T0448

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
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479 480 481 482
483 484 485 486
487 488 489 490
491 492 493 494
495 496 497 498
499 500 501 502
503 504 505 506
507 508 509 510
511 512 513 514

T0448

protein Q88SR8 from Lactobacillus plantarum

Target type: Server only

Target sequence:

>T0448 Q88SR8, Lactobacillus plantarum, 232 residues
MIAMIVKGGLAMAISNGHVSFKRPAWLGDSITANNGLATVHYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHHHHHH

Structure:
Method: X-ray, res=2.12Å, R/Rfree=0.19/0.22
Determined by: NESG
PDB ID: 3dc7

3dc7_A cartoon
Cartoon diagram of 448: 3dc7 chain A residues

PyMOL of 3dc7

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

SGNH hydrolase from Flavodoxin-like fold.

CASP category:

Comparative modeling:medium.

Closest templates:

3bzw.

Target sequence - PDB file inconsistencies:

T0448    3dc7.pdb    T0448.pdb    PyMOL    PyMOL of domains    

T0448    1 MIAMIVKGGLAMAISNGHVSFKRPAWLGDSITANNGLATVHYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHHHHHH 232
           ~~~~~~~~~~~~~~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~
3dc7A   18 -----------------HVSFKRPAWLGDSITANNGLATVHYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHHHH-- 230

Residue change log: change 72, 109, 117, 118, 169, 186, MSE to MET;

Single domain protein: target 18-230 ; pdb 18-230

Sequence classification:

SGNH_hydrolase in CDD.

Server predictions:

T0448:pdb 18-230:seq 18-230:CM_medium;   alignment

distribution of first scores
First models for T0448: 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 #
T0448 T0448 T0448 T0448
First score First Z-score Best score Best Z-score
1 BAKER−ROBETTA 76.29 71.36 67.18 1.55 1.66 1.49 76.29 71.36 67.18 1.28 1.30 1.21 BAKER−ROBETTA 1
2 HHpred4 76.06 70.34 68.14 1.52 1.55 1.60 76.06 70.34 68.14 1.25 1.17 1.34 HHpred4 2
3 HHpred5 75.94 71.56 69.44 1.51 1.68 1.75 75.94 71.56 69.44 1.23 1.32 1.52 HHpred5 3
4 HHpred2 75.70 69.21 67.89 1.48 1.44 1.57 75.70 69.21 67.89 1.20 1.04 1.31 HHpred2 4
5 FFASsuboptimal 75.47 70.15 66.61 1.45 1.53 1.42 75.82 71.52 67.44 1.22 1.32 1.25 FFASsuboptimal 5
6 PS2−server 74.41 68.70 62.54 1.33 1.38 0.95 74.41 68.70 62.54 1.02 0.97 0.56 PS2−server 6
7 GS−KudlatyPred 73.94 69.17 66.10 1.28 1.43 1.36 73.94 69.17 66.10 0.95 1.03 1.06 GS−KudlatyPred 7
8 FFASstandard 73.94 68.31 65.50 1.28 1.34 1.29 73.94 68.94 65.55 0.95 1.00 0.98 FFASstandard 8
9 LEE−SERVER 73.94 64.94 67.98 1.28 0.98 1.58 75.35 68.70 68.16 1.15 0.97 1.35 LEE−SERVER 9
10 FAMSD 73.83 69.21 63.09 1.26 1.44 1.02 73.83 69.21 64.59 0.94 1.04 0.85 FAMSD 10
11 RAPTOR 73.83 63.89 66.03 1.26 0.87 1.35 74.18 69.01 66.76 0.99 1.01 1.15 RAPTOR 11
12 FFASflextemplate 73.47 68.94 65.55 1.22 1.41 1.30 73.94 68.94 65.55 0.95 1.00 0.98 FFASflextemplate 12
13 Fiser−M4T 73.24 64.32 61.65 1.19 0.92 0.85 73.24 64.32 61.65 0.85 0.44 0.44 Fiser−M4T 13
14 keasar−server 73.00 68.08 65.38 1.17 1.32 1.28 73.94 68.86 65.56 0.95 0.99 0.98 keasar−server 14
15 pipe_int 73.00 68.08 63.72 1.17 1.32 1.09 73.00 68.08 63.72 0.82 0.90 0.73 pipe_int 15
16 GS−MetaServer2 73.00 67.61 65.51 1.17 1.27 1.29 73.00 67.61 65.51 0.82 0.84 0.98 GS−MetaServer2 16
17 3D−JIGSAW_AEP 72.89 67.80 64.06 1.15 1.29 1.13 72.89 67.80 64.06 0.80 0.86 0.77 3D−JIGSAW_AEP 17
18 fais−server 72.89 66.39 65.57 1.15 1.14 1.30 72.89 66.39 65.57 0.80 0.69 0.98 fais−server 18
19 SAM−T02−server 72.77 66.59 63.52 1.14 1.16 1.07 72.77 66.59 63.52 0.79 0.72 0.70 SAM−T02−server 19
20 SAM−T06−server 69.60 58.88 63.02 0.77 0.34 1.01 72.77 66.75 63.34 0.79 0.74 0.67 SAM−T06−server 20
21 CpHModels 69.48 64.63 57.82 0.76 0.95 0.41 69.48 64.63 57.82 0.32 0.48 -0.10 CpHModels 21
22 MULTICOM−CMFR 68.19 56.14 61.18 0.61 0.05 0.80 70.19 63.54 61.35 0.42 0.34 0.40 MULTICOM−CMFR 22
23 Pushchino 67.37 62.44 48.61 0.52 0.72 -0.65 67.37 62.44 48.61 0.02 0.21 -1.38 Pushchino 23
24 YASARA 66.90 60.17 56.50 0.46 0.48 0.26 69.72 63.54 59.72 0.36 0.34 0.17 YASARA 24
25 MULTICOM−REFINE 66.43 59.47 58.31 0.41 0.41 0.47 66.43 59.47 58.31 -0.11 -0.15 -0.03 MULTICOM−REFINE 25
26 3DShot2 64.79 55.09 52.02 0.22 -0.06 -0.25 64.79 55.09 52.02 -0.34 -0.69 -0.90 3DShot2 26
27 Phyre_de_novo 62.68 57.67 53.60 -0.03 0.22 -0.07 66.43 59.16 54.68 -0.11 -0.19 -0.53 Phyre_de_novo 27
28 Zhang−Server 62.32 53.09 56.49 -0.07 -0.27 0.26 72.53 65.02 65.00 0.75 0.52 0.91 Zhang−Server 28
29 pro−sp3−TASSER 60.91 50.31 51.64 -0.23 -0.56 -0.30 60.91 50.31 56.25 -0.89 -1.27 -0.31 pro−sp3−TASSER 29
30 METATASSER 60.09 43.66 52.68 -0.33 -1.26 -0.18 63.97 55.05 56.38 -0.46 -0.69 -0.30 METATASSER 30
31 FEIG 59.62 48.20 53.21 -0.38 -0.78 -0.12 60.33 53.99 53.21 -0.97 -0.82 -0.74 FEIG 31
32 MULTICOM−RANK 59.51 51.84 50.97 -0.39 -0.40 -0.37 66.90 58.73 58.91 -0.04 -0.24 0.06 MULTICOM−RANK 32
33 MULTICOM−CLUSTER 59.51 51.84 50.97 -0.39 -0.40 -0.37 70.19 65.96 60.56 0.42 0.64 0.29 MULTICOM−CLUSTER 33
34 COMA−M 59.27 50.59 51.86 -0.42 -0.53 -0.27 59.62 53.91 51.86 -1.07 -0.83 -0.93 COMA−M 34
35 Pcons_multi 59.16 50.94 51.96 -0.43 -0.50 -0.26 59.16 51.56 51.96 -1.14 -1.12 -0.91 Pcons_multi 35
36 MUProt 58.57 53.09 50.50 -0.50 -0.27 -0.43 66.90 60.56 59.31 -0.04 -0.02 0.11 MUProt 36
37 BioSerf 58.33 49.34 51.88 -0.53 -0.66 -0.27 58.33 49.34 51.88 -1.25 -1.39 -0.92 BioSerf 37
38 Distill 58.10 51.29 49.46 -0.56 -0.46 -0.55 59.04 51.29 49.46 -1.15 -1.15 -1.26 Distill 38
39 Pcons_local 57.86 47.85 45.80 -0.58 -0.82 -0.97 57.86 47.85 46.46 -1.32 -1.57 -1.68 Pcons_local 39
40 SAM−T08−server 57.28 49.22 50.57 -0.65 -0.68 -0.42 75.23 71.01 66.78 1.13 1.25 1.15 SAM−T08−server 40
41 Pcons_dot_net 57.16 50.98 46.80 -0.66 -0.49 -0.85 58.33 53.17 48.90 -1.25 -0.92 -1.34 Pcons_dot_net 41
42 Phyre2 57.04 51.41 49.43 -0.68 -0.45 -0.55 66.31 60.05 53.76 -0.13 -0.08 -0.66 Phyre2 42
43 PSI 56.69 51.29 46.73 -0.72 -0.46 -0.86 56.69 51.29 49.50 -1.48 -1.15 -1.26 PSI 43
44 MUSTER 56.57 49.69 50.50 -0.73 -0.63 -0.43 56.57 49.69 50.50 -1.50 -1.34 -1.12 MUSTER 44
45 Poing 56.45 48.71 49.33 -0.75 -0.73 -0.56 66.78 58.18 54.15 -0.06 -0.31 -0.61 Poing 45
46 3D−JIGSAW_V3 56.22 50.74 45.82 -0.77 -0.52 -0.97 72.42 67.88 63.37 0.74 0.87 0.68 3D−JIGSAW_V3 46
47 Phragment 56.22 50.51 49.25 -0.77 -0.54 -0.57 66.43 59.39 53.74 -0.11 -0.16 -0.66 Phragment 47
48 ACOMPMOD 55.40 44.52 45.85 -0.87 -1.17 -0.96 55.40 46.63 45.85 -1.67 -1.72 -1.76 ACOMPMOD 48
49 GeneSilicoMetaServer 54.81 48.40 46.75 -0.94 -0.76 -0.86 56.92 48.40 46.75 -1.45 -1.50 -1.64 GeneSilicoMetaServer 49
50 circle 54.70 43.90 44.38 -0.95 -1.24 -1.13 73.94 69.17 64.44 0.95 1.03 0.83 circle 50
51 mGenTHREADER 53.17 47.53 43.96 -1.13 -0.86 -1.18 53.17 47.53 43.96 -1.98 -1.61 -2.03 mGenTHREADER 51
52 LOOPP_Server 52.11 45.77 43.54 -1.25 -1.04 -1.23 67.02 62.79 58.17 -0.03 0.25 -0.05 LOOPP_Server 52
53 3Dpro 52.11 41.59 48.69 -1.25 -1.48 -0.64 70.42 65.73 61.99 0.45 0.61 0.49 3Dpro 53
54 forecast 51.99 44.01 42.85 -1.26 -1.23 -1.31 52.11 45.54 49.24 -2.13 -1.85 -1.29 forecast 54
55 nFOLD3 51.99 42.84 43.96 -1.26 -1.35 -1.18 72.42 67.80 63.78 0.74 0.86 0.74 nFOLD3 55
56 COMA 51.76 44.95 45.14 -1.29 -1.13 -1.04 60.33 52.66 51.86 -0.97 -0.98 -0.93 COMA 56
57 FUGUE_KM 50.70 46.71 35.26 -1.41 -0.94 -2.18 56.34 48.20 42.21 -1.53 -1.52 -2.27 FUGUE_KM 57
58 FOLDpro 50.59 37.68 39.50 -1.42 -1.90 -1.69 52.70 45.34 45.79 -2.05 -1.87 -1.77 FOLDpro 58
59 panther_server 49.65 43.70 38.40 -1.53 -1.26 -1.82 54.46 46.48 44.20 -1.80 -1.73 -1.99 panther_server 59
60 rehtnap 48.83 44.29 30.44 -1.63 -1.20 -2.73 51.06 45.15 33.45 -2.28 -1.90 -3.49 rehtnap 60
61 FALCON_CONSENSUS 48.59 41.55 42.01 -1.66 -1.49 -1.40 74.30 68.35 66.27 1.00 0.93 1.08 FALCON_CONSENSUS 61
62 FALCON 48.59 41.55 42.01 -1.66 -1.49 -1.40 58.69 48.44 66.27 -1.20 -1.50 1.08 FALCON 62
63 MUFOLD−Server 38.97 32.63 27.76 -2.77 -2.43 -3.04 38.97 32.63 27.76 -3.99 -3.42 -4.29 MUFOLD−Server 63
64 mariner1 23.83 19.52 19.32 -4.52 -3.82 -4.01 55.05 46.28 50.00 -1.72 -1.76 -1.19 mariner1 64
65 MUFOLD−MD 17.61 15.65 22.19 -5.24 -4.22 -3.68 19.13 16.12 25.72 -6.79 -5.43 -4.57 MUFOLD−MD 65
66 RBO−Proteus 15.26 13.81 21.30 -5.51 -4.42 -3.78 15.26 13.81 22.20 -7.33 -5.72 -5.06 RBO−Proteus 66
67 RANDOM 12.48 10.50 12.48 -5.83 -4.77 -4.79 12.48 10.50 12.48 -7.73 -6.12 -6.42 RANDOM 67
68 OLGAFS 9.27 7.86 -5.34 -6.20 -5.05 -6.84 9.27 7.86 -5.34 -8.18 -6.44 -8.90 OLGAFS 68
69 BHAGEERATH                   -5.83 -4.77 -4.79                   -7.73 -6.12 -6.42 BHAGEERATH 69
70 Frankenstein                   -5.83 -4.77 -4.79                   -7.73 -6.12 -6.42 Frankenstein 70
71 huber−torda−server                   -5.83 -4.77 -4.79                   -7.73 -6.12 -6.42 huber−torda−server 71
72 mahmood−torda−server                   -5.83 -4.77 -4.79                   -7.73 -6.12 -6.42 mahmood−torda−server 72
73 schenk−torda−server                   -5.83 -4.77 -4.79                   -7.73 -6.12 -6.42 schenk−torda−server 73
74 test_http_server_01                   -5.83 -4.77 -4.79                   -7.73 -6.12 -6.42 test_http_server_01 74