T0514

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

T0514

invasion associated protein B from Bartonella henselae

Target type: Server only

Target sequence:

>T0514 INVASION ASSOCIATED PROTEIN B, BARTONELLA HENSELAE, 145 residues
SSLTETYGLWSINCGIQEGKKVCFMHRQEVNDQNRVVVAMSVVLNADGVVSGNLTVPFGILVSKPVRLQVDEGKAVIETGIRTCVPAGCIVPIVFDKNYVAALRAGKHLKLAMTIAAPGEPPLNDLFVQLNGFSNALNRLIALQK

Structure:
Method: X-ray, res=2.35Å, R/Rfree=0.24/0.27
Determined by: NYSGRC
PDB ID: 3dtd

3dtd_A cartoon
Cartoon diagram of 514: 3dtd chain A

PyMOL of 3dtd

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Immunoglobulin-like topology (in a broad sense) with extra 3-stranded meander β-sheet at the N-terminus covered by an extra-C-terminal α-helix. This extra-region may even be viewed as a separate β3α domain. Another interesting aspect of this structure is topological similarity to circularly permuted reversed ferredoxin-like fold, if the two helices are considered core elements, but the strands in one of the sheets are treated as insertions and extensions.

3dtd_A cartoon
Cartoon diagram of 514: 3dtd chain A possible domains:
42-72, 171-186 (blue) and 73-170 (red)

3dtd_A cartoon
Cartoon diagram of 514: 3dtd chain A
IG-like core colored rainbow

3dtd_A cartoon
Cartoon diagram of 514: 3dtd chain A
circular permutation of
reversed ferredoxin-like core colored rainbow

CASP category:

Fold recognition.

Closest templates:

2zf8, 2jug.

Target sequence - PDB file inconsistencies:

T0514    3dtd.pdb    T0514.pdb    PyMOL    PyMOL of domains    

T0514    1 SSLTETYGLWSINCGIQEGKKVCFMHRQEVNDQNRVVVAMSVVLNADGVVSGNLTVPFGILVSKPVRLQVDEGKAVIETGIRTCVPAGCIVPIVFDKNYVAALRAGKHLKLAMTIAAPGEPPLNDLFVQLNGFSNALNRLIALQK- 145
           ~||||||||||||||||~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~
3dtdA   42 -SLTETYGLWSINCGIQ---KVCFMHRQEVNDQNRVVVAMSVVLNADGVVSGNLTVPFGILVSKPVRLQVDEGKAVIETGIRTCVPAGCIVPIVFDKNYVAALRAGKHLKLAMTIAAPGEPPLNDLFVQLNGFSNALNRLIALQKE 186

Single domain protein: target 2-17, 21-145 ; pdb 42-57, 61-185

Sequence classification:

Invasion associated locus B protein IalB in Pfam.

Server predictions:

T0514:pdb 42-185:seq 2-145:FR;   alignment

distribution of first scores
First models for T0514: 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 #
T0514 T0514 T0514 T0514
First score First Z-score Best score Best Z-score
1 pro−sp3−TASSER 50.71 37.23 51.86 3.35 2.71 2.52 50.89 38.83 51.97 2.96 2.65 2.26 pro−sp3−TASSER 1
2 MUProt 43.79 36.70 44.79 2.54 2.63 1.81 43.79 36.70 44.79 2.16 2.34 1.50 MUProt 2
3 MULTICOM−CMFR 43.62 35.46 44.71 2.52 2.45 1.80 43.62 35.46 44.71 2.14 2.15 1.50 MULTICOM−CMFR 3
4 MULTICOM−CLUSTER 43.44 33.92 44.71 2.50 2.23 1.80 43.44 33.92 44.71 2.12 1.93 1.50 MULTICOM−CLUSTER 4
5 MULTICOM−REFINE 43.09 35.99 44.71 2.46 2.53 1.80 43.09 35.99 44.71 2.08 2.23 1.50 MULTICOM−REFINE 5
6 MULTICOM−RANK 43.09 33.16 44.73 2.46 2.12 1.80 43.09 33.16 44.73 2.08 1.81 1.50 MULTICOM−RANK 6
7 METATASSER 39.36 32.15 40.79 2.02 1.97 1.40 44.50 34.81 51.73 2.24 2.06 2.24 METATASSER 7
8 HHpred4 35.11 29.55 30.88 1.53 1.59 0.39 35.11 29.55 30.88 1.18 1.28 0.03 HHpred4 8
9 HHpred5 33.33 28.84 35.01 1.32 1.49 0.81 33.33 28.84 35.01 0.98 1.17 0.47 HHpred5 9
10 FAMSD 29.61 25.00 30.90 0.88 0.93 0.40 29.61 25.00 30.90 0.56 0.61 0.03 FAMSD 10
11 RBO−Proteus 28.90 25.59 43.83 0.80 1.01 1.71 28.90 25.59 44.55 0.48 0.69 1.48 RBO−Proteus 11
12 GS−KudlatyPred 28.37 23.88 39.21 0.74 0.77 1.24 29.61 25.59 40.55 0.56 0.69 1.06 GS−KudlatyPred 12
13 forecast 26.24 19.62 22.50 0.49 0.15 -0.46 26.24 20.15 22.50 0.18 -0.11 -0.86 forecast 13
14 MUSTER 25.89 20.21 27.22 0.45 0.23 0.02 49.11 42.49 45.14 2.76 3.19 1.54 MUSTER 14
15 Zhang−Server 25.89 19.74 37.98 0.45 0.16 1.11 39.01 29.85 44.04 1.62 1.32 1.42 Zhang−Server 15
16 PSI 25.53 21.39 42.69 0.41 0.40 1.59 26.95 22.81 44.00 0.26 0.28 1.42 PSI 16
17 circle 23.94 20.15 22.62 0.22 0.22 -0.44 24.11 20.15 27.44 -0.06 -0.11 -0.33 circle 17
18 BAKER−ROBETTA 23.58 19.80 41.73 0.18 0.17 1.50 29.61 25.59 43.32 0.56 0.69 1.35 BAKER−ROBETTA 18
19 LEE−SERVER 23.23 22.28 37.59 0.14 0.53 1.08 23.23 22.28 37.59 -0.16 0.21 0.74 LEE−SERVER 19
20 MUFOLD−MD 21.63 18.14 37.07 -0.05 -0.07 1.02 27.13 19.86 41.37 0.28 -0.15 1.14 MUFOLD−MD 20
21 FEIG 20.21 18.85 28.74 -0.21 0.03 0.18 23.23 21.45 40.28 -0.16 0.08 1.03 FEIG 21
22 FALCON_CONSENSUS 20.21 18.44 28.24 -0.21 -0.03 0.13 20.21 18.44 32.42 -0.50 -0.36 0.19 FALCON_CONSENSUS 22
23 FALCON 20.21 18.44 28.24 -0.21 -0.03 0.13 21.45 18.44 32.72 -0.36 -0.36 0.23 FALCON 23
24 mGenTHREADER 19.86 18.79 19.22 -0.26 0.03 -0.79 19.86 18.79 19.22 -0.54 -0.31 -1.20 mGenTHREADER 24
25 Frankenstein 19.68 16.90 29.15 -0.28 -0.25 0.22 20.57 17.85 29.15 -0.46 -0.45 -0.15 Frankenstein 25
26 BioSerf 19.50 17.79 33.35 -0.30 -0.12 0.64 19.50 17.79 33.35 -0.58 -0.46 0.29 BioSerf 26
27 RAPTOR 19.33 18.50 33.94 -0.32 -0.02 0.70 23.94 20.75 37.94 -0.08 -0.02 0.78 RAPTOR 27
28 keasar−server 19.33 17.91 25.91 -0.32 -0.10 -0.11 19.86 18.20 25.91 -0.54 -0.40 -0.49 keasar−server 28
29 mariner1 19.33 13.77 25.80 -0.32 -0.70 -0.12 20.39 19.33 30.54 -0.48 -0.23 -0.00 mariner1 29
30 Phyre_de_novo 18.62 16.25 25.52 -0.40 -0.34 -0.15 18.97 16.25 31.37 -0.64 -0.69 0.08 Phyre_de_novo 30
31 SAM−T06−server 18.62 15.48 26.25 -0.40 -0.46 -0.08 18.62 15.48 26.25 -0.68 -0.80 -0.46 SAM−T06−server 31
32 FFASsuboptimal 18.44 16.67 19.99 -0.42 -0.28 -0.71 18.44 16.67 20.00 -0.70 -0.62 -1.12 FFASsuboptimal 32
33 SAM−T08−server 17.91 14.95 26.65 -0.48 -0.53 -0.04 17.91 14.95 26.65 -0.76 -0.88 -0.42 SAM−T08−server 33
34 HHpred2 17.91 14.54 21.19 -0.48 -0.59 -0.59 17.91 14.54 21.19 -0.76 -0.94 -0.99 HHpred2 34
35 3D−JIGSAW_V3 17.55 15.31 22.39 -0.53 -0.48 -0.47 25.53 21.39 22.39 0.10 0.07 -0.87 3D−JIGSAW_V3 35
36 MUFOLD−Server 17.55 13.12 20.09 -0.53 -0.80 -0.70 17.55 14.42 20.09 -0.80 -0.96 -1.11 MUFOLD−Server 36
37 ACOMPMOD 17.38 15.90 21.73 -0.54 -0.40 -0.53 18.79 15.90 21.73 -0.66 -0.74 -0.94 ACOMPMOD 37
38 Distill 17.38 14.89 26.34 -0.54 -0.54 -0.07 19.15 16.84 28.78 -0.62 -0.60 -0.19 Distill 38
39 nFOLD3 17.02 13.47 18.12 -0.59 -0.75 -0.90 22.52 18.38 27.50 -0.24 -0.37 -0.33 nFOLD3 39
40 3DShot2 17.02 13.36 26.95 -0.59 -0.76 -0.00 17.02 13.36 26.95 -0.86 -1.11 -0.38 3DShot2 40
41 Phyre2 16.84 14.01 24.71 -0.61 -0.67 -0.23 20.75 18.62 35.63 -0.44 -0.33 0.53 Phyre2 41
42 CpHModels 16.67 15.48 22.07 -0.63 -0.46 -0.50 16.67 15.48 22.07 -0.90 -0.80 -0.90 CpHModels 42
43 3D−JIGSAW_AEP 16.67 15.37 17.53 -0.63 -0.47 -0.96 16.67 15.37 18.75 -0.90 -0.82 -1.25 3D−JIGSAW_AEP 43
44 Pcons_dot_net 16.49 14.95 17.43 -0.65 -0.53 -0.97 19.50 16.43 19.43 -0.58 -0.66 -1.18 Pcons_dot_net 44
45 Poing 16.31 12.18 28.65 -0.67 -0.94 0.17 24.11 19.39 31.16 -0.06 -0.22 0.06 Poing 45
46 Phragment 15.78 14.18 22.66 -0.73 -0.65 -0.44 17.38 14.18 26.56 -0.82 -0.99 -0.43 Phragment 46
47 fais−server 15.78 13.42 23.69 -0.73 -0.76 -0.34 19.86 16.79 34.84 -0.54 -0.61 0.45 fais−server 47
48 huber−torda−server 15.60 15.31 12.28 -0.75 -0.48 -1.49 15.78 15.31 15.61 -1.00 -0.82 -1.58 huber−torda−server 48
49 FUGUE_KM 15.43 14.84 14.16 -0.77 -0.55 -1.30 17.55 14.84 14.16 -0.80 -0.89 -1.74 FUGUE_KM 49
50 COMA 15.43 12.23 13.85 -0.77 -0.93 -1.33 17.38 16.08 21.85 -0.82 -0.71 -0.92 COMA 50
51 COMA−M 15.43 12.23 13.85 -0.77 -0.93 -1.33 17.38 16.08 21.85 -0.82 -0.71 -0.92 COMA−M 51
52 PS2−server 15.07 11.29 13.90 -0.81 -1.07 -1.33 20.39 17.32 27.34 -0.48 -0.53 -0.34 PS2−server 52
53 LOOPP_Server 14.72 11.64 8.43 -0.86 -1.01 -1.88 25.00 20.86 28.35 0.04 -0.00 -0.24 LOOPP_Server 53
54 RANDOM 14.69 12.46 14.69 -0.86 -0.90 -1.25 14.69 12.46 14.69 -1.12 -1.24 -1.68 RANDOM 54
55 Pcons_multi 14.54 11.70 18.29 -0.88 -1.01 -0.88 17.20 14.95 21.25 -0.84 -0.88 -0.99 Pcons_multi 55
56 GS−MetaServer2 14.18 10.88 8.00 -0.92 -1.13 -1.93 20.92 19.86 25.83 -0.42 -0.15 -0.50 GS−MetaServer2 56
57 GeneSilicoMetaServer 14.18 10.88 8.00 -0.92 -1.13 -1.93 20.92 19.86 25.83 -0.42 -0.15 -0.50 GeneSilicoMetaServer 57
58 schenk−torda−server 13.65 13.36 17.81 -0.98 -0.76 -0.93 15.78 13.42 17.81 -1.00 -1.10 -1.35 schenk−torda−server 58
59 SAM−T02−server 13.12 11.05 14.14 -1.04 -1.10 -1.31 13.12 11.05 14.14 -1.30 -1.45 -1.74 SAM−T02−server 59
60 OLGAFS 12.94 9.99 10.61 -1.06 -1.25 -1.66 13.30 11.53 10.61 -1.28 -1.38 -2.11 OLGAFS 60
61 FFASstandard 12.77 10.64 4.09 -1.08 -1.16 -2.33 12.77 10.64 4.89 -1.34 -1.51 -2.72 FFASstandard 61
62 3Dpro 12.59 11.47 15.90 -1.10 -1.04 -1.13 16.31 12.41 15.90 -0.94 -1.25 -1.55 3Dpro 62
63 FOLDpro 12.59 11.47 15.90 -1.10 -1.04 -1.13 16.31 12.41 15.90 -0.94 -1.25 -1.55 FOLDpro 63
64 FFASflextemplate 11.70 10.05 4.89 -1.21 -1.25 -2.24 12.77 10.64 4.89 -1.34 -1.51 -2.72 FFASflextemplate 64
65 Pcons_local 11.70 9.93 1.36 -1.21 -1.26 -2.60 13.30 11.17 1.36 -1.28 -1.44 -3.09 Pcons_local 65
66 rehtnap 9.93 9.81 -7.22 -1.42 -1.28 -3.47 9.93 9.81 -7.22 -1.66 -1.64 -4.00 rehtnap 66
67 BHAGEERATH                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 BHAGEERATH 67
68 Fiser−M4T                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 Fiser−M4T 68
69 Pushchino                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 Pushchino 69
70 YASARA                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 YASARA 70
71 mahmood−torda−server                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 mahmood−torda−server 71
72 panther_server                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 panther_server 72
73 pipe_int                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 pipe_int 73
74 test_http_server_01                   -0.86 -0.90 -1.25                   -1.12 -1.24 -1.68 test_http_server_01 74