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SNRK

ID: 1505262285 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 337 (277)
Sequences: 21219 (12231.2)
Seq/Len: 76.603
Nf(neff/√len): 734.9

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: 76.603).

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
111_F196_L3.8481.00
242_Q247_R3.6381.00
104_E230_S3.0111.00
26_H29_T2.9301.00
239_R249_A2.9061.00
24_A35_V2.8801.00
23_L32_K2.8631.00
235_D257_H2.7951.00
24_A33_V2.7291.00
118_I192_L2.7201.00
11_K23_L2.6781.00
137_V148_T2.6481.00
189_I240_M2.6401.00
8_D27_V2.6241.00
200_V233_C2.6151.00
62_Q68_R2.5981.00
119_S123_K2.5041.00
8_D25_R2.4481.00
119_S252_E2.4151.00
84_E146_K2.4021.00
113_Q144_L2.3751.00
131_L195_I2.3471.00
115_V254_I2.3421.00
235_D239_R2.3271.00
35_V82_I2.3071.00
183_D186_A2.2101.00
196_L236_L2.1951.00
111_F192_L2.1861.00
12_T20_V2.1791.00
117_A147_L2.0791.00
115_V192_L2.0481.00
119_S255_E2.0151.00
12_T22_K2.0131.00
244_D247_R1.9551.00
114_I136_V1.9451.00
25_R32_K1.9411.00
70_Y84_E1.9281.00
104_E259_W1.9071.00
12_T15_R1.8831.00
10_D25_R1.8541.00
6_L26_H1.7501.00
92_F134_E1.7221.00
103_N106_L1.7031.00
107_A200_V1.6981.00
250_S253_E1.6801.00
25_R30_G1.6461.00
22_K37_V1.6421.00
136_V145_V1.6401.00
31_E70_Y1.6331.00
189_I251_L1.6321.00
249_A254_I1.6081.00
40_K74_D1.5761.00
10_D23_L1.5591.00
23_L85_L1.5581.00
63_H120_Y1.5471.00
236_L240_M1.5311.00
208_E213_E1.5251.00
198_M204_P1.5001.00
67_V83_L1.4901.00
239_R257_H1.4851.00
136_V195_I1.4771.00
221_C243_R1.4751.00
69_L81_L1.4651.00
37_V80_Y1.4551.00
33_V82_I1.4511.00
201_C229_V1.4491.00
239_R242_Q1.4401.00
173_A187_V1.4201.00
132_K168_S1.4161.00
68_R84_E1.3880.99
232_E258_P1.3730.99
240_M254_I1.3460.99
110_Y145_V1.3390.99
139_F144_L1.3310.99
87_D141_K1.3180.99
234_K238_T1.3170.99
65_N116_H1.3080.99
249_A253_E1.3010.99
208_E217_M1.2910.99
54_E57_C1.2850.99
114_I145_V1.2830.99
239_R253_E1.2830.99
208_E214_T1.2740.99
123_K252_E1.2710.99
133_P171_Y1.2700.99
26_H31_E1.2660.99
60_L155_K1.2640.99
90_D93_D1.2620.99
186_A250_S1.2460.98
32_K85_L1.2420.98
118_I131_L1.2390.98
33_V70_Y1.2350.98
236_L249_A1.2230.98
67_V86_G1.2220.98
130_D135_N1.2190.98
236_L254_I1.2100.98
140_E144_L1.1900.98
236_L257_H1.1900.98
113_Q145_V1.1850.98
242_Q249_A1.1790.98
194_V204_P1.1750.98
197_F205_P1.1730.98
108_K262_G1.1670.97
54_E58_M1.1660.97
231_K234_K1.1600.97
86_G146_K1.1580.97
67_V148_T1.1550.97
189_I254_I1.1530.97
108_K259_W1.1520.97
60_L124_L1.1440.97
98_H106_L1.1420.97
167_G172_S1.1350.97
37_V78_K1.1300.97
35_V80_Y1.1300.97
152_F166_C1.1280.97
7_Y71_E1.1240.97
21_V34_A1.1230.97
229_V233_C1.1100.96
57_C153_S1.1000.96
237_I241_L1.0960.96
176_I187_V1.0820.96
232_E262_G1.0740.95
173_A176_I1.0740.95
55_V81_L1.0680.95
131_L147_L1.0680.95
115_V255_E1.0680.95
116_H255_E1.0630.95
69_L72_V1.0590.95
107_A199_L1.0440.94
132_K135_N1.0330.94
170_A190_W1.0280.94
116_H119_S1.0260.94
251_L255_E1.0140.93
128_H131_L1.0100.93
178_L219_M1.0070.93
94_Y102_L1.0020.92
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  
3fe3A20.94071000.184Contact Map
4bkyA10.91691000.188Contact Map
4redA20.95551000.196Contact Map
3h4jB20.97331000.199Contact Map
4cfeA20.9051000.201Contact Map
4gv1A10.93181000.23Contact Map
4lqsA10.85161000.232Contact Map
4ejnA10.80121000.234Contact Map
3utoA20.97631000.237Contact Map
4aw2A10.92881000.238Contact 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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