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T0836

ID: 1404168992 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (166)
Sequences: 184 (87.9)
Seq/Len: 1.108
Nf(neff/√len): 6.8

HHblits Results: (2013_03)
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: 1.108).

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
49_F97_A2.4430.99
62_F91_F2.2460.99
99_W143_T1.9290.95
50_G95_A1.9020.95
95_A197_A1.8590.94
180_L183_R1.7820.92
91_F94_A1.7650.91
61_N188_L1.7490.91
50_G197_A1.7330.90
132_F135_I1.5900.84
56_L91_F1.5900.84
95_A146_F1.5820.84
114_E175_A1.5330.81
115_A150_W1.4980.79
154_W180_L1.4880.79
50_G135_I1.4870.79
142_A146_F1.4840.78
154_W158_K1.4440.76
75_L78_A1.4330.75
47_V197_A1.3940.72
137_T142_A1.3840.71
50_G142_A1.3840.71
95_A135_I1.3460.68
65_I119_G1.3450.68
178_A183_R1.3370.67
100_V104_L1.3370.67
62_F89_F1.3350.67
95_A142_A1.3270.67
156_N160_A1.3230.66
47_V50_G1.2960.64
64_Q67_V1.2930.64
135_I192_M1.2910.63
61_N65_I1.2710.62
39_Q137_T1.2700.62
156_N177_T1.2610.61
45_L118_L1.2420.59
166_A173_K1.2400.59
163_I168_A1.2330.58
59_Y190_I1.2120.56
62_F158_K1.2050.56
50_G195_T1.1980.55
112_L164_V1.1920.54
179_M183_R1.1900.54
47_V193_L1.1790.53
49_F193_L1.1570.51
61_N89_F1.1520.51
84_A161_L1.1520.51
72_P89_F1.1460.50
78_A83_I1.1390.49
45_L101_M1.1330.49
51_I133_T1.1300.48
114_E179_M1.1020.46
82_Y123_G1.1000.46
68_M80_S1.0940.45
51_I104_L1.0930.45
60_F88_L1.0920.45
61_N186_T1.0890.45
73_A78_A1.0850.44
156_N174_A1.0820.44
62_F65_I1.0810.44
156_N175_A1.0800.44
161_L178_A1.0790.44
64_Q179_M1.0780.43
56_L94_A1.0720.43
69_P142_A1.0640.42
77_P110_G1.0640.42
147_F158_K1.0550.41
71_I141_L1.0460.41
56_L160_A1.0460.41
110_G123_G1.0450.40
103_V146_F1.0450.40
95_A176_K1.0420.40
106_A139_M1.0400.40
132_F146_F1.0350.40
80_S83_I1.0310.39
127_G130_M1.0290.39
42_F108_N1.0270.39
118_L193_L1.0270.39
115_A169_D1.0210.38
173_K177_T1.0120.37
160_A183_R1.0090.37
65_I71_I1.0080.37
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: (28Jun14)
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  
1kqfC10.88734.50.974Contact Map
1j2rA40.30883.10.976Contact Map
3hd7A20.1522.30.978Contact Map
2hc9A10.31372.10.978Contact Map
3kzwA120.31371.50.98Contact Map
1c1yB10.26961.30.981Contact Map
3peiA10.33331.30.981Contact Map
3kr4A120.30391.30.981Contact Map
1gytA120.2991.20.981Contact Map
4l35A10.71081.10.981Contact 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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