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T0834 -force run

ID: 1403892752 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 219 (219)
Sequences: 61 (52.3)
Seq/Len: 0.279
Nf(neff/√len): 3.5

Jackhmmer Results: (2014_04_16)
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: 0.279).

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
37_L89_S1.8070.60
14_F19_A1.8050.60
102_H210_N1.6400.49
185_L211_I1.6060.47
48_E196_S1.5580.43
2_S73_L1.5370.42
32_F164_S1.5310.42
30_T37_L1.5090.40
55_Q70_L1.5060.40
58_Y123_L1.5040.40
136_A211_I1.4990.40
37_L168_L1.4920.39
3_L6_R1.3920.33
2_S37_L1.3860.33
114_E157_S1.3810.32
113_A118_A1.3780.32
160_S164_S1.3600.31
32_F118_A1.3480.31
77_P104_G1.3450.30
13_L194_S1.3410.30
101_I128_H1.3220.29
138_G175_I1.3220.29
58_Y209_G1.3130.29
136_A168_L1.3110.29
7_I14_F1.3110.29
90_L102_H1.3070.28
3_L111_R1.3030.28
9_L59_K1.2950.28
31_D193_L1.2860.27
74_I116_Y1.2690.26
84_L163_G1.2640.26
134_N146_N1.2620.26
39_P117_P1.2510.25
135_A139_T1.2470.25
116_Y126_Y1.2380.25
60_L174_D1.2370.25
122_N157_S1.2260.24
151_A197_L1.2220.24
23_Y66_G1.2220.24
51_L81_T1.2210.24
80_F184_W1.2160.24
13_L183_T1.2140.24
207_Q218_H1.2110.23
5_E216_E1.2010.23
61_A211_I1.1940.23
70_L191_A1.1920.23
215_V218_H1.1850.22
91_S160_S1.1690.22
88_S167_D1.1590.21
91_S207_Q1.1460.21
188_A211_I1.1440.20
51_L77_P1.1380.20
130_Q149_E1.1340.20
14_F127_M1.1330.20
39_P131_E1.1240.20
117_P132_R1.1190.19
31_D107_T1.1170.19
61_A108_Y1.1150.19
4_P51_L1.1110.19
52_K173_G1.1050.19
17_N59_K1.0950.18
51_L104_G1.0950.18
154_A194_S1.0950.18
148_G175_I1.0940.18
168_L200_A1.0800.18
43_L46_T1.0780.18
155_L184_W1.0770.18
30_T182_E1.0760.18
23_Y213_W1.0730.18
110_F173_G1.0720.18
163_G188_A1.0700.17
128_H141_L1.0690.17
151_A178_L1.0690.17
136_A150_D1.0670.17
160_S188_A1.0640.17
188_A198_L1.0640.17
118_A186_T1.0620.17
130_Q159_A1.0610.17
83_S142_Y1.0600.17
41_S60_L1.0600.17
149_E154_A1.0580.17
8_D14_F1.0560.17
107_T170_L1.0560.17
155_L207_Q1.0560.17
23_Y82_R1.0540.17
166_S189_N1.0540.17
84_L160_S1.0540.17
162_F217_D1.0530.17
108_Y174_D1.0520.17
116_Y178_L1.0510.17
98_S176_Y1.0500.17
26_R29_Q1.0490.17
114_E202_N1.0490.17
21_T91_S1.0490.17
124_L166_S1.0470.17
136_A185_L1.0460.17
128_H131_E1.0380.16
59_K146_N1.0380.16
35_R163_G1.0350.16
15_D119_Q1.0320.16
79_V104_G1.0320.16
173_G177_Y1.0310.16
90_L108_Y1.0260.16
74_I218_H1.0250.16
11_V47_S1.0250.16
5_E184_W1.0230.16
30_T130_Q1.0200.16
80_F155_L1.0200.16
72_P141_L1.0150.15
174_D205_F1.0140.15
83_S195_Y1.0130.15
37_L133_P1.0090.15
2_S32_F1.0070.15
196_S199_S1.0060.15
83_S107_T1.0050.15
56_L87_G1.0040.15
9_L84_L1.0030.15
135_A171_R1.0020.15
107_T214_D1.0000.15
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: (05Jul14)
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  
3f0iA20.502325.80.967Contact Map
3rdwA20.48417.10.969Contact Map
1s3cA10.58458.90.973Contact Map
3fz4A10.49328.60.973Contact Map
3hshA60.25116.20.975Contact Map
3n3fA20.2425.90.975Contact Map
1pbuA10.64385.30.976Contact Map
2eboA30.2745.30.976Contact Map
1vw4b10.5895.10.976Contact Map
3gkxA20.49774.80.976Contact 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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