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CcmC-02

ID: 1517605241 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 245 (236)
Sequences: 1570 (862.1)
Seq/Len: 6.653
Nf(neff/√len): 56.1

Jackhmmer Results: (2016_04)
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: 6.653).

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
96_M213_S2.7941.00
64_A107_A2.7661.00
29_S215_T2.5521.00
79_F83_V2.2961.00
72_A170_L2.2671.00
36_G205_S2.1701.00
78_A93_V2.1471.00
96_M217_T2.0931.00
33_L208_G2.0291.00
75_A167_V2.0171.00
79_F164_L1.9881.00
54_Y58_Y1.9831.00
54_Y57_I1.9781.00
70_I213_S1.9641.00
199_R203_R1.9491.00
124_V129_L1.9251.00
67_S132_E1.8871.00
26_A215_T1.8691.00
47_D50_Q1.8681.00
105_F109_V1.8361.00
90_N156_G1.8171.00
149_F155_A1.8171.00
212_L216_L1.7791.00
32_V211_L1.7741.00
91_L221_M1.7711.00
35_V204_W1.7701.00
38_I43_F1.7681.00
121_T124_V1.7611.00
132_E136_L1.7601.00
127_A182_T1.7331.00
52_N55_R1.6981.00
174_H178_E1.6971.00
65_I210_L1.6871.00
85_Q157_R1.6631.00
136_L140_V1.6581.00
105_F136_L1.6491.00
63_A106_I1.6471.00
70_I96_M1.6411.00
224_L227_L1.6191.00
146_W159_A1.6141.00
133_L137_F1.6051.00
74_M163_V1.6011.00
73_S96_M1.5831.00
38_I42_G1.5781.00
10_I13_R1.5721.00
72_A167_V1.5530.99
81_G90_N1.5240.99
90_N146_W1.5220.99
67_S107_A1.4910.99
168_V172_I1.4880.99
57_I202_L1.4850.99
107_A132_E1.4790.99
44_A54_Y1.4680.99
207_F211_L1.4610.99
104_T132_E1.4490.99
65_I206_I1.4400.99
46_A52_N1.4330.99
189_R199_R1.4220.99
28_A211_L1.4120.99
97_A142_V1.4110.99
92_A221_M1.4030.99
82_L164_L1.3920.99
93_V142_V1.3530.98
40_G55_R1.3490.98
19_G222_R1.3470.98
39_W43_F1.3390.98
58_Y198_M1.3280.98
5_L8_L1.3240.98
9_A13_R1.3240.98
138_L166_G1.3230.98
32_V207_F1.3200.98
142_V163_V1.3110.98
91_L228_M1.2830.97
29_S212_L1.2730.97
46_A55_R1.2720.97
24_W27_I1.2690.97
43_F58_Y1.2680.97
172_I179_W1.2600.97
108_L133_L1.2550.97
170_L173_I1.2530.97
27_I31_V1.2480.96
99_I217_T1.2460.96
25_L211_L1.2430.96
205_S208_G1.2270.96
93_V163_V1.2120.96
185_Q188_T1.2070.96
86_M89_A1.1890.95
138_L163_V1.1890.95
71_Y100_G1.1880.95
74_M97_A1.1860.95
116_K122_W1.1830.95
75_A79_F1.1750.95
16_Q20_W1.1730.95
94_A224_L1.1730.95
53_S118_M1.1490.94
7_Q12_P1.1440.94
203_R207_F1.1270.93
33_L212_L1.1180.92
235_V238_L1.1090.92
116_K121_T1.0920.91
15_Y18_C1.0860.91
12_P16_Q1.0820.91
14_L221_M1.0760.90
69_G210_L1.0740.90
161_I164_L1.0690.90
66_W210_L1.0650.90
189_R192_Q1.0590.90
8_L17_I1.0550.89
155_A159_A1.0540.89
13_R16_Q1.0460.89
103_F213_S1.0320.88
25_L214_A1.0310.88
26_A30_V1.0290.88
94_A146_W1.0230.87
7_Q13_R1.0210.87
109_V112_S1.0160.87
174_H177_V1.0130.87
109_V113_A1.0120.87
134_V147_H1.0110.86
98_P220_R1.0040.86
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: (06Aug15)
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  
4he8J20.579628.10.963Contact Map
2cfqA10.840821.10.966Contact Map
4uvmA10.8816160.967Contact Map
4tphA20.7429150.968Contact Map
4ikvA10.84913.80.968Contact Map
2kluA10.224511.90.969Contact Map
4oh3A20.889811.30.969Contact Map
4xnjA1010.50.97Contact Map
1vhfA10.33069.50.97Contact Map
1p1lA10.33069.40.97Contact 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.

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