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b1

ID: 1518105022 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 191 (187)
Sequences: 312 (191.4)
Seq/Len: 1.668
Nf(neff/√len): 14.0

Jackhmmer Results: (2016_04)
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: 1.668).

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
76_C81_V2.5541.00
158_L162_F2.4721.00
103_C107_P2.3751.00
76_C103_C1.8670.97
5_L9_Q1.7580.96
59_N146_V1.6720.94
66_L76_C1.6670.94
75_P81_V1.6530.93
103_C109_S1.6220.93
12_G16_A1.5800.91
90_L93_T1.5640.91
76_C164_P1.5340.90
90_L163_W1.5250.89
17_L68_G1.5130.89
90_L94_E1.4820.87
137_S146_V1.4600.86
109_S112_N1.4530.86
106_I120_V1.4140.84
128_Q136_F1.3740.81
178_V182_Q1.3700.81
179_K182_Q1.3690.81
138_A145_S1.3650.81
159_F163_W1.3550.80
153_G173_L1.3480.80
4_K10_K1.3420.79
38_V173_L1.3380.79
30_T146_V1.3160.77
29_I136_F1.3110.77
68_G72_P1.3030.76
75_P90_L1.2970.76
76_C90_L1.2900.75
41_L116_A1.2710.74
23_M167_L1.2670.73
168_L175_I1.2640.73
165_T168_L1.2620.73
53_C135_C1.2550.72
126_K129_E1.2430.71
59_N136_F1.2300.70
90_L96_T1.2260.70
88_A173_L1.2240.70
49_Q95_D1.2190.69
171_G175_I1.1910.67
65_E69_K1.1910.67
26_C147_L1.1880.66
27_A171_G1.1860.66
23_M182_Q1.1840.66
35_V77_L1.1810.66
50_E136_F1.1740.65
163_W171_G1.1660.64
76_C94_E1.1650.64
76_C79_V1.1610.64
103_C163_W1.1590.64
150_R158_L1.1590.64
177_M185_S1.1540.63
19_L23_M1.1530.63
17_L72_P1.1420.62
53_C76_C1.1400.62
66_L164_P1.1300.61
54_H68_G1.1240.60
27_A49_Q1.1240.60
72_P109_S1.1240.60
157_L168_L1.1210.60
133_F136_F1.1200.60
87_W146_V1.1150.59
74_Y81_V1.1110.59
123_V148_F1.1090.59
76_C107_P1.1010.58
11_R14_T1.0890.56
39_L42_Y1.0880.56
60_I170_G1.0870.56
138_A165_T1.0810.56
81_V107_P1.0790.55
17_L33_I1.0790.55
53_C81_V1.0540.53
90_L103_C1.0500.52
27_A147_L1.0500.52
70_K76_C1.0480.52
6_V136_F1.0480.52
5_L11_R1.0460.52
9_Q18_C1.0450.52
73_Q120_V1.0400.51
20_G171_G1.0390.51
183_Y186_I1.0380.51
156_A167_L1.0360.51
57_E166_F1.0340.51
17_L102_Q1.0330.51
19_L177_M1.0320.50
56_I87_W1.0320.50
68_G109_S1.0150.49
80_N147_L1.0150.49
170_G181_N1.0130.48
5_L188_A1.0100.48
134_Y140_R1.0080.48
158_L177_M1.0050.48
68_G171_G1.0050.48
75_P150_R1.0050.48
169_T173_L1.0040.47
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  
2m8rA10.199240.941Contact Map
3wu2F20.172814.50.947Contact Map
1rh5B10.23564.80.957Contact Map
2zxeG10.20424.70.957Contact Map
4w25210.24614.20.958Contact Map
3uh0A10.31413.70.959Contact Map
2m20A20.20423.70.96Contact Map
2ww9B10.23563.70.96Contact Map
3mp7B10.22513.20.961Contact Map
2jo1A10.2672.70.962Contact 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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