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T0813

ID: 1402423047 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 307 (284)
Sequences: 2353 (1738.7)
Seq/Len: 8.285
Nf(neff/√len): 103.2

HHblits Results: (2013_03)
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: 8.285).

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
9_A66_A3.4631.00
7_T32_T3.4491.00
163_R175_E3.0681.00
281_R285_R2.8181.00
252_A262_Q2.7741.00
32_T54_R2.7531.00
96_T122_G2.5881.00
45_R134_D2.5561.00
163_R167_E2.5321.00
73_V81_V2.4301.00
80_A84_E2.3961.00
58_S61_E2.3801.00
255_S259_A2.3711.00
8_I24_I2.3561.00
40_E44_K2.3251.00
22_R136_G2.2811.00
269_D272_K2.2391.00
255_S262_Q2.1061.00
16_I98_V2.0581.00
7_T34_V2.0321.00
125_I185_L2.0261.00
43_L55_Y1.9371.00
10_L21_A1.8531.00
128_T137_F1.8031.00
13_I35_V1.8011.00
230_A285_R1.7931.00
25_R53_D1.7751.00
244_K268_G1.7671.00
252_A266_R1.7631.00
82_A109_M1.7261.00
23_D169_L1.7021.00
177_D180_H1.6931.00
24_I165_F1.6901.00
9_A62_A1.6701.00
122_G148_L1.6681.00
147_I176_M1.6541.00
20_I169_L1.6111.00
37_T42_T1.6081.00
26_E138_A1.6081.00
160_A163_R1.6021.00
67_D90_K1.5891.00
20_I70_V1.5891.00
120_V162_L1.5841.00
79_G83_A1.5811.00
264_A272_K1.5521.00
263_R267_W1.5421.00
71_V81_V1.5401.00
90_K93_A1.5341.00
21_A51_L1.5251.00
146_C166_W1.5121.00
13_I37_T1.4911.00
71_V78_S1.4760.99
60_A88_H1.4720.99
160_A164_L1.4660.99
230_A281_R1.4630.99
35_V52_G1.4490.99
262_Q266_R1.4310.99
118_H155_D1.4250.99
164_L167_E1.4150.99
7_T65_G1.4150.99
44_K48_E1.4020.99
94_I158_A1.3790.99
71_V82_A1.3740.99
43_L52_G1.3700.99
224_D228_L1.3670.99
196_A229_A1.3540.99
9_A36_T1.3490.99
106_I178_P1.3470.99
75_V101_T1.3380.99
155_D158_A1.3350.99
75_V99_G1.3230.99
237_R274_F1.3010.98
231_S277_F1.2960.98
86_A113_L1.2930.98
275_D279_R1.2880.98
240_C247_I1.2720.98
89_L95_V1.2700.98
193_H236_W1.2540.98
183_K249_E1.2500.98
166_W173_V1.2480.98
11_I81_V1.2470.98
271_D275_D1.2460.98
148_L163_R1.2450.98
191_L247_I1.2320.98
78_S99_G1.2280.97
94_I162_L1.2110.97
237_R270_G1.2080.97
68_L94_I1.1950.97
11_I85_I1.1940.97
96_T162_L1.1840.97
248_L266_R1.1770.96
38_R73_V1.1740.96
10_L17_G1.1670.96
49_L133_P1.1650.96
16_I141_F1.1650.96
180_H213_E1.1630.96
11_I36_T1.1590.96
79_G108_Q1.1590.96
122_G166_W1.1590.96
122_G146_C1.1580.96
23_D139_G1.1570.96
156_E160_A1.1540.96
69_V89_L1.1510.96
16_I126_A1.1470.96
45_R48_E1.1450.96
159_V175_E1.1420.96
34_V65_G1.1370.95
25_R33_I1.1330.95
15_L239_V1.1280.95
8_I68_L1.1270.95
264_A269_D1.1200.95
241_L270_G1.1120.95
69_V93_A1.0970.94
150_P159_V1.0910.94
9_A63_V1.0910.94
21_A33_I1.0900.94
103_G179_K1.0850.94
52_G55_Y1.0840.94
103_G107_A1.0730.93
140_L190_H1.0730.93
221_G224_D1.0640.93
274_F278_T1.0630.93
24_I29_L1.0610.93
94_I161_R1.0600.93
165_F169_L1.0540.92
97_D106_I1.0500.92
60_A84_E1.0490.92
85_I88_H1.0470.92
164_L168_T1.0400.92
43_L57_L1.0380.92
125_I188_V1.0300.91
234_T274_F1.0270.91
109_M119_F1.0230.91
40_E57_L1.0210.91
92_G118_H1.0130.90
224_D227_R1.0120.90
68_L162_L1.0120.90
240_C277_F1.0100.90
142_R170_G1.0090.90
195_I198_N1.0070.90
20_I98_V1.0060.90
186_A243_N1.0050.90
231_S239_V1.0030.90
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: (07Jun14)
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  
3ktdA40.95441000.371Contact Map
2g5cA40.91211000.381Contact Map
3b1fA10.91531000.388Contact Map
3ggoA40.92511000.394Contact Map
2f1kA40.89581000.417Contact Map
2pv7A20.87951000.439Contact Map
2izzA50.8731000.635Contact Map
4e12A10.82411000.638Contact Map
4kqwA20.91531000.639Contact Map
1zejA10.866499.90.645Contact 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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