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T0836 30-204

ID: 1405651922 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 175 (173)
Sequences: 630 (262.9)
Seq/Len: 3.642
Nf(neff/√len): 20.0

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: 3.642).

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
21_G66_A2.2071.00
33_F62_F1.9221.00
115_V119_N1.9011.00
32_N36_I1.7560.99
151_L154_R1.6900.99
125_W129_K1.6430.99
18_V21_G1.6000.98
92_A95_Y1.5990.98
64_W67_L1.5890.98
149_A154_R1.5700.98
62_F65_A1.5620.98
127_N131_A1.5000.97
150_M154_R1.4950.97
33_F36_I1.4840.97
33_F60_F1.4750.97
147_K151_L1.4610.96
154_R173_L1.4090.95
66_A69_T1.3940.95
134_I168_A1.3760.94
138_D141_A1.3620.94
127_N145_A1.3310.93
32_N35_Q1.3250.93
4_H41_Q1.3160.93
9_F13_F1.3120.92
70_W114_T1.3120.92
144_K148_T1.3070.92
130_I133_G1.2950.92
134_I139_A1.2900.92
117_F168_A1.2890.92
20_F68_A1.2710.91
125_W149_A1.2690.91
37_R46_L1.2610.90
131_A145_A1.2600.90
127_N148_T1.2560.90
16_L72_M1.2380.89
42_I46_L1.2340.89
43_P47_K1.2230.88
145_A159_L1.2200.88
91_L95_Y1.2160.88
131_A154_R1.2160.88
82_Y107_G1.2040.87
127_N157_T1.2020.87
40_P46_L1.2000.87
71_V75_L1.1920.87
130_I145_A1.1910.87
41_Q110_M1.1700.85
131_A135_V1.1510.84
55_A116_M1.1420.83
36_I44_A1.1360.83
27_L65_A1.1210.82
33_F37_R1.1130.81
131_A136_E1.1100.81
27_L62_F1.1070.81
39_M49_A1.1060.81
118_F122_V1.1010.80
125_W151_L1.1000.80
4_H32_N1.0990.80
25_I45_E1.0940.80
33_F45_E1.0940.80
43_P46_L1.0800.78
46_L53_Y1.0770.78
135_V151_L1.0730.78
32_N41_Q1.0720.78
123_F127_N1.0710.78
3_G116_M1.0710.78
149_A159_L1.0710.78
27_L58_A1.0690.77
32_N44_A1.0690.77
144_K147_K1.0680.77
113_A117_F1.0660.77
127_N149_A1.0570.76
121_W160_S1.0550.76
130_I137_A1.0540.76
99_V102_G1.0480.75
111_W115_V1.0470.75
42_I45_E1.0420.75
41_Q45_E1.0400.75
52_K55_A1.0370.74
36_I39_M1.0300.74
9_F12_I1.0290.73
39_M58_A1.0290.73
137_A144_K1.0270.73
158_L165_A1.0260.73
32_N37_R1.0250.73
32_N39_M1.0200.73
6_A32_N1.0180.72
142_K145_A1.0170.72
93_G97_P1.0080.71
147_K159_L1.0060.71
42_I49_A1.0050.71
13_F80_R1.0050.71
148_T159_L1.0010.71
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: (12Jul14)
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  
2qzuA10.38863.40.971Contact Map
2b34A80.3230.972Contact Map
2kluA10.36572.90.972Contact Map
3b5qA20.34292.60.973Contact Map
1c1yB10.31432.20.973Contact Map
1b4uB20.33711.90.975Contact Map
3wraA20.33711.80.975Contact Map
1ifpA10.17141.70.975Contact Map
1u6hB10.13711.60.975Contact Map
3ed4A40.37711.60.975Contact 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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