T0406

Targets
387 388 389 390
391 392 393 394
395 396 397 398
399 400 401 402
403 404 405 406
407 408 409 410
411 412 413 414
415 416 417 418
419 420 421 422
423 424 425 426
427 428 429 430
431 432 433 434
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443 444 445 446
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483 484 485 486
487 488 489 490
491 492 493 494
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503 504 505 506
507 508 509 510
511 512 513 514

T0406

DinB-like protein (NP_980948.1) from Bacillus cereus

Target type: Server only

Target sequence:

>T0406 NP_980948.1, BACILLUS CEREUS, 167 residues
MYQTIEGFLQSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPVILSGTGLKFEGETKDYPVPTSAKTIADGYRKVNTAFVEALQSEWTDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQAGLTVPGVYGPAKEEWATAGMEAPKM

Structure:
Method: X-ray, res=2.01Å, R/Rfree=0.23/0.27
Determined by: JCSG
PDB ID: 3di5

3di5_A cartoon
Cartoon diagram of 406: 3di5 chain A

PyMOL of 3di5

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

DinB/YfiT-like putative metalloenzymes.

CASP category:

Comparative modeling:medium.

Closest templates:

2qe9, 2f22, 2hkv, 2p1a, 2ou6.

Target sequence - PDB file inconsistencies:

T0406    3di5.pdb    T0406.pdb    PyMOL    PyMOL of domains    

T0406    1 MYQTIEGFLQSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPVILSGTGLKFEGETKDYPVPTSAKTIADGYRKVNTAFVEALQSEWTDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQAGLTVPGVYGPAKEEWATAGMEAPKM 167
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~~~~~~~
3di5A    1 MYQTIEGFLQSWTYETESTQKMLDVLTDESLSQEIAPGHWTLGRVAWHIVTAIPVILSGTGLKFEGETKDYPVPTSAKTIADGYRKVNTAFVEALQSEWTDKDLTTINDFFGRPMPNSIFLMTLINHQNHHRGQMTVLMRQAGLTVPGVY----------------- 150

Residue change log: change 1, 22, 115, 122, 135, 139, MSE to MET;

Single domain protein: target 1-150 ; pdb 1-150

Sequence classification:

DinB family (PF05163) in Pfam.

Comments:

This protein is a close homolog of T0481.

Server predictions:

T0406:pdb 1-150:seq 1-150:CM_medium;   alignment

distribution of first scores
First models for T0406: 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 #
T0406 T0406 T0406 T0406
First score First Z-score Best score Best Z-score
1 LEE−SERVER 73.00 65.78 67.77 1.54 1.88 1.74 73.33 66.22 67.77 1.75 1.77 1.84 LEE−SERVER 1
2 HHpred5 72.00 65.22 65.12 1.44 1.82 1.39 72.00 65.22 65.12 1.56 1.64 1.39 HHpred5 2
3 METATASSER 69.67 60.78 65.59 1.18 1.34 1.45 71.83 62.39 67.57 1.53 1.26 1.81 METATASSER 3
4 RAPTOR 69.50 59.50 62.26 1.17 1.20 1.02 69.50 60.61 62.32 1.19 1.02 0.91 RAPTOR 4
5 pro−sp3−TASSER 68.83 60.06 67.24 1.09 1.26 1.67 69.33 61.00 67.69 1.16 1.07 1.83 pro−sp3−TASSER 5
6 Phyre_de_novo 67.67 58.33 63.32 0.97 1.07 1.16 67.67 58.67 63.32 0.92 0.76 1.08 Phyre_de_novo 6
7 GS−KudlatyPred 67.17 59.61 59.14 0.91 1.21 0.62 67.17 59.61 59.14 0.85 0.89 0.37 GS−KudlatyPred 7
8 Zhang−Server 67.17 54.56 64.76 0.91 0.66 1.35 67.17 55.94 64.76 0.85 0.40 1.33 Zhang−Server 8
9 FEIG 66.83 58.50 63.42 0.88 1.09 1.17 68.17 59.50 63.69 0.99 0.87 1.15 FEIG 9
10 nFOLD3 66.67 62.67 55.54 0.86 1.54 0.15 66.67 62.67 57.23 0.77 1.30 0.04 nFOLD3 10
11 SAM−T08−server 65.67 59.22 65.28 0.75 1.17 1.41 65.67 61.00 65.28 0.62 1.07 1.42 SAM−T08−server 11
12 COMA−M 65.33 56.22 61.37 0.71 0.84 0.91 65.33 56.22 61.37 0.57 0.44 0.75 COMA−M 12
13 Pcons_multi 64.67 51.89 61.85 0.64 0.36 0.97 67.67 60.00 61.85 0.92 0.94 0.83 Pcons_multi 13
14 Pcons_local 63.67 55.56 55.98 0.54 0.76 0.21 63.67 55.56 58.68 0.33 0.35 0.29 Pcons_local 14
15 FAMSD 62.67 53.56 55.66 0.43 0.55 0.17 62.67 53.56 56.00 0.18 0.08 -0.17 FAMSD 15
16 BAKER−ROBETTA 62.67 50.22 59.73 0.43 0.18 0.69 63.00 55.11 60.45 0.23 0.29 0.59 BAKER−ROBETTA 16
17 FALCON 62.50 52.39 56.61 0.41 0.42 0.29 65.67 60.67 59.14 0.62 1.03 0.37 FALCON 17
18 Phyre2 62.33 51.89 58.24 0.39 0.36 0.50 63.67 58.67 58.42 0.33 0.76 0.25 Phyre2 18
19 Poing 62.33 51.78 58.23 0.39 0.35 0.50 63.50 58.83 59.77 0.30 0.78 0.48 Poing 19
20 Phragment 62.33 51.78 58.21 0.39 0.35 0.50 63.33 58.44 59.47 0.28 0.73 0.43 Phragment 20
21 COMA 62.17 53.61 54.82 0.37 0.55 0.06 62.83 55.17 61.37 0.21 0.29 0.75 COMA 21
22 Pcons_dot_net 62.17 53.61 57.41 0.37 0.55 0.39 63.67 55.56 60.45 0.33 0.35 0.59 Pcons_dot_net 22
23 BioSerf 62.17 51.17 56.23 0.37 0.28 0.24 62.17 51.17 56.23 0.11 -0.24 -0.13 BioSerf 23
24 SAM−T06−server 62.00 49.06 57.81 0.35 0.05 0.44 65.17 61.06 57.81 0.55 1.08 0.14 SAM−T06−server 24
25 PS2−server 61.67 52.11 56.69 0.32 0.39 0.30 61.67 52.11 59.18 0.03 -0.11 0.38 PS2−server 25
26 3D−JIGSAW_AEP 61.50 48.83 60.82 0.30 0.03 0.83 61.50 48.83 60.82 0.01 -0.55 0.66 3D−JIGSAW_AEP 26
27 PSI 61.50 47.94 59.79 0.30 -0.07 0.70 66.00 61.00 60.20 0.67 1.07 0.55 PSI 27
28 keasar−server 61.33 51.78 55.99 0.28 0.35 0.21 62.00 53.39 57.87 0.08 0.06 0.15 keasar−server 28
29 HHpred2 61.33 47.33 55.67 0.28 -0.14 0.17 61.33 47.33 55.67 -0.02 -0.75 -0.22 HHpred2 29
30 mGenTHREADER 61.17 50.39 53.59 0.27 0.20 -0.10 61.17 50.39 53.59 -0.04 -0.34 -0.58 mGenTHREADER 30
31 pipe_int 60.83 50.83 56.32 0.23 0.25 0.25 66.83 59.94 59.51 0.80 0.93 0.43 pipe_int 31
32 MULTICOM−RANK 60.67 51.78 51.63 0.21 0.35 -0.36 60.67 51.78 58.39 -0.11 -0.16 0.24 MULTICOM−RANK 32
33 MULTICOM−CLUSTER 60.67 51.78 51.63 0.21 0.35 -0.36 62.83 56.61 56.58 0.21 0.49 -0.07 MULTICOM−CLUSTER 33
34 CpHModels 60.67 51.22 53.25 0.21 0.29 -0.15 60.67 51.22 53.25 -0.11 -0.23 -0.63 CpHModels 34
35 HHpred4 60.50 55.72 57.23 0.19 0.78 0.37 60.50 55.72 57.23 -0.14 0.37 0.04 HHpred4 35
36 GeneSilicoMetaServer 60.50 44.17 50.93 0.19 -0.48 -0.45 62.50 54.50 53.34 0.16 0.21 -0.62 GeneSilicoMetaServer 36
37 Frankenstein 60.33 49.67 52.64 0.17 0.12 -0.23 66.17 59.06 61.05 0.70 0.82 0.70 Frankenstein 37
38 3Dpro 59.83 52.72 53.32 0.12 0.45 -0.14 59.83 52.72 53.32 -0.24 -0.03 -0.62 3Dpro 38
39 3DShot2 59.83 46.67 54.35 0.12 -0.21 -0.00 59.83 46.67 54.35 -0.24 -0.84 -0.45 3DShot2 39
40 circle 59.00 49.44 57.99 0.03 0.10 0.47 61.67 51.89 57.99 0.03 -0.14 0.17 circle 40
41 MULTICOM−REFINE 58.17 44.17 59.34 -0.06 -0.48 0.64 62.33 54.33 59.36 0.13 0.18 0.41 MULTICOM−REFINE 41
42 3D−JIGSAW_V3 57.83 50.39 51.54 -0.10 0.20 -0.37 60.83 50.39 59.70 -0.09 -0.34 0.47 3D−JIGSAW_V3 42
43 rehtnap 57.83 46.72 57.48 -0.10 -0.20 0.40 59.00 47.33 58.44 -0.36 -0.75 0.25 rehtnap 43
44 MUProt 57.83 46.39 59.36 -0.10 -0.24 0.65 63.17 54.61 59.36 0.26 0.22 0.41 MUProt 44
45 MULTICOM−CMFR 57.67 43.00 59.34 -0.11 -0.61 0.64 62.83 54.72 59.34 0.21 0.23 0.40 MULTICOM−CMFR 45
46 YASARA 57.17 52.39 55.10 -0.17 0.42 0.09 57.17 52.39 55.10 -0.63 -0.08 -0.32 YASARA 46
47 FUGUE_KM 56.83 42.44 45.64 -0.20 -0.67 -1.13 58.33 46.44 51.76 -0.46 -0.87 -0.89 FUGUE_KM 47
48 FFASsuboptimal 56.83 33.39 51.79 -0.20 -1.66 -0.34 58.17 43.72 53.21 -0.48 -1.24 -0.64 FFASsuboptimal 48
49 FFASflextemplate 56.50 35.83 51.21 -0.24 -1.39 -0.41 56.50 47.33 52.31 -0.73 -0.75 -0.79 FFASflextemplate 49
50 FFASstandard 56.50 32.50 52.65 -0.24 -1.76 -0.22 59.50 47.50 53.35 -0.29 -0.73 -0.62 FFASstandard 50
51 SAM−T02−server 55.67 40.33 50.28 -0.33 -0.90 -0.53 58.00 53.78 50.28 -0.51 0.11 -1.14 SAM−T02−server 51
52 MUSTER 55.33 42.67 50.65 -0.37 -0.65 -0.48 61.33 42.67 58.78 -0.02 -1.38 0.31 MUSTER 52
53 GS−MetaServer2 55.17 50.50 47.99 -0.38 0.21 -0.83 60.33 53.44 59.01 -0.16 0.06 0.35 GS−MetaServer2 53
54 fais−server 55.17 48.17 51.20 -0.38 -0.04 -0.41 55.17 48.17 51.20 -0.93 -0.64 -0.98 fais−server 54
55 panther_server 53.83 47.94 43.86 -0.53 -0.07 -1.36 64.00 59.67 51.34 0.38 0.90 -0.96 panther_server 55
56 FOLDpro 52.33 41.56 38.62 -0.69 -0.77 -2.04 58.33 41.56 50.83 -0.46 -1.53 -1.05 FOLDpro 56
57 ACOMPMOD 48.83 43.17 44.55 -1.07 -0.59 -1.27 52.67 47.56 50.65 -1.29 -0.72 -1.08 ACOMPMOD 57
58 Pushchino 47.00 37.67 35.94 -1.27 -1.19 -2.39 47.00 37.67 35.94 -2.13 -2.05 -3.58 Pushchino 58
59 MUFOLD−Server 36.17 31.00 36.46 -2.43 -1.92 -2.32 36.17 31.00 36.46 -3.73 -2.94 -3.49 MUFOLD−Server 59
60 forecast 27.67 23.44 33.15 -3.35 -2.75 -2.75 32.33 27.89 36.96 -4.30 -3.35 -3.41 forecast 60
61 FALCON_CONSENSUS 27.17 24.28 31.91 -3.41 -2.66 -2.91 62.50 52.39 56.61 0.16 -0.08 -0.06 FALCON_CONSENSUS 61
62 MUFOLD−MD 24.50 21.17 40.35 -3.70 -3.00 -1.82 26.83 21.56 40.53 -5.11 -4.20 -2.80 MUFOLD−MD 62
63 Distill 23.50 17.06 1.98 -3.80 -3.45 -6.79 25.50 20.56 13.71 -5.30 -4.33 -7.37 Distill 63
64 RBO−Proteus 21.17 17.83 35.29 -4.06 -3.36 -2.48 32.00 28.44 41.80 -4.34 -3.28 -2.58 RBO−Proteus 64
65 RANDOM 19.68 16.46 19.68 -4.22 -3.51 -4.50 19.68 16.46 19.68 -6.16 -4.88 -6.35 RANDOM 65
66 mariner1 19.17 14.94 17.63 -4.27 -3.68 -4.77 27.00 22.33 30.90 -5.08 -4.10 -4.44 mariner1 66
67 LOOPP_Server 17.33 15.44 15.70 -4.47 -3.62 -5.02 49.50 35.94 45.70 -1.76 -2.28 -1.92 LOOPP_Server 67
68 schenk−torda−server 14.17 11.11 8.96 -4.81 -4.10 -5.89 14.17 11.83 11.01 -6.97 -5.50 -7.83 schenk−torda−server 68
69 mahmood−torda−server 13.67 11.44 9.10 -4.87 -4.06 -5.87 16.00 14.33 19.40 -6.70 -5.17 -6.40 mahmood−torda−server 69
70 OLGAFS 10.33 7.22 -17.75 -5.23 -4.52 -9.35 13.00 11.22 -8.71 -7.15 -5.58 -11.19 OLGAFS 70
71 BHAGEERATH                   -4.22 -3.51 -4.50                   -6.16 -4.88 -6.35 BHAGEERATH 71
72 Fiser−M4T                   -4.22 -3.51 -4.50                   -6.16 -4.88 -6.35 Fiser−M4T 72
73 huber−torda−server                   -4.22 -3.51 -4.50                   -6.16 -4.88 -6.35 huber−torda−server 73
74 test_http_server_01                   -4.22 -3.51 -4.50                   -6.16 -4.88 -6.35 test_http_server_01 74