67 0.33 0.61 0.17 COMA 13
14 FFASstandard 82.65 79.08 81.82 0.60 1.04 0.31 84.18 79.08 82.28 0.63 0.80 -0.12 FFASstandard 14
15 FFASflextemplate 82.65 79.08 81.82 0.60 1.04 0.31 84.44 80.70 81.82 0.69 1.13 -0.22 FFASflextemplate 15
16 MULTICOM−CMFR 81.89 76.62 83.93 0.49 0.73 0.58 82.91 79.34 84.23 0.33 0.85 0.29 MULTICOM−CMFR 16
17 Phyre_de_novo 81.89 74.75 85.13 0.49 0.49 0.74 81.89 74.75 85.13 0.09 -0.08 0.48 Phyre_de_novo 17
18 Zhang−Server 81.63 75.68 84.96 0.46 0.61 0.72 83.93 79.68 86.71 0.57 0.92 0.81 Zhang−Server 18
19 PS2−server 81.63 74.32 82.55 0.46 0.44 0.41 82.65 74.32 89.34 0.27 -0.17 1.37 PS2−server 19
20 RAPTOR 81.63 73.30 83.13 0.46 0.31 0.48 81.63 73.30 83.14 0.03 -0.38 0.06 RAPTOR 20
21 MULTICOM−CLUSTER 81.38 73.89 83.48 0.43 0.39 0.53 83.16 77.72 84.38 0.39 0.52 0.32 MULTICOM−CLUSTER 21
22 fais−server 81.12 72.28 82.61 0.39 0.18 0.41 81.12 73.47 87.41 -0.09 -0.34 0.96 fais−server 22
23 HHpred2 81.12 67.86 83.39 0.39 -0.37 0.51 81.12 67.86 83.39 -0.09 -1.48 0.11 HHpred2 23
24 FFASsuboptimal 80.87 76.79 80.72 0.36 0.75 0.17 83.67 79.76 81.90 0.51 0.94 -0.20 FFASsuboptimal 24
25 Frankenstein 80.87 76.79 83.44 0.36 0.75 0.52 85.97 80.02 83.44 1.05 0.99 0.13 Frankenstein 25
26 3D−JIGSAW_V3 80.87 76.28 83.82 0.36 0.69 0.57 80.87 76.28 85.84 -0.15 0.23 0.63 3D−JIGSAW_V3 26
27 nFOLD3 80.87 75.77 82.57 0.36 0.62 0.41 80.87 75.77 82.57 -0.15 0.13 -0.06 nFOLD3 27
28 Pcons_dot_net 80.87 68.11 81.97 0.36 -0.34 0.33 82.14 77.64 84.28 0.15 0.51 0.30 Pcons_dot_net 28
29 Pcons_multi 80.87 68.11 81.97 0.36 -0.34 0.33 80.87 73.38 83.67 -0.15 -0.36 0.17 Pcons_multi 29
30 ACOMPMOD 80.61 75.34 82.24 0.32 0.57 0.37 80.61 75.34 82.24 -0.21 0.04 -0.13 ACOMPMOD 30
31 LOOPP_Server 80.61 74.83 80.86 0.32 0.50 0.19 84.18 75.51 84.01 0.63 0.07 0.25 LOOPP_Server 31
32 METATASSER 80.61 69.73 80.54 0.32 -0.14 0.15 80.61 74.32 84.94 -0.21 -0.17 0.44 METATASSER 32
33 pro−sp3−TASSER 80.36 73.72 82.02 0.29 0.36 0.34 80.36 73.72 83.87 -0.27 -0.29 0.22 pro−sp3−TASSER 33
34 GS−MetaServer2 80.36 72.36 82.85 0.29 0.19 0.44 84.69 74.32 87.09 0.75 -0.17 0.89 GS−MetaServer2 34
35 GeneSilicoMetaServer 80.36 72.36 82.85 0.29 0.19 0.44 84.69 79.34 82.85 0.75 0.85 0.00 GeneSilicoMetaServer 35
36 HHpred4 80.10 72.28 82.66 0.26 0.18 0.42 80.10 72.28 82.66 -0.33 -0.58 -0.04 HHpred4 36
37 Pushchino 79.85 73.55 82.38 0.22 0.34 0.38 79.85 73.55 82.38 -0.39 -0.33 -0.10 Pushchino 37
38 GS−KudlatyPred 79.85 73.55 82.95 0.22 0.34 0.46 79.85 73.55 86.02 -0.39 -0.33 0.67 GS−KudlatyPred 38
39 3Dpro 79.85 70.66 83.83 0.22 -0.02 0.57 79.85 70.66 83.83 -0.39 -0.91 0.21 3Dpro 39
40 FALCON 79.85 70.66 80.96 0.22 -0.02 0.20 79.85 71.51 81.80 -0.39 -0.74 -0.22 FALCON 40
41 MULTICOM−REFINE 79.59 74.66 83.45 0.19 0.48 0.52 83.67 78.06 83.99 0.51 0.59 0.24 MULTICOM−REFINE 41
42 FUGUE_KM 79.59 71.60 81.27 0.19 0.10 0.24 79.59 71.60 81.27 -0.45 -0.72 -0.33 FUGUE_KM 42
43 MUProt 78.57 73.64 83.67 0.05 0.35 0.55 83.67 78.49 84.02 0.51 0.68 0.25 MUProt 43
44 Poing 78.57 70.41 80.75 0.05 -0.05 0.17 84.95 79.51 89.32 0.81 0.89 1.36 Poing 44
45 Phyre2 78.57 70.41 80.75 0.05 -0.05 0.17 84.44 79.00 89.39 0.69 0.78 1.38 Phyre2 45
46 Phragment 78.57 70.41 80.75 0.05 -0.05 0.17 84.18 78.74 89.33 0.63 0.73 1.37 Phragment 46
47 MUSTER 78.57 66.33 84.57 0.05 -0.57 0.67 82.91 76.28 84.57 0.33 0.23 0.36 MUSTER 47
48 MUFOLD−MD 78.32 65.22 73.78 0.02 -0.71 -0.73 78.32 65.22 73.78 -0.75 -2.02 -1.91 MUFOLD−MD 48
49 SAM−T06−server 78.06 66.50 84.17 -0.01 -0.54 0.61 83.67 76.70 84.17 0.51 0.31 0.28 SAM−T06−server 49
50 Fiser−M4T 77.81 72.36 79.62 -0.05 0.19 0.03 77.81 72.36 79.62 -0.87 -0.57 -0.68 Fiser−M4T 50
51 3D−JIGSAW_AEP 77.55 63.44 82.09 -0.08 -0.93 0.35 77.55 66.58 82.75 -0.93 -1.74 -0.02 3D−JIGSAW_AEP 51
52 CpHModels 77.30 72.36 73.68 -0.12 0.19 -0.74 77.30 72.36 73.68 -0.99 -0.57 -1.93 CpHModels 52
53 MULTICOM−RANK 76.53 73.81 83.07 -0.22 0.38 0.47 82.40 76.11 85.48 0.21 0.19 0.56 MULTICOM−RANK 53
54 COMA−M 75.51 68.54 81.84 -0.35 -0.29 0.31 77.30 70.15 83.67 -0.99 -1.02 0.17 COMA−M 54
55 FAMSD 75.25 65.05 84.02 -0.39 -0.73 0.60 86.48 81.46 84.02 1.17 1.28 0.25 FAMSD 55
56 BAKER−ROBETTA 67.86 55.61 61.93 -1.37 -1.92 -2.26 71.68 67.60 74.06 -2.31 -1.54 -1.85 BAKER−ROBETTA 56
57 Pcons_local 66.58 61.82 58.16 -1.54 -1.13 -2.75 79.59 76.87 81.22 -0.45 0.35 -0.34 Pcons_local 57
58 pipe_int 65.82 58.67 66.24 -1.64 -1.53 -1.70 65.82 58.67 66.24 -3.69 -3.35 -3.50 pipe_int 58
59 panther_server 64.54 59.61 66.38 -1.81 -1.41 -1.68 83.93 80.02 79.33 0.57 0.99 -0.74 panther_server 59
60 FEIG 59.69 53.91 59.70 -2.45 -2.13 -2.55 75.25 69.13 78.30 -1.47 -1.22 -0.96 FEIG 60
61 RBO−Proteus 59.44 50.94 70.78 -2.49 -2.50 -1.12 59.44 52.98 70.78 -5.19 -4.51 -2.54 RBO−Proteus 61
62 FOLDpro 58.16 53.74 60.65 -2.66 -2.15 -2.43 68.11 61.65 67.66 -3.15 -2.74 -3.20 FOLDpro 62
63 rehtnap 55.10 48.81 49.77 -3.06 -2.77 -3.83 66.33 61.40 50.58 -3.57 -2.80 -6.80 rehtnap 63
64 FALCON_CONSENSUS 54.59 47.11 56.56 -3.13 -2.99 -2.95 79.08 70.92 79.85 -0.57 -0.86 -0.63 FALCON_CONSENSUS 64
65 forecast 54.34 41.24 49.11 -3.17 -3.73 -3.92 75.00 67.52 81.62 -1.53 -1.55 -0.26 forecast 65
66 mariner1 52.55 43.88 56.11 -3.40 -3.39 -3.01 56.12 53.06 58.71 -5.98 -4.49 -5.09 mariner1 66
67 Distill 19.39 19.39 24.43 -7.81 -6.48 -7.11 20.92 19.39 27.94 -14.27 -11.33 -11.57 Distill 67
68 RANDOM 18.92 15.66 18.92 -7.87 -6.95 -7.82 18.92 15.66 18.92 -14.74 -12.09 -13.47 RANDOM 68
69 schenk−torda−server 16.84 13.95 15.28 -8.15 -7.16 -8.29 16.84 14.80 16.02 -15.23 -12.27 -14.08 schenk−torda−server 69
70 mahmood−torda−server 15.05 12.33 19.20 -8.39 -7.37 -7.78 19.13 16.24 24.85 -14.69 -11.97 -12.22 mahmood−torda−server 70
71 OLGAFS 13.27 11.22 8.27 -8.62 -7.51 -9.20 71.68 66.58 58.12 -2.31 -1.74 -5.21 OLGAFS 71
72 huber−torda−server 0.00 0.00 -6.88 -10.38 -8.92 -11.15 0.00 0.00 -6.88 -19.19 -15.28 -18.91 huber−torda−server 72
73 BHAGEERATH                   -7.87 -6.95 -7.82                   -14.74 -12.09 -13.47 BHAGEERATH 73
74 test_http_server_01                   -7.87 -6.95 -7.82                   -14.74 -12.09 -13.47 test_http_server_01 74