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T0825

ID: 1403119573 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 205 (200)
Sequences: 342 (297.5)
Seq/Len: 1.710
Nf(neff/√len): 21.0

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: 1.710).

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
82_H100_S3.4171.00
164_H186_D2.9531.00
164_H182_S2.8541.00
100_S110_W2.6741.00
82_H110_W2.4891.00
19_A23_K2.4171.00
123_H141_S2.3761.00
59_S69_W2.2250.99
141_S151_W2.1690.99
164_H184_S2.1530.99
41_H59_S2.0630.99
99_A139_I2.0030.99
66_V100_S1.9910.98
182_S192_W1.9240.98
140_A173_F1.8820.98
41_H69_W1.7810.96
99_A132_F1.7290.95
93_P136_G1.7100.95
82_H102_S1.7020.95
148_V182_S1.6790.94
79_L100_S1.6740.94
122_G151_W1.6640.94
107_V141_S1.5750.91
58_A98_I1.5460.90
61_S69_W1.5110.89
102_S110_W1.5100.89
81_G110_W1.5030.89
184_S188_T1.5010.89
44_S57_I1.4920.88
17_A57_I1.4170.84
164_H168_V1.3950.83
122_G141_S1.3940.83
41_H63_D1.3750.82
163_G192_W1.3280.79
123_H143_S1.3020.77
95_G101_A1.2790.75
40_G69_W1.2690.74
18_S28_W1.2690.74
36_Q148_V1.2610.74
129_G142_A1.2590.73
11_P54_G1.2550.73
25_V59_S1.2450.72
52_P95_G1.2400.72
24_T99_A1.2290.71
148_V168_V1.2210.70
91_F173_F1.2150.70
102_S106_T1.1900.67
123_H151_W1.1830.67
89_V184_S1.1790.66
81_G123_H1.1720.66
102_S151_W1.1610.65
99_A130_V1.1330.62
127_V151_W1.1220.61
143_S151_W1.1220.61
136_G140_A1.1180.60
13_G95_G1.1140.60
160_T183_A1.1100.59
88_G101_A1.1080.59
82_H86_V1.1060.59
181_A191_L1.1040.59
17_A50_F1.0980.58
25_V28_W1.0910.57
51_S96_Q1.0840.57
132_F180_I1.0840.57
151_W187_K1.0780.56
130_V145_D1.0740.56
151_W190_K1.0670.55
109_L132_F1.0640.55
67_K108_K1.0580.54
123_H145_D1.0560.54
46_W120_L1.0530.53
101_A127_V1.0370.52
170_G183_A1.0270.51
123_H148_V1.0250.50
60_A102_S1.0240.50
61_S193_N1.0230.50
41_H61_S1.0210.50
17_A154_N1.0200.50
4_V160_T1.0200.50
110_W151_W1.0190.50
150_L178_Q1.0180.50
67_K101_A1.0100.49
140_A180_I1.0070.48
123_H147_T1.0010.48
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: (14Jun14)
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  
2ymuA211000.219Contact Map
1vyhC1011000.234Contact Map
1nr0A10.99511000.235Contact Map
3sfzA10.98541000.251Contact Map
4lg9A111000.264Contact Map
3mkqA311000.264Contact Map
3w15A10.98541000.267Contact Map
3f3fA40.99511000.268Contact Map
3dwlC20.95121000.275Contact Map
4j87A111000.285Contact 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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