T0481

X-ray 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
435 436 438 439
440 441 442 443
444 445 446 447
448 449 450 451
452 453 454 455
456 457 458 459
461 463 465 470
477 478 479 481
483 485 486 487
488 489 490 491
493 494 495 496
497 501 502 503
504 505 506 507
508 509 510 511
512 513 514

T0481

DinB-like protein (NP_389123.1) from Bacillus subtilis

Target type: Server only

Target sequence:

>T0481 NP_389123.1, Bacillus subtilis, 154 residues
MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM

Structure:
Method: X-ray, res=2.3Å, R/Rfree=0.22/0.27
Determined by: JCSG
PDB ID: 3dka

3dka_A cartoon
Cartoon diagram of 481: 3dka chain A

PyMOL of 3dka

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

DinB/YfiT-like putative metalloenzymes.

CASP category:

Comparative modeling:medium.

Closest templates:

2qe9.

Target sequence - PDB file inconsistencies:

T0481    3dka.pdb    T0481.pdb    PyMOL    PyMOL of domains    

T0481    1 MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM 154
           ~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~|||||||||||||||||||||||||||||||||~~~|||||||||||||||||||||||||||||||||||||||||||||
3dkaA    5 ----NQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQN----TETDLNVLAKTYTEKTVAILEQLTEEQLDREID---AFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM 154

Residue change log: change 39, 125, 142, 154, MSE to MET;

Single domain protein: target 5-69, 74-106, 110-154 ; pdb 5-69, 74-106, 110-154

Sequence classification:

DinB family (PF05163) in Pfam.

Comments:

This protein is a close homolog of T0406:

Server predictions:

T0481:pdb 5-154:seq 5-154:CM_medium;   alignment

distribution of first scores
First models for T0481: 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 #
T0481 T0481 T0481 T0481
First score First Z-score Best score Best Z-score
1 LEE−SERVER 72.73 65.27 70.03 1.44 2.31 1.70 72.73 66.14 71.89 1.63 2.40 2.06 LEE−SERVER 1
2 pro−sp3−TASSER 71.15 58.10 71.49 1.23 1.30 1.92 73.25 63.23 72.90 1.72 1.90 2.24 pro−sp3−TASSER 2
3 Pcons_multi 70.98 56.82 69.29 1.21 1.12 1.59 73.25 62.30 70.63 1.72 1.74 1.83 Pcons_multi 3
4 FEIG 69.93 60.96 65.12 1.08 1.70 0.97 73.25 66.61 69.14 1.72 2.48 1.56 FEIG 4
5 METATASSER 69.93 60.55 67.35 1.08 1.65 1.30 69.93 60.55 68.14 1.13 1.44 1.38 METATASSER 5
6 RAPTOR 69.93 57.69 67.64 1.08 1.24 1.35 70.98 62.35 68.14 1.32 1.75 1.38 RAPTOR 6
7 MULTICOM−CMFR 69.23 52.62 65.37 0.99 0.53 1.01 69.23 56.18 67.33 1.01 0.68 1.23 MULTICOM−CMFR 7
8 MULTICOM−CLUSTER 68.36 58.68 67.28 0.87 1.38 1.29 68.36 58.68 67.28 0.86 1.11 1.22 MULTICOM−CLUSTER 8
9 Phyre_de_novo 67.66 58.68 68.03 0.78 1.38 1.41 67.66 58.68 68.03 0.73 1.11 1.36 Phyre_de_novo 9
10 MULTICOM−RANK 67.31 54.49 66.44 0.74 0.79 1.17 68.36 54.49 66.96 0.86 0.39 1.17 MULTICOM−RANK 10
11 CpHModels 66.96 54.95 59.58 0.69 0.86 0.15 66.96 54.95 59.58 0.61 0.47 -0.17 CpHModels 11
12 Zhang−Server 66.08 50.41 64.61 0.58 0.22 0.90 70.11 60.78 65.77 1.17 1.48 0.95 Zhang−Server 12
13 SAM−T08−server 65.73 52.51 67.97 0.53 0.51 1.40 65.73 54.78 67.97 0.39 0.44 1.35 SAM−T08−server 13
14 MULTICOM−REFINE 65.21 49.71 63.07 0.46 0.12 0.67 66.26 52.16 64.67 0.48 -0.01 0.75 MULTICOM−REFINE 14
15 Frankenstein 64.86 55.77 63.66 0.42 0.97 0.76 64.86 55.77 63.66 0.24 0.61 0.57 Frankenstein 15
16 MUProt 64.86 50.17 63.18 0.42 0.18 0.69 65.56 51.63 63.18 0.36 -0.10 0.48 MUProt 16
17 3DShot2 64.86 48.13 58.84 0.42 -0.10 0.04 64.86 48.13 58.84 0.24 -0.70 -0.30 3DShot2 17
18 BioSerf 64.86 46.15 59.16 0.42 -0.38 0.09 64.86 46.15 59.16 0.24 -1.04 -0.25 BioSerf 18
19 Pcons_dot_net 64.51 48.78 59.56 0.37 -0.01 0.15 64.51 49.18 63.56 0.17 -0.52 0.55 Pcons_dot_net 19
20 GS−KudlatyPred 64.34 51.17 62.41 0.35 0.32 0.57 65.39 52.68 62.41 0.33 0.08 0.34 GS−KudlatyPred 20
21 3Dpro 64.16 51.05 59.36 0.33 0.31 0.12 64.16 51.05 59.36 0.11 -0.20 -0.21 3Dpro 21
22 Poing 64.16 49.59 60.23 0.33 0.10 0.25 64.16 49.59 60.23 0.11 -0.45 -0.05 Poing 22
23 Phragment 63.99 50.00 59.79 0.30 0.16 0.18 63.99 50.00 59.88 0.08 -0.38 -0.12 Phragment 23
24 Phyre2 63.99 49.77 60.07 0.30 0.13 0.22 63.99 49.77 60.07 0.08 -0.42 -0.08 Phyre2 24
25 HHpred2 62.94 55.36 53.72 0.17 0.91 -0.72 62.94 55.36 53.72 -0.10 0.54 -1.23 HHpred2 25
26 3D−JIGSAW_AEP 62.94 48.95 61.87 0.17 0.01 0.49 63.99 49.88 63.30 0.08 -0.40 0.50 3D−JIGSAW_AEP 26
27 mGenTHREADER 62.59 55.13 54.34 0.12 0.88 -0.63 62.59 55.13 54.34 -0.17 0.50 -1.12 mGenTHREADER 27
28 HHpred4 62.59 50.93 55.23 0.12 0.29 -0.49 62.59 50.93 55.23 -0.17 -0.22 -0.96 HHpred4 28
29 HHpred5 62.59 50.93 55.23 0.12 0.29 -0.49 62.59 50.93 55.23 -0.17 -0.22 -0.96 HHpred5 29
30 Pcons_local 62.24 51.05 56.38 0.08 0.31 -0.32 64.51 55.59 59.56 0.17 0.58 -0.17 Pcons_local 30
31 MUSTER 62.24 47.20 59.81 0.08 -0.23 0.19 65.21 50.06 62.10 0.30 -0.37 0.29 MUSTER 31
32 BAKER−ROBETTA 62.24 46.62 63.56 0.08 -0.32 0.74 62.24 50.52 63.56 -0.23 -0.29 0.55 BAKER−ROBETTA 32
33 PS2−server 62.06 44.64 55.79 0.05 -0.59 -0.41 62.59 53.50 59.39 -0.17 0.22 -0.21 PS2−server 33
34 panther_server 61.89 48.02 51.55 0.03 -0.12 -1.04 61.89 49.13 56.81 -0.29 -0.53 -0.67 panther_server 34
35 keasar−server 61.89 47.61 61.13 0.03 -0.18 0.38 61.89 47.96 61.26 -0.29 -0.73 0.13 keasar−server 35
36 COMA−M 61.89 44.23 62.37 0.03 -0.65 0.57 66.26 51.11 64.34 0.48 -0.19 0.69 COMA−M 36
37 PSI 61.71 57.75 55.83 0.01 1.25 -0.41 63.64 57.75 62.07 0.02 0.95 0.28 PSI 37
38 pipe_int 61.71 45.22 62.23 0.01 -0.51 0.54 61.71 45.22 62.23 -0.32 -1.20 0.31 pipe_int 38
39 FAMSD 61.36 47.03 59.83 -0.04 -0.26 0.19 61.89 53.38 59.83 -0.29 0.20 -0.13 FAMSD 39
40 fais−server 61.19 44.52 56.77 -0.06 -0.61 -0.27 62.76 55.13 56.77 -0.14 0.50 -0.68 fais−server 40
41 GeneSilicoMetaServer 61.01 47.49 54.50 -0.08 -0.19 -0.60 61.01 47.84 54.52 -0.45 -0.75 -1.09 GeneSilicoMetaServer 41
42 3D−JIGSAW_V3 61.01 45.75 60.81 -0.08 -0.44 0.33 63.46 54.02 65.14 -0.01 0.31 0.84 3D−JIGSAW_V3 42
43 MUFOLD−Server 60.84 52.10 58.13 -0.11 0.46 -0.06 62.24 52.56 59.31 -0.23 0.06 -0.22 MUFOLD−Server 43
44 FFASflextemplate 60.66 46.80 56.25 -0.13 -0.29 -0.34 60.66 48.43 56.25 -0.51 -0.65 -0.77 FFASflextemplate 44
45 FFASsuboptimal 60.66 46.80 56.25 -0.13 -0.29 -0.34 61.71 48.08 57.88 -0.32 -0.71 -0.48 FFASsuboptimal 45
46 COMA 60.66 46.10 59.80 -0.13 -0.39 0.18 60.66 46.33 64.34 -0.51 -1.01 0.69 COMA 46
47 FUGUE_KM 60.49 45.69 53.58 -0.15 -0.45 -0.74 60.49 49.01 53.58 -0.54 -0.55 -1.26 FUGUE_KM 47
48 nFOLD3 60.31 45.45 58.39 -0.17 -0.48 -0.03 62.41 51.92 58.39 -0.20 -0.05 -0.39 nFOLD3 48
49 circle 60.14 52.21 59.03 -0.20 0.47 0.07 61.01 52.21 59.09 -0.45 0.00 -0.26 circle 49
50 FFASstandard 60.14 46.27 55.91 -0.20 -0.37 -0.39 62.94 57.92 57.86 -0.10 0.98 -0.48 FFASstandard 50
51 LOOPP_Server 59.27 50.06 52.63 -0.31 0.17 -0.88 59.79 51.52 55.27 -0.66 -0.12 -0.95 LOOPP_Server 51
52 SAM−T06−server 58.92 45.92 63.47 -0.36 -0.41 0.73 62.24 51.28 63.47 -0.23 -0.16 0.53 SAM−T06−server 52
53 Pushchino 58.92 43.24 51.53 -0.36 -0.79 -1.04 58.92 43.24 51.53 -0.82 -1.54 -1.63 Pushchino 53
54 GS−MetaServer2 58.39 46.97 50.42 -0.42 -0.27 -1.21 64.16 53.79 60.47 0.11 0.27 -0.01 GS−MetaServer2 54
55 forecast 58.39 42.54 61.16 -0.42 -0.89 0.39 59.62 43.06 62.11 -0.69 -1.58 0.29 forecast 55
56 rehtnap 58.22 48.08 47.77 -0.45 -0.11 -1.60 58.22 48.08 47.77 -0.94 -0.71 -2.31 rehtnap 56
57 SAM−T02−server 58.22 43.41 50.84 -0.45 -0.77 -1.15 61.01 54.08 56.24 -0.45 0.32 -0.78 SAM−T02−server 57
58 ACOMPMOD 54.90 48.48 50.61 -0.88 -0.05 -1.18 60.14 48.48 54.90 -0.60 -0.64 -1.02 ACOMPMOD 58
59 FOLDpro 48.95 32.40 39.51 -1.65 -2.32 -2.83 64.51 50.64 60.31 0.17 -0.27 -0.04 FOLDpro 59
60 RBO−Proteus 26.22 22.96 41.88 -4.61 -3.65 -2.48 29.37 26.81 41.88 -6.05 -4.37 -3.38 RBO−Proteus 60
61 Distill 25.70 20.57 31.78 -4.67 -3.98 -3.98 26.22 21.68 33.42 -6.61 -5.26 -4.91 Distill 61
62 MUFOLD−MD 24.13 21.27 37.48 -4.88 -3.89 -3.13 24.48 22.67 38.89 -6.92 -5.09 -3.92 MUFOLD−MD 62
63 FALCON_CONSENSUS 22.20 19.87 33.97 -5.13 -4.08 -3.65 25.00 21.39 35.16 -6.83 -5.31 -4.60 FALCON_CONSENSUS 63
64 FALCON 20.98 17.72 33.51 -5.29 -4.38 -3.72 58.74 52.45 55.42 -0.85 0.04 -0.92 FALCON 64
65 RANDOM 19.49 16.60 19.49 -5.48 -4.54 -5.80 19.49 16.60 19.49 -7.80 -6.13 -7.44 RANDOM 65
66 schenk−torda−server 17.66 14.63 18.14 -5.72 -4.82 -6.00 17.66 14.63 18.14 -8.13 -6.47 -7.68 schenk−torda−server 66
67 mariner1 16.43 12.59 16.07 -5.88 -5.11 -6.31 20.80 19.64 26.56 -7.57 -5.61 -6.16 mariner1 67
68 mahmood−torda−server 15.91 13.58 20.11 -5.95 -4.97 -5.71 15.91 13.75 20.11 -8.44 -6.62 -7.32 mahmood−torda−server 68
69 OLGAFS 15.21 14.63 -14.77 -6.04 -4.82 -10.89 15.38 14.80 -14.67 -8.53 -6.44 -13.63 OLGAFS 69
70 BHAGEERATH                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 BHAGEERATH 70
71 Fiser−M4T                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 Fiser−M4T 71
72 YASARA                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 YASARA 72
73 huber−torda−server                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 huber−torda−server 73
74 test_http_server_01                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 test_http_server_01 74