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ctaa

ID: 1500395164 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 306 (296)
Sequences: 2308 (1536.3)
Seq/Len: 7.797
Nf(neff/√len): 89.3

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: 7.797).

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
121_A180_A3.0071.00
65_G104_A2.6011.00
21_I280_F2.4761.00
171_Y226_W2.3601.00
106_L122_L2.3171.00
178_T219_A2.3111.00
71_V100_L2.2861.00
75_A97_I2.2841.00
196_L203_G2.2381.00
10_V138_T2.1991.00
125_G177_Y2.1321.00
22_G63_A2.1231.00
254_F288_V2.1021.00
35_C42_C2.0811.00
69_I73_S1.9941.00
168_I226_W1.9931.00
17_L280_F1.9331.00
29_T56_I1.8761.00
102_L106_L1.8731.00
8_L73_S1.8321.00
196_L199_P1.8201.00
247_G291_Y1.8141.00
15_V70_L1.7951.00
13_T138_T1.7821.00
131_F287_G1.7761.00
75_A94_I1.7551.00
231_A252_L1.7301.00
193_N198_S1.7291.00
194_V221_L1.7181.00
273_G277_A1.6991.00
260_L264_M1.6921.00
135_L287_G1.6741.00
171_Y223_L1.6641.00
213_Q217_R1.6581.00
20_L283_A1.6541.00
13_T135_L1.6361.00
268_S271_A1.6321.00
72_L97_I1.6221.00
256_T260_L1.6191.00
231_A235_I1.6141.00
227_I255_I1.5951.00
261_S281_F1.5821.00
77_W81_K1.5781.00
106_L126_I1.5431.00
250_S288_V1.5321.00
249_I253_I1.5311.00
20_L24_A1.5231.00
68_I104_A1.5211.00
254_F284_C1.4690.99
251_C285_L1.4590.99
214_M218_A1.4520.99
87_R91_F1.4500.99
264_M268_S1.4430.99
224_F259_A1.4410.99
79_W94_I1.4200.99
213_Q266_V1.4160.99
229_V233_H1.4130.99
40_P43_H1.4080.99
75_A79_W1.4050.99
165_M293_L1.3900.99
172_S289_L1.3880.99
58_W62_F1.3620.99
76_F80_R1.3380.99
175_V223_L1.3330.99
72_L104_A1.3270.98
96_S133_S1.3230.98
191_C197_C1.3220.98
19_V64_S1.3170.98
92_L137_L1.3060.98
3_K7_A1.2880.98
168_I227_I1.2770.98
12_T70_L1.2720.98
25_L29_T1.2680.98
259_A263_I1.2680.98
166_I293_L1.2650.98
261_S277_A1.2620.98
105_L108_A1.2530.98
159_K163_F1.2520.98
98_I102_L1.2520.98
35_C40_P1.2500.97
291_Y295_L1.2470.97
24_A279_S1.2430.97
105_L109_L1.2430.97
132_A286_F1.2390.97
247_G288_V1.2370.97
64_S68_I1.2320.97
106_L109_L1.2310.97
31_S56_I1.2280.97
128_L283_A1.2240.97
108_A112_V1.2230.97
228_I232_V1.2210.97
164_H226_W1.2210.97
15_V67_S1.2190.97
221_L225_V1.2170.97
55_I59_S1.2160.97
234_A248_W1.2090.97
91_F95_M1.1910.96
5_L141_I1.1840.96
262_G278_H1.1820.96
8_L77_W1.1730.96
164_H168_I1.1710.96
224_F256_T1.1660.96
247_G295_L1.1610.96
286_F290_C1.1580.96
224_F255_I1.1560.95
65_G69_I1.1430.95
28_K33_Q1.1410.95
170_I174_I1.1390.95
57_E111_V1.1310.95
111_V123_H1.1290.95
163_F167_G1.1270.95
110_A120_M1.1260.95
6_K142_F1.1230.94
76_F79_W1.1230.94
251_C292_F1.1230.94
125_G173_Y1.1220.94
165_M292_F1.1210.94
255_I259_A1.1210.94
254_F281_F1.1140.94
218_A222_L1.1100.94
131_F283_A1.1000.94
30_G186_E1.0960.94
91_F94_I1.0930.93
132_A290_C1.0890.93
23_G26_V1.0830.93
66_I70_L1.0800.93
22_G56_I1.0760.93
18_I63_A1.0600.92
82_I90_T1.0580.92
235_I249_I1.0560.92
232_V235_I1.0530.92
110_A119_I1.0510.92
175_V178_T1.0510.92
264_M274_F1.0460.91
102_L126_I1.0430.91
252_L256_T1.0410.91
104_A108_A1.0360.91
135_L139_L1.0360.91
25_L276_L1.0350.91
9_G74_L1.0280.90
246_W249_I1.0270.90
261_S274_F1.0250.90
242_K246_W1.0220.90
43_H54_S1.0100.89
231_A248_W1.0090.89
109_L113_F1.0090.89
284_C288_V1.0030.89
52_P56_I1.0000.89
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  
2jwaA20.137321.40.954Contact Map
1kqfC10.477115.60.957Contact Map
2ks1B10.143810.40.961Contact Map
3cx5C20.52619.80.961Contact Map
4i0uA100.205980.962Contact Map
4gd3A20.44127.20.963Contact Map
1wqbA10.10135.40.965Contact Map
4ogqA10.54584.70.966Contact Map
4o6yA20.51964.20.967Contact Map
1pp9C20.540.967Contact 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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