T0508

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
435 436 437 438
439 440 441 442
443 444 445 446
447 448 449 450
451 452 453 454
455 456 457 458
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479 480 481 482
483 484 485 486
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491 492 493 494
495 496 497 498
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503 504 505 506
507 508 509 510
511 512 513 514

T0508

methyltransferase involved in cell division from Thermoplasma volcanium

Target type: Server only

Target sequence:

>T0508 Methyltransferase, Thermoplasma volcanium, 197 residues
MTGDRRDEYYWKAKKEQLRSRAAFKLEFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSLARKIISIDLQEMEEIAGVRFIRCDIFKETIFDDIDRALREEGIEKVDDVVSDAMAKVSGIPSRDHAVSYQIGQRVMEIAVRYLRNGGNVLLKQFQGDMTNDFIAIWRKNFSSYKISKPPASRGSSSEIYIMFFGFKAP

Structure:
Method: X-ray, res=1.45Å, R/Rfree=0.17/0.20
Determined by: NYSGRC
PDB ID: 3dou

3dou cartoon
Cartoon diagram of 508: 3dou, cofactor SAM is shown as 'sticks'.

PyMOL of 3dou

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

SAM-dependent methyltransferase fold.

CASP category:

Comparative modeling:easy.

Closest templates:

1ej0, 2nyu, 2plw.

Target sequence - PDB file inconsistencies:

T0508    3dou.pdb    T0508.pdb    PyMOL    PyMOL of domains    

T0508    1 MTGDRRDEYYWKAKKEQLRSRAAFKLEFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSLARKIISIDLQEMEEIAGVRFIRCDIFKETIFDDIDRALREEGIEKVDDVVSDAMAKVSGIPSRDHAVSYQIGQRVMEIAVRYLRNGGNVLLKQFQGDMTNDFIAIWRKNFSSYKISKPPASRGSSSEIYIMFFGFKAP 197
           ~~~~~~~~~~~~~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~|||||||||||||:
3douA   17 ----------------QLRSRAAFKLEFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSLARKIISIDLQEMEEIAGVRFIRCDIFKETIFDDIDRALREEGIEKVDDVVSDAMAKVSGIPSRDHAVSYQIGQRVMEIAVRYLRNGGNVLLKQFQGDMTNDFIAIWRKNFSSYKISKP------SSEIYIMFFGFKAE 197

Residue change log: change 197 E to P; change 71, 113, 135, 157, 190, MSE to MET;

Single domain protein: target 17-177, 184-197 ; pdb 17-177, 184-197

Sequence classification:

FtsJ-like methyltransferase (PF01728) in Pfam.

Server predictions:

T0508:pdb 17-197:seq 17-197:CM_easy;   alignment

distribution of first scores
First models for T0508: 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 #
T0508 T0508 T0508 T0508
First score First Z-score Best score Best Z-score
1 HHpred5 88.86 87.05 88.22 1.35 1.30 1.14 88.86 87.05 88.22 1.68 1.39 1.36 HHpred5 1
2 BAKER−ROBETTA 88.57 81.71 88.39 1.27 0.33 1.19 88.57 86.67 88.39 1.56 1.30 1.42 BAKER−ROBETTA 2
3 LEE−SERVER 88.14 85.48 87.77 1.14 1.01 1.02 88.14 85.48 88.59 1.37 0.98 1.50 LEE−SERVER 3
4 MULTICOM−CLUSTER 88.14 83.86 88.08 1.14 0.72 1.11 88.14 85.43 88.08 1.37 0.97 1.30 MULTICOM−CLUSTER 4
5 GS−KudlatyPred 88.00 85.81 87.50 1.11 1.07 0.95 88.00 85.81 88.14 1.31 1.07 1.33 GS−KudlatyPred 5
6 Zhang−Server 87.71 85.62 87.56 1.02 1.04 0.97 88.14 86.62 88.07 1.37 1.28 1.30 Zhang−Server 6
7 MULTICOM−RANK 87.71 85.43 86.76 1.02 1.00 0.76 87.71 85.43 86.76 1.19 0.97 0.79 MULTICOM−RANK 7
8 Phyre_de_novo 86.71 84.62 86.55 0.74 0.85 0.71 86.71 84.62 86.55 0.76 0.76 0.71 Phyre_de_novo 8
9 MUProt 86.71 78.71 86.03 0.74 -0.22 0.57 87.00 85.95 86.43 0.88 1.11 0.67 MUProt 9
10 METATASSER 86.57 84.86 86.24 0.70 0.90 0.62 87.00 85.57 86.87 0.88 1.01 0.84 METATASSER 10
11 MULTICOM−REFINE 86.43 84.33 86.21 0.66 0.80 0.62 87.00 85.29 86.70 0.88 0.93 0.77 MULTICOM−REFINE 11
12 MUSTER 86.43 82.24 85.79 0.66 0.42 0.51 86.43 82.29 86.07 0.64 0.15 0.53 MUSTER 12
13 MUFOLD−Server 86.29 81.81 85.87 0.62 0.34 0.53 86.43 81.81 85.87 0.64 0.02 0.45 MUFOLD−Server 13
14 HHpred4 86.14 83.86 85.81 0.58 0.72 0.51 86.14 83.86 85.81 0.51 0.56 0.43 HHpred4 14
15 COMA 86.14 81.38 85.95 0.58 0.27 0.55 86.14 81.38 87.45 0.51 -0.09 1.06 COMA 15
16 MULTICOM−CMFR 86.14 80.62 85.84 0.58 0.13 0.52 86.14 80.95 85.84 0.51 -0.21 0.44 MULTICOM−CMFR 16
17 COMA−M 86.14 75.48 86.70 0.58 -0.81 0.74 87.86 86.52 87.45 1.25 1.26 1.06 COMA−M 17
18 RAPTOR 85.86 84.71 85.05 0.50 0.87 0.31 86.00 84.71 85.43 0.45 0.78 0.28 RAPTOR 18
19 LOOPP_Server 85.86 84.33 85.52 0.50 0.80 0.44 85.86 84.33 85.52 0.39 0.68 0.32 LOOPP_Server 19
20 Pcons_dot_net 85.71 83.91 85.48 0.46 0.73 0.43 85.71 83.91 85.48 0.32 0.57 0.30 Pcons_dot_net 20
21 Pcons_multi 85.71 83.91 85.48 0.46 0.73 0.43 88.00 84.09 87.52 1.31 0.62 1.09 Pcons_multi 21
22 circle 85.71 83.52 84.98 0.46 0.65 0.30 85.86 83.52 84.98 0.39 0.47 0.11 circle 22
23 ACOMPMOD 85.57 83.29 85.90 0.42 0.61 0.54 85.57 83.29 85.90 0.26 0.41 0.46 ACOMPMOD 23
24 HHpred2 85.57 83.29 86.08 0.42 0.61 0.58 85.57 83.29 86.08 0.26 0.41 0.53 HHpred2 24
25 Poing 85.57 83.00 86.38 0.42 0.56 0.66 85.57 83.00 86.38 0.26 0.33 0.65 Poing 25
26 Phyre2 85.57 83.00 86.38 0.42 0.56 0.66 85.57 83.00 86.38 0.26 0.33 0.65 Phyre2 26
27 Phragment 85.57 83.00 86.38 0.42 0.56 0.66 85.57 83.00 86.38 0.26 0.33 0.65 Phragment 27
28 forecast 85.57 78.43 84.19 0.42 -0.27 0.09 86.14 82.62 84.46 0.51 0.23 -0.09 forecast 28
29 GS−MetaServer2 85.43 83.43 84.99 0.38 0.64 0.30 85.43 83.43 84.99 0.20 0.44 0.11 GS−MetaServer2 29
30 Frankenstein 85.43 83.43 85.79 0.38 0.64 0.51 85.43 83.43 85.79 0.20 0.44 0.42 Frankenstein 30
31 3D−JIGSAW_V3 85.43 82.57 84.74 0.38 0.48 0.23 85.57 83.57 85.05 0.26 0.48 0.14 3D−JIGSAW_V3 31
32 3D−JIGSAW_AEP 85.43 82.38 86.13 0.38 0.45 0.60 86.86 84.38 86.13 0.82 0.69 0.55 3D−JIGSAW_AEP 32
33 GeneSilicoMetaServer 85.43 81.71 83.77 0.38 0.33 -0.02 85.71 83.62 84.99 0.32 0.49 0.11 GeneSilicoMetaServer 33
34 FAMSD 85.43 79.71 85.96 0.38 -0.04 0.55 85.43 82.95 85.96 0.20 0.32 0.49 FAMSD 34
35 Pcons_local 85.29 83.67 85.10 0.34 0.68 0.33 85.29 83.67 85.10 0.14 0.51 0.16 Pcons_local 35
36 PSI 85.29 75.38 84.74 0.34 -0.83 0.23 85.29 75.38 84.75 0.14 -1.67 0.02 PSI 36
37 pipe_int 84.71 78.71 85.31 0.17 -0.22 0.38 85.29 82.91 85.31 0.14 0.31 0.24 pipe_int 37
38 Fiser−M4T 84.57 79.71 84.05 0.13 -0.04 0.05 84.57 79.71 84.05 -0.17 -0.53 -0.25 Fiser−M4T 38
39 nFOLD3 84.43 82.33 84.35 0.09 0.44 0.13 84.43 82.33 84.35 -0.23 0.16 -0.13 nFOLD3 39
40 PS2−server 84.29 82.19 83.83 0.05 0.41 -0.00 84.29 82.19 83.83 -0.29 0.12 -0.33 PS2−server 40
41 FUGUE_KM 84.14 82.14 83.61 0.01 0.40 -0.06 84.14 82.14 83.61 -0.35 0.11 -0.42 FUGUE_KM 41
42 pro−sp3−TASSER 84.00 79.52 85.73 -0.03 -0.07 0.49 86.29 84.14 85.73 0.57 0.63 0.40 pro−sp3−TASSER 42
43 BioSerf 83.43 78.29 83.95 -0.19 -0.30 0.03 83.43 78.29 83.95 -0.66 -0.90 -0.29 BioSerf 43
44 3DShot2 83.14 74.19 82.11 -0.27 -1.04 -0.45 83.14 74.19 82.11 -0.79 -1.98 -0.99 3DShot2 44
45 FALCON_CONSENSUS 82.71 77.48 83.17 -0.39 -0.44 -0.18 82.71 79.29 83.17 -0.97 -0.64 -0.59 FALCON_CONSENSUS 45
46 SAM−T08−server 82.57 79.71 82.66 -0.43 -0.04 -0.31 84.14 82.05 83.71 -0.35 0.08 -0.38 SAM−T08−server 46
47 FALCON 82.57 79.14 82.93 -0.43 -0.14 -0.24 82.71 79.29 83.17 -0.97 -0.64 -0.59 FALCON 47
48 Pushchino 82.43 80.05 80.88 -0.47 0.02 -0.77 82.43 80.05 80.88 -1.09 -0.44 -1.47 Pushchino 48
49 3Dpro 82.43 79.09 82.34 -0.47 -0.15 -0.39 82.43 79.09 82.34 -1.09 -0.69 -0.90 3Dpro 49
50 rehtnap 82.43 79.09 82.69 -0.47 -0.15 -0.30 82.43 79.09 82.69 -1.09 -0.69 -0.77 rehtnap 50
51 fais−server 81.57 79.00 81.41 -0.72 -0.17 -0.64 84.86 82.95 84.43 -0.04 0.32 -0.10 fais−server 51
52 mGenTHREADER 81.57 68.24 81.45 -0.72 -2.12 -0.63 81.57 68.24 81.45 -1.46 -3.54 -1.25 mGenTHREADER 52
53 FFASsuboptimal 81.43 77.52 82.67 -0.76 -0.44 -0.31 81.43 77.71 82.67 -1.52 -1.06 -0.78 FFASsuboptimal 53
54 FFASstandard 81.14 78.09 82.70 -0.84 -0.33 -0.30 81.14 78.09 82.70 -1.65 -0.96 -0.77 FFASstandard 54
55 FFASflextemplate 81.00 75.19 81.86 -0.88 -0.86 -0.52 81.00 76.95 81.86 -1.71 -1.26 -1.09 FFASflextemplate 55
56 Distill 79.29 74.24 71.89 -1.36 -1.03 -3.12 79.29 74.24 74.37 -2.45 -1.97 -3.97 Distill 56
57 panther_server 78.86 74.38 77.68 -1.48 -1.01 -1.61 84.00 81.43 82.72 -0.41 -0.08 -0.76 panther_server 57
58 CpHModels 78.14 75.86 77.41 -1.69 -0.74 -1.68 78.14 75.86 77.41 -2.95 -1.54 -2.80 CpHModels 58
59 huber−torda−server 76.29 73.14 71.19 -2.21 -1.23 -3.30 80.57 74.67 81.18 -1.90 -1.85 -1.35 huber−torda−server 59
60 SAM−T02−server 71.14 58.19 72.78 -3.67 -3.95 -2.89 71.14 66.67 72.78 -5.97 -3.95 -4.58 SAM−T02−server 60
61 SAM−T06−server 70.29 57.33 72.18 -3.91 -4.11 -3.04 71.00 65.09 72.18 -6.03 -4.37 -4.81 SAM−T06−server 61
62 RBO−Proteus 48.57 42.67 63.17 -10.07 -6.77 -5.40 51.71 47.24 64.99 -14.36 -9.05 -7.58 RBO−Proteus 62
63 FOLDpro 33.86 29.86 33.61 -14.23 -9.10 -13.11 40.86 38.29 46.49 -19.05 -11.40 -14.69 FOLDpro 63
64 FEIG 33.71 29.48 41.28 -14.28 -9.17 -11.11 81.14 72.38 78.89 -1.65 -2.45 -2.23 FEIG 64
65 mariner1 33.71 28.48 39.08 -14.28 -9.35 -11.68 86.00 83.91 85.02 0.45 0.57 0.13 mariner1 65
66 OLGAFS 29.14 22.67 27.59 -15.57 -10.41 -14.68 29.14 22.67 27.59 -24.11 -15.50 -21.96 OLGAFS 66
67 MUFOLD−MD 26.29 21.76 42.88 -16.38 -10.57 -10.69 43.00 37.67 54.41 -18.12 -11.56 -11.64 MUFOLD−MD 67
68 RANDOM 15.71 13.11 15.71 -19.38 -12.15 -17.78 15.71 13.11 15.71 -29.91 -18.01 -26.53 RANDOM 68
69 schenk−torda−server 11.14 9.05 14.36 -20.67 -12.88 -18.14 12.57 11.67 16.71 -31.26 -18.39 -26.14 schenk−torda−server 69
70 BHAGEERATH                   -19.38 -12.15 -17.78                   -29.91 -18.01 -26.53 BHAGEERATH 70
71 YASARA                   -19.38 -12.15 -17.78                   -29.91 -18.01 -26.53 YASARA 71
72 keasar−server                   -19.38 -12.15 -17.78                   -29.91 -18.01 -26.53 keasar−server 72
73 mahmood−torda−server                   -19.38 -12.15 -17.78                   -29.91 -18.01 -26.53 mahmood−torda−server 73
74 test_http_server_01                   -19.38 -12.15 -17.78                   -29.91 -18.01 -26.53 test_http_server_01 74