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KNL1-2-rwd

ID: 1507225013 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 148 (141)
Sequences: 155 (91.7)
Seq/Len: 1.099
Nf(neff/√len): 7.7

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: 1.099).

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 > 50% 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
75_F84_F2.4270.99
22_C31_M2.1580.98
93_Y115_I1.8100.93
7_L12_V1.6830.88
45_L83_K1.5870.84
115_I136_I1.5760.84
98_P102_T1.5570.83
95_P128_Y1.5510.82
2_L25_Q1.5330.81
125_E131_N1.5040.79
8_I16_E1.4940.79
109_N115_I1.4860.78
59_Y131_N1.4600.77
29_P105_N1.3980.72
111_S114_D1.3770.70
118_I137_Y1.3660.70
100_P117_T1.3510.68
4_V46_G1.3450.68
90_L102_T1.3230.66
59_Y64_I1.2580.60
94_Y128_Y1.2400.59
114_D135_Q1.2330.58
45_L100_P1.2240.57
103_I114_D1.2010.55
119_L123_P1.1900.54
31_M43_R1.1770.53
28_L35_F1.1630.51
22_C32_L1.1530.50
48_E94_Y1.1460.50
2_L16_E1.1410.49
31_M61_L1.1380.49
113_D130_K1.1360.49
27_Q57_P1.1340.49
124_L140_L1.1330.48
35_F130_K1.1310.48
49_I67_N1.1260.48
20_K23_T1.1200.47
37_L47_E1.1200.47
11_Y20_K1.1170.47
34_E79_A1.1130.47
117_T123_P1.1130.47
26_H115_I1.1050.46
2_L5_H1.1020.46
21_T115_I1.0950.45
49_I112_Q1.0860.44
48_E85_E1.0840.44
8_I126_N1.0800.43
92_A102_T1.0760.43
43_R84_F1.0750.43
12_V20_K1.0710.43
16_E24_T1.0710.43
77_S122_V1.0690.42
96_S138_Q1.0670.42
37_L41_H1.0640.42
90_L106_H1.0600.42
22_C43_R1.0590.41
62_M69_N1.0580.41
128_Y140_L1.0560.41
35_F113_D1.0560.41
44_L134_K1.0560.41
31_M79_A1.0540.41
63_N71_L1.0530.41
49_I127_N1.0520.41
32_L36_S1.0510.41
92_A98_P1.0490.41
24_T36_S1.0470.40
14_E57_P1.0380.40
69_N136_I1.0370.39
119_L122_V1.0360.39
27_Q89_F1.0350.39
13_E16_E1.0310.39
53_K114_D1.0310.39
57_P70_E1.0290.39
127_N131_N1.0230.38
74_L85_E1.0200.38
51_Y119_L1.0160.38
3_L20_K1.0120.37
46_G55_W1.0100.37
7_L49_I1.0100.37
11_Y58_N1.0090.37
6_K49_I1.0020.36
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  
4nfaA10.94591000.051Contact Map
4y1lC1059.20.922Contact Map
1jatB10.709551.20.926Contact Map
2yz0A10.777310.935Contact Map
1jatA10.702730.40.935Contact Map
4ccgA20.743225.70.937Contact Map
2r0jA10.682424.40.938Contact Map
2a7lA20.702724.10.938Contact Map
1ayzA30.702722.30.939Contact Map
1yh2A10.729720.90.94Contact 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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