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ccr6

ID: 1515681596 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 374 (309)
Sequences: 2634 (1647.9)
Seq/Len: 8.524
Nf(neff/√len): 93.7

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: 8.524).

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
60_G96_V5.7021.00
87_N172_W3.5831.00
232_F236_F2.7071.00
229_F233_C2.6541.00
180_S184_V2.4001.00
111_W114_S2.3951.00
144_Y149_Q2.3261.00
77_A82_D2.3241.00
138_C171_V2.2561.00
116_A120_L2.2331.00
135_L168_C2.1091.00
188_K195_D1.9991.00
123_G127_I1.9031.00
123_G183_F1.8581.00
267_Q305_A1.8061.00
127_I176_V1.8011.00
67_V312_N1.7471.00
115_N187_Q1.7391.00
166_I170_V1.7171.00
144_Y148_V1.7161.00
172_W313_P1.6991.00
68_V86_L1.6951.00
118_C197_C1.6531.00
36_C288_C1.6141.00
273_V297_T1.6101.00
91_A172_W1.6061.00
255_V319_I1.5881.00
142_D157_R1.5571.00
67_V71_F1.5471.00
71_F86_L1.5421.00
234_Y313_P1.5391.00
101_F121_L1.5101.00
235_T239_K1.4670.99
267_Q312_N1.4550.99
130_N222_G1.4500.99
133_M137_T1.4410.99
44_F48_F1.4380.99
272_M276_V1.4260.99
293_L297_T1.4220.99
87_N135_L1.4210.99
231_I235_T1.4190.99
104_V113_F1.4170.99
47_L51_I1.4130.99
68_V93_I1.4070.99
87_N313_P1.3970.99
219_L275_L1.3930.99
238_V253_I1.3890.99
227_L264_L1.3640.99
144_Y232_F1.3570.99
49_V53_Y1.3480.99
230_M260_V1.3450.99
266_C304_L1.3370.99
140_S260_V1.3150.99
92_D132_G1.3130.99
118_C313_P1.3030.99
87_N168_C1.2940.98
98_T102_W1.2890.98
67_V313_P1.2770.98
63_G310_C1.2770.98
67_V317_A1.2750.98
267_Q313_P1.2710.98
142_D237_I1.2660.98
70_T323_F1.2660.98
219_L224_F1.2570.98
165_K169_L1.2560.98
62_L65_I1.2480.98
323_F327_F1.2450.98
91_A316_Y1.2310.98
83_V164_S1.2240.98
65_I93_I1.2200.97
92_D312_N1.2110.97
133_M263_F1.2100.97
141_M229_F1.2020.97
128_N168_C1.2010.97
223_F264_L1.1940.97
67_V267_Q1.1900.97
132_G308_H1.1900.97
115_N119_K1.1870.97
96_V320_G1.1830.97
136_L230_M1.1800.97
134_L137_T1.1730.97
91_A131_C1.1530.96
87_N91_A1.1470.96
60_G310_C1.1470.96
257_I315_L1.1390.96
92_D308_H1.1320.96
63_G306_F1.1200.95
84_Y164_S1.1150.95
99_L136_L1.1110.95
100_P313_P1.1100.95
190_N261_L1.1070.95
34_L38_L1.1040.95
50_P103_A1.1030.95
225_I279_A1.0960.94
98_T121_L1.0950.94
153_S157_R1.0930.94
264_L268_I1.0920.94
86_L90_I1.0920.94
234_Y260_V1.0890.94
146_A150_A1.0880.94
236_F239_K1.0820.94
187_Q200_K1.0710.94
234_Y254_R1.0710.94
118_C172_W1.0680.93
141_M233_C1.0650.93
118_C269_P1.0640.93
84_Y167_I1.0620.93
34_L37_S1.0610.93
223_F227_L1.0570.93
307_L311_L1.0550.93
67_V91_A1.0460.92
111_W313_P1.0420.92
83_V168_C1.0410.92
241_L252_A1.0410.92
135_L171_V1.0400.92
58_V62_L1.0370.92
137_T230_M1.0350.92
142_D256_I1.0350.92
61_L93_I1.0330.92
223_F313_P1.0320.92
33_M38_L1.0300.92
91_A140_S1.0300.92
100_P223_F1.0260.92
234_Y317_A1.0240.91
115_N301_T1.0210.91
33_M37_S1.0200.91
335_W340_K1.0200.91
274_L277_T1.0150.91
142_D252_A1.0130.91
162_P166_I1.0130.91
85_L139_I1.0110.91
139_I230_M1.0110.91
113_F117_T1.0070.90
134_L222_G1.0070.90
146_A157_R1.0050.90
80_M306_F1.0050.90
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: (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  
3oduA20.80481000.372Contact Map
4pxzA10.74061000.378Contact Map
4mbsA20.78611000.386Contact Map
3vw7A10.74061000.397Contact Map
2rh1A10.74331000.401Contact Map
4iarA10.72731000.402Contact Map
3uonA10.72731000.406Contact Map
4grvA10.75671000.409Contact Map
3pblA20.70321000.412Contact Map
4dklA10.7461000.414Contact 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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