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1a0l

ID: 1516177889 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 244 (236)
Sequences: 13358 (9550.6)
Seq/Len: 56.602
Nf(neff/√len): 621.7

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: 56.602).

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
125_C200_C4.5051.00
29_C45_C3.5341.00
75_S96_E3.0171.00
11_K147_Q2.9631.00
31_G39_V2.9611.00
38_W96_E2.8521.00
38_W94_L2.8161.00
6_E146_K2.7711.00
15_Q128_T2.6501.00
17_S27_H2.6201.00
12_W147_Q2.5591.00
73_P98_E2.5521.00
46_V93_A2.4461.00
32_S208_Q2.4341.00
60_L101_V2.3731.00
90_A233_Y2.3311.00
76_R96_E2.2471.00
33_L101_V2.2411.00
44_H194_S2.1981.00
37_Q100_P2.1881.00
40_L208_Q2.1751.00
148_V187_R2.1661.00
190_C218_C2.1401.00
37_Q96_E2.1141.00
97_L101_V2.1031.00
214_W226_I2.0961.00
16_V31_G2.0841.00
81_P240_Y2.0501.00
12_W128_T2.0331.00
158_C181_C2.0171.00
6_E144_P1.9911.00
127_V189_S1.9891.00
16_V60_L1.9271.00
78_I240_Y1.9111.00
36_P100_P1.8921.00
1_I4_G1.8811.00
59_Q71_L1.8691.00
35_H38_W1.8451.00
178_D232_Y1.8411.00
74_V95_L1.8111.00
234_L238_H1.7971.00
92_I233_Y1.7921.00
89_G178_D1.7771.00
75_S98_E1.7751.00
103_V109_T1.7531.00
128_T199_V1.7401.00
72_L101_V1.6981.00
72_L98_E1.6861.00
125_C152_I1.6261.00
82_Q90_A1.6251.00
127_V148_V1.6171.00
16_V39_V1.5991.00
19_R27_H1.5311.00
7_A12_W1.5021.00
14_W199_V1.4871.00
228_T233_Y1.4521.00
110_V208_Q1.4381.00
180_L198_L1.4281.00
10_S63_Q1.4221.00
41_T46_V1.4181.00
188_D225_G1.4171.00
14_W111_T1.4151.00
64_H143_F1.4101.00
59_Q62_E1.4101.00
212_V215_G1.3930.99
62_E69_D1.3810.99
80_H90_A1.3780.99
124_P149_K1.3630.99
229_R232_Y1.3500.99
133_V146_K1.3470.99
15_Q145_L1.3470.99
32_S211_V1.3370.99
32_S110_V1.3320.99
79_V93_A1.3120.99
153_M224_P1.3080.99
198_L227_Y1.3080.99
9_R63_Q1.3070.99
126_W149_K1.3060.99
42_A211_V1.3030.99
200_C209_A1.2960.99
189_S212_V1.2800.99
46_V79_V1.2770.99
179_M214_W1.2750.99
66_Y143_F1.2630.99
14_W206_W1.2530.99
57_R71_L1.2510.99
137_E220_Q1.2390.98
90_A178_D1.2380.98
72_L99_E1.2370.98
127_V150_V1.2330.98
110_V199_V1.2300.98
77_I95_L1.2240.98
44_H91_D1.2190.98
18_L58_V1.2150.98
33_L60_L1.2070.98
78_I96_E1.2060.98
15_Q130_W1.2010.98
8_P11_K1.1820.98
15_Q30_G1.1800.98
154_E157_I1.1590.97
64_H144_P1.1540.97
92_I228_T1.1350.97
6_E63_Q1.1280.97
195_G198_L1.1280.97
142_P146_K1.1220.97
39_V58_V1.1130.96
151_P183_G1.1020.96
38_W240_Y1.0890.96
5_Q147_Q1.0860.96
216_E223_R1.0840.96
182_A198_L1.0800.95
32_S40_L1.0740.95
10_S106_H1.0600.95
236_W240_Y1.0580.95
155_N229_R1.0540.95
124_P151_P1.0480.94
199_V206_W1.0400.94
12_W206_W1.0260.94
89_G176_R1.0260.94
80_H83_F1.0260.94
12_W126_W1.0040.93
84_Y87_Q1.0020.92
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  
2f83A10.8689100-0.03Contact Map
4nzqA10.9467100-0.016Contact Map
2xxlA20.9426100-0.012Contact Map
3nxpA10.9385100-0.007Contact Map
4kkdA20.9631100-0.004Contact Map
2b9lA10.97131000.003Contact Map
2f9nA40.98361000.008Contact Map
2anyA10.95491000.014Contact Map
1z8gA10.94671000.015Contact Map
4crgA10.93851000.017Contact 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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