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PilG

ID: 1513362345 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 403 (401)
Sequences: 4947 (3644.1)
Seq/Len: 12.337
Nf(neff/√len): 182.0

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: 12.337).

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
8_G37_L4.7121.00
67_T128_Y4.6161.00
204_W208_V4.3271.00
20_L28_V4.0721.00
106_K119_H3.7761.00
240_S243_G3.3431.00
113_L117_M3.3021.00
28_V42_I2.9611.00
22_A28_V2.7691.00
342_K345_E2.5991.00
205_P383_G2.5551.00
274_A348_N2.5501.00
82_K339_M2.4831.00
157_G356_E2.4451.00
84_L107_V2.3821.00
75_E146_N2.3541.00
102_D120_Y2.3301.00
245_Y301_K2.3061.00
204_W207_Q2.2961.00
159_K163_K2.2541.00
70_F83_C2.2051.00
192_A214_K2.2041.00
271_R355_E2.1981.00
128_Y148_L2.1641.00
207_Q211_N2.1481.00
309_N314_Q2.1281.00
71_A149_A2.1101.00
66_F100_I2.1051.00
181_S185_L2.0781.00
102_D106_K2.0671.00
88_A101_R2.0521.00
7_Q17_K2.0381.00
6_W18_G2.0361.00
84_L100_I2.0201.00
288_T307_R2.0101.00
39_P42_I2.0091.00
118_V133_R1.9661.00
7_Q41_K1.9371.00
174_A178_I1.9311.00
70_F145_L1.9241.00
182_V186_F1.9201.00
178_I182_V1.9141.00
140_N143_M1.8981.00
85_E104_K1.8981.00
25_P29_E1.8861.00
291_G304_E1.8861.00
156_V160_S1.8841.00
263_K357_E1.8731.00
205_P390_L1.8681.00
4_Y25_P1.8631.00
161_K363_N1.8631.00
306_V320_M1.8631.00
248_D297_K1.8211.00
154_K359_D1.8051.00
106_K111_V1.7831.00
104_K108_E1.7811.00
248_D296_N1.7571.00
389_Y393_F1.7561.00
117_M132_I1.7521.00
28_V39_P1.7401.00
68_R153_E1.7301.00
278_G344_E1.7001.00
106_K116_A1.6991.00
271_R352_G1.6881.00
273_L286_A1.6781.00
88_A104_K1.6611.00
205_P208_V1.6561.00
173_V177_I1.6171.00
114_S136_E1.6051.00
99_V123_I1.6001.00
10_S14_E1.5941.00
137_S285_P1.5931.00
10_S16_R1.5711.00
314_Q318_D1.5561.00
170_S174_A1.5431.00
379_V383_G1.5371.00
261_F265_A1.5341.00
111_V115_E1.5311.00
263_K361_M1.5241.00
157_G161_K1.5221.00
208_V211_N1.5151.00
23_T27_L1.5091.00
128_Y152_I1.5051.00
270_A330_M1.4881.00
31_Y35_L1.4861.00
27_L31_Y1.4761.00
259_E263_K1.4651.00
71_A146_N1.4501.00
75_E349_K1.4491.00
209_V387_A1.4281.00
168_Y172_V1.4221.00
68_R149_A1.4201.00
291_G307_R1.4191.00
161_K359_D1.3960.99
80_I113_L1.3890.99
285_P288_T1.3830.99
308_L311_S1.3770.99
278_G348_N1.3700.99
287_I303_M1.3620.99
307_R311_S1.3520.99
297_K300_E1.3400.99
24_N27_L1.3380.99
195_Y395_L1.3330.99
134_S138_S1.3320.99
271_R351_A1.3320.99
382_G386_V1.3290.99
154_K355_E1.3270.99
7_Q15_I1.3250.99
287_I310_V1.3210.99
273_L347_L1.3100.99
190_K193_E1.3060.99
3_L19_V1.3050.99
184_M212_I1.3020.99
191_F393_F1.2970.99
180_I384_I1.2930.99
19_V45_K1.2650.99
146_N150_D1.2600.99
211_N215_N1.2600.99
75_E142_D1.2570.99
103_I117_M1.2460.98
6_W32_L1.2360.98
106_K120_Y1.2330.98
267_A358_V1.2310.98
302_A326_F1.2310.98
125_D128_Y1.2280.98
208_V212_I1.2230.98
266_V330_M1.2140.98
5_E45_K1.2080.98
70_F80_I1.1990.98
309_N319_P1.1970.98
320_M334_V1.1940.98
191_F389_Y1.1830.98
273_L283_L1.1820.98
28_V31_Y1.1810.98
249_K253_R1.1730.98
18_G32_L1.1730.98
8_G18_G1.1680.97
25_P44_E1.1590.97
60_D159_K1.1590.97
246_V249_K1.1580.97
8_G39_P1.1550.97
180_I380_I1.1520.97
151_Y155_I1.1450.97
370_E374_I1.1410.97
183_I384_I1.1370.97
203_P206_T1.1330.97
283_L316_I1.1320.97
3_L21_E1.1270.97
74_L145_L1.1240.97
265_A299_I1.1240.97
115_E118_V1.1200.96
215_N223_L1.1200.96
172_V381_V1.1150.96
374_I377_L1.1080.96
201_S207_Q1.1050.96
172_V377_L1.1020.96
245_Y297_K1.1020.96
184_M188_I1.0970.96
330_M350_V1.0960.96
267_A355_E1.0940.96
365_L369_I1.0910.96
210_I214_K1.0830.96
202_L206_T1.0810.95
67_T148_L1.0810.95
133_R292_E1.0800.95
263_K358_V1.0790.95
276_L286_A1.0710.95
184_M216_F1.0660.95
64_A152_I1.0640.95
111_V116_A1.0640.95
175_V179_V1.0610.95
334_V343_L1.0530.95
348_N352_G1.0500.94
308_L312_A1.0500.94
306_V334_V1.0490.94
20_L31_Y1.0490.94
214_K217_G1.0460.94
274_A351_A1.0410.94
167_I170_S1.0330.94
5_E43_T1.0310.94
269_T273_L1.0290.94
133_R137_S1.0240.93
244_R297_K1.0220.93
134_S272_T1.0200.93
5_E17_K1.0150.93
175_V375_V1.0140.93
77_G280_G1.0110.93
31_Y34_R1.0070.93
142_D344_E1.0060.93
392_I396_G1.0050.93
58_V96_F1.0030.93
64_A149_A1.0020.92
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  
3c1qA20.300299.90.714Contact Map
4hhxA10.250699.90.719Contact Map
2whnA20.27399.80.744Contact Map
3tweA20.0645190.961Contact Map
4g3bA20.057113.50.964Contact Map
3hd7A20.225810.30.966Contact Map
4ev6A50.47899.70.966Contact Map
2lmcA10.11919.70.966Contact Map
4i0uA100.48149.10.967Contact Map
2m8rA10.27058.70.967Contact 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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