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PilO

ID: 1513362572 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 195 (182)
Sequences: 2246 (1845.9)
Seq/Len: 12.341
Nf(neff/√len): 136.8

HHblits Results: (2016_02)
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: 12.341).

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
111_N151_D2.9551.00
108_A115_I2.9501.00
141_D144_D2.8661.00
35_L40_F2.5401.00
92_P157_R2.4991.00
113_L140_G2.2791.00
112_N144_D2.0691.00
52_D55_N2.0421.00
53_I57_N1.9801.00
100_L159_I1.9141.00
49_L52_D1.8811.00
55_N59_K1.8431.00
131_E180_K1.8411.00
47_A50_K1.8011.00
78_I81_K1.7671.00
145_I175_V1.7611.00
162_D180_K1.7471.00
108_A148_F1.7381.00
16_T20_I1.7341.00
113_L148_F1.7091.00
138_F175_V1.7051.00
32_F36_K1.6731.00
116_I139_A1.6461.00
15_T18_E1.6401.00
42_T45_K1.6031.00
119_K135_S1.5771.00
97_I101_L1.5211.00
54_I58_F1.5171.00
14_A18_E1.5081.00
139_A174_R1.4781.00
74_N78_I1.4691.00
45_K49_L1.4671.00
103_S155_M1.4571.00
46_I49_L1.4040.99
41_P44_E1.4000.99
34_F38_Y1.3950.99
114_E139_A1.3210.99
70_R74_N1.3200.99
166_F175_V1.3090.99
33_L37_F1.3060.99
60_I64_Q1.2840.99
117_S137_E1.2620.99
121_V135_S1.2620.99
38_Y41_P1.2530.99
72_I76_Q1.2460.98
107_T151_D1.2290.98
135_S176_F1.2230.98
47_A51_K1.2190.98
137_E176_F1.2180.98
45_K48_I1.2120.98
49_L53_I1.2090.98
91_L157_R1.2080.98
96_E99_D1.1960.98
66_L70_R1.1950.98
39_Y43_K1.1900.98
40_F44_E1.1900.98
48_I52_D1.1870.98
53_I56_L1.1640.97
76_Q79_Q1.1610.97
110_R151_D1.1500.97
159_I181_T1.1490.97
75_K79_Q1.1480.97
100_L181_T1.1280.97
51_K55_N1.1160.96
99_D103_S1.1120.96
31_L34_F1.1100.96
135_S178_V1.1080.96
104_L148_F1.0970.96
18_E21_L1.0970.96
57_N61_K1.0920.96
58_F61_K1.0880.96
139_A172_E1.0810.95
50_K54_I1.0760.95
38_Y42_T1.0760.95
97_I157_R1.0680.95
137_E174_R1.0660.95
160_V182_F1.0630.95
63_Y67_V1.0580.95
52_D56_L1.0530.95
34_F39_Y1.0490.94
82_K86_F1.0390.94
73_L76_Q1.0250.93
85_E88_K1.0230.93
102_K118_F1.0200.93
98_P102_K1.0190.93
123_E183_Q1.0120.93
58_F62_R1.0110.93
142_F146_I1.0080.93
61_K65_N1.0010.92
62_R66_L1.0000.92
158_L181_T1.0000.92
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  
2rjzA20.671899.70.444Contact Map
4bhqA20.487295.30.809Contact Map
1uv7A20.384675.50.867Contact Map
2rddB10.189750.30.887Contact Map
2fhmA10.461533.40.898Contact Map
1ulrA10.446225.80.904Contact Map
3trgA10.4872240.905Contact Map
3rvyA20.235920.20.908Contact Map
1w2iA20.4615200.908Contact Map
4hi1A30.446217.40.911Contact 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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