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CobBSIRT2_1

ID: 1506435164 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 304 (284)
Sequences: 1700 (1170)
Seq/Len: 5.986
Nf(neff/√len): 69.4

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: 5.986).

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
39_A94_T4.2831.00
101_R105_D3.7481.00
104_K127_E3.3621.00
15_V231_L2.9241.00
13_E282_L2.6131.00
15_V266_V2.5341.00
169_C172_C2.3321.00
19_M27_V2.3291.00
233_I275_G2.2911.00
61_P65_A2.2801.00
38_S273_D2.2761.00
281_E286_K2.2711.00
143_C148_C2.2631.00
26_R201_K2.2251.00
271_E274_Q2.2221.00
31_V112_C2.1321.00
143_C172_C2.0601.00
102_L106_K2.0261.00
100_M112_C1.9951.00
235_K271_E1.9811.00
206_L231_L1.9461.00
96_C276_C1.9431.00
122_R133_E1.9251.00
29_C103_L1.9151.00
148_C172_C1.8801.00
215_Q219_S1.8281.00
96_C273_D1.7951.00
29_C100_M1.7661.00
111_R198_D1.7231.00
142_H151_E1.7121.00
48_S53_D1.6911.00
215_Q218_A1.6881.00
119_T137_T1.6811.00
30_L205_L1.6721.00
66_I82_L1.6261.00
113_Y198_D1.5530.99
38_S95_I1.5360.99
140_T179_D1.5260.99
8_D17_R1.5230.99
96_C208_M1.5110.99
62_Y65_A1.5100.99
278_A281_E1.4840.99
236_E269_L1.4730.99
145_S174_S1.4550.99
102_L105_D1.4410.99
127_E130_D1.4260.98
268_W275_G1.4170.98
29_C206_L1.4140.98
94_T273_D1.3940.98
278_A282_L1.3930.98
95_I277_L1.3780.98
291_D295_R1.3780.98
11_T14_G1.3600.98
148_C169_C1.3570.98
28_I202_V1.3560.98
28_I205_L1.3460.98
150_H170_E1.3420.97
177_K182_F1.3310.97
19_M283_L1.3310.97
187_L216_P1.3170.97
43_D46_S1.3100.97
190_R194_C1.3040.97
286_K290_E1.2950.97
183_F214_V1.2940.97
178_P185_E1.2940.97
151_E179_D1.2930.97
14_G18_Y1.2930.97
12_L279_L1.2830.96
60_L82_L1.2700.96
13_E17_R1.2610.96
143_C169_C1.2600.96
13_E16_A1.2580.96
288_E292_L1.2510.96
18_Y229_P1.2510.96
75_H78_P1.2470.96
58_Y66_I1.2470.96
31_V35_I1.2250.95
45_R50_G1.2230.95
101_R104_K1.2210.95
104_K130_D1.2070.95
208_M276_C1.2060.95
31_V121_E1.2040.94
33_A36_S1.1980.94
142_H179_D1.1900.94
73_K144_V1.1890.94
49_T53_D1.1730.93
37_T43_D1.1690.93
97_H135_H1.1670.93
150_H171_D1.1580.93
152_Y176_V1.1510.93
208_M272_C1.1500.92
18_Y24_C1.1410.92
33_A135_H1.1320.92
65_A68_E1.1290.92
115_Q135_H1.1230.91
76_P175_L1.1140.91
31_V100_M1.1110.91
233_I279_L1.1080.91
177_K185_E1.1010.90
188_P193_S1.1000.90
290_E295_R1.0980.90
214_V218_A1.0960.90
33_A45_R1.0940.90
84_K164_E1.0940.90
76_P79_F1.0890.90
133_E137_T1.0820.89
122_R131_L1.0810.89
144_V174_S1.0810.89
111_R132_V1.0800.89
17_R20_Q1.0750.89
45_R115_Q1.0720.89
141_S157_M1.0720.89
233_I268_W1.0710.88
134_A217_F1.0660.88
77_E81_A1.0580.88
254_G257_F1.0550.87
184_G214_V1.0470.87
232_L239_G1.0470.87
205_L221_I1.0440.87
32_G36_S1.0430.87
97_H115_Q1.0390.86
99_F276_C1.0390.86
274_Q277_L1.0380.86
91_F119_T1.0380.86
181_V185_E1.0360.86
71_Y78_P1.0350.86
99_F103_L1.0300.86
19_M22_E1.0290.86
65_A71_Y1.0250.85
224_A264_R1.0220.85
82_L86_L1.0200.85
30_L217_F1.0140.85
60_L177_K1.0140.85
67_F79_F1.0130.84
269_L272_C1.0090.84
36_S42_P1.0050.84
132_V190_R1.0050.84
289_L293_V1.0050.84
16_A282_L1.0040.84
92_K96_C1.0020.84
44_F50_G1.0010.83
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  
4rmhA10.96051000.117Contact Map
2hjhA20.91451000.186Contact Map
1q14A10.87171000.187Contact Map
4iaoA20.91121000.19Contact Map
4bn4A10.89471000.195Contact Map
1q1aA10.8981000.201Contact Map
5btrA301000.21Contact Map
4kxqA10.89471000.231Contact Map
1yc5A10.75661000.251Contact Map
3u31A10.84541000.255Contact 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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