GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0827 212-369

ID: 1406135254 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 158 (155)
Sequences: 434 (351.9)
Seq/Len: 2.800
Nf(neff/√len): 28.3

Jackhmmer Results: (2014_04_16)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 2.800).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
25_P29_K2.2111.00
59_G67_I1.9720.99
26_L30_A1.9390.99
26_L33_F1.8160.99
75_S101_T1.7890.99
18_S22_W1.7190.98
7_Q14_F1.6810.98
18_S23_Q1.6120.97
48_P51_S1.6110.97
56_V67_I1.6070.97
7_Q19_A1.5990.97
53_D59_G1.5810.97
98_C108_V1.4860.95
88_D91_G1.4700.94
75_S82_G1.4630.94
59_G105_R1.4330.93
25_P30_A1.4300.93
7_Q15_A1.4280.93
7_Q18_S1.4230.93
25_P31_L1.3940.92
144_R151_Y1.3680.91
110_Q131_E1.3590.91
7_Q10_V1.3500.90
15_A23_Q1.3440.90
74_L101_T1.3440.90
30_A33_F1.3350.90
17_A20_E1.3150.89
77_L82_G1.3060.88
94_L97_L1.2620.86
27_S33_F1.2590.86
98_C116_R1.2380.84
26_L32_Q1.2320.84
10_V17_A1.2210.83
11_G90_G1.2180.83
46_K50_N1.2170.83
99_K145_A1.2140.83
72_S79_P1.2130.83
7_Q22_W1.2050.82
8_D19_A1.1910.81
20_E59_G1.1820.80
57_A110_Q1.1640.79
82_G97_L1.1610.79
96_I148_V1.1570.78
15_A19_A1.1370.77
108_V137_Y1.1360.76
53_D98_C1.1360.76
59_G108_V1.1330.76
58_A66_E1.1290.76
68_A93_P1.1270.76
78_K117_R1.1220.75
12_D19_A1.1070.74
35_E56_V1.1020.73
103_L143_D1.0940.73
151_Y155_S1.0920.72
84_K93_P1.0710.70
85_I88_D1.0660.70
5_I9_A1.0640.70
16_L20_E1.0620.69
30_A86_F1.0560.69
85_I93_P1.0560.69
41_R44_I1.0550.69
4_E24_D1.0530.68
9_A21_G1.0520.68
27_S93_P1.0480.68
5_I86_F1.0480.68
104_P129_N1.0460.68
101_T154_W1.0460.68
53_D107_C1.0360.67
79_P83_A1.0350.66
65_R133_V1.0330.66
8_D11_G1.0320.66
57_A60_E1.0270.66
35_E38_Q1.0230.65
10_V13_V1.0190.65
87_T93_P1.0180.65
8_D84_K1.0100.64
10_V22_W1.0100.64
14_F17_A1.0070.63
52_L97_L1.0050.63
95_A136_V1.0040.63
19_A23_Q1.0000.63
110_Q127_D1.0000.63
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (12Jul14)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
1b0nA10.6203350.898Contact Map
3qwgA20.487329.80.902Contact Map
3op9A10.639229.10.902Contact Map
3pxpA30.708927.40.904Contact Map
4o8bA10.582318.40.911Contact Map
4jcyA20.53815.70.914Contact Map
3r1fA180.696212.40.917Contact Map
3fmyA10.3987120.918Contact Map
1neqA10.468411.20.919Contact Map
1y7yA20.417711.10.919Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

Page generated in 0.0161 seconds.