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KNL1 C-term -force run

ID: 1507040272 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 150 (149)
Sequences: 130 (84.3)
Seq/Len: 0.872
Nf(neff/√len): 6.9

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: 0.872).

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
126_F135_F1.9180.92
10_T109_N1.6620.83
73_C82_M1.6590.83
53_L76_Q1.5960.79
110_Y115_I1.5880.79
126_F131_A1.5000.73
86_F147_S1.4670.71
4_F87_S1.4390.68
62_Y71_K1.4050.66
37_V149_P1.4040.66
11_I45_E1.4030.66
137_I140_F1.4010.65
108_P114_N1.3890.64
62_Y109_N1.3780.64
15_I79_L1.3680.63
55_V97_G1.3490.61
11_I41_S1.3430.61
128_S131_A1.3320.60
30_R71_K1.3180.58
88_L98_E1.2760.55
48_A86_F1.2670.54
122_L133_A1.2570.53
29_K68_S1.2500.52
108_P121_E1.2380.51
47_Q66_K1.2250.50
34_I100_I1.2220.50
10_T60_F1.2060.49
88_L92_H1.2030.48
73_C101_E1.1970.48
108_P113_M1.1900.47
4_F26_F1.1850.47
79_L115_I1.1850.47
82_M94_R1.1830.46
71_K74_T1.1800.46
82_M112_L1.1780.46
39_F44_D1.1730.46
85_E119_N1.1640.45
48_A52_S1.1570.44
38_N118_N1.1510.44
109_N122_L1.1470.43
59_I67_E1.1420.43
58_L63_V1.1180.41
93_C97_G1.1110.40
127_S136_E1.1080.40
88_L97_G1.1030.39
5_T15_I1.1010.39
15_I86_F1.0890.38
112_L143_A1.0880.38
125_L136_E1.0870.38
31_Y117_I1.0830.38
101_E112_L1.0830.38
24_F47_Q1.0820.38
2_A12_Q1.0790.37
84_E119_N1.0790.37
36_D45_E1.0730.37
78_Q140_F1.0700.37
5_T53_L1.0690.37
13_L17_F1.0680.37
67_E75_T1.0650.36
78_Q149_P1.0640.36
51_S99_E1.0620.36
109_N113_M1.0610.36
34_I63_V1.0600.36
15_I21_V1.0570.36
126_F132_F1.0550.35
27_L34_I1.0520.35
6_F13_L1.0480.35
93_C98_E1.0460.35
24_F27_L1.0420.34
127_S137_I1.0370.34
124_L132_F1.0360.34
64_E69_W1.0330.34
11_I40_Q1.0280.33
106_W126_F1.0270.33
3_V90_V1.0250.33
57_K64_E1.0210.33
39_F43_L1.0200.33
36_D70_K1.0170.32
76_Q121_E1.0170.32
17_F139_L1.0110.32
48_A57_K1.0040.31
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  
4nfaA10.98100-0.012Contact Map
4ccgA20.4242.50.936Contact Map
1fxtA10.386737.90.937Contact Map
1jatA10.433.50.939Contact Map
1yh2A10.406732.80.94Contact Map
1jatB10.393332.40.94Contact Map
2r0jA10.3831.50.94Contact Map
1tteA10.393328.30.941Contact Map
4y1lC1027.40.942Contact Map
1wzvA20.3827.10.942Contact 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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