OPENSEQ.org
Rv2633c

ID: 1518566728 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 161 (146)
Sequences: 2176 (1581.3)
Seq/Len: 14.904
Nf(neff/√len): 130.9

HHblits Results: (2016_02)
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: 14.904).

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
12_T15_K3.2901.00
7_L114_I3.1471.00
10_H138_I2.4671.00
80_T94_E2.2291.00
123_T126_E2.2171.00
31_R92_E2.0011.00
15_K106_A1.9351.00
15_K103_E1.8951.00
48_I134_M1.7701.00
2_N119_P1.6961.00
137_R141_L1.6431.00
32_H36_D1.6321.00
51_D137_R1.5701.00
99_R103_E1.5631.00
56_A60_A1.5251.00
129_E133_K1.5001.00
70_E104_A1.4941.00
73_Q101_V1.4751.00
126_E129_E1.4601.00
72_R76_D1.4451.00
21_V92_E1.4000.99
43_D75_V1.3960.99
143_G146_L1.3850.99
18_G102_L1.3660.99
20_K34_L1.3400.99
22_G103_E1.3370.99
77_Q94_E1.3360.99
137_R140_Q1.3190.99
27_N30_E1.3170.99
14_L38_M1.3080.99
2_N127_L1.2940.99
107_D111_R1.2880.99
132_D136_A1.2770.99
144_S147_Y1.2700.99
22_G96_N1.2550.99
133_K136_A1.2530.99
7_L134_M1.2350.98
46_F74_V1.2340.98
2_N5_D1.2320.98
14_L106_A1.2310.98
69_A73_Q1.2040.98
64_I68_H1.2030.98
71_H109_E1.1940.98
53_Y118_T1.1880.98
65_T69_A1.1840.98
21_V95_W1.1710.98
4_Y119_P1.1690.97
33_V37_E1.1690.97
102_L106_A1.1530.97
8_K110_E1.1530.97
128_E132_D1.1480.97
74_V102_L1.1440.97
3_A134_M1.1430.97
39_L82_L1.1420.97
8_K12_T1.1360.97
30_E33_V1.1270.97
8_K119_P1.1240.97
54_Y108_V1.0990.96
35_F81_L1.0970.96
124_D128_E1.0950.96
24_A31_R1.0920.96
81_L95_W1.0920.96
42_L98_F1.0830.96
39_L78_L1.0820.96
38_M95_W1.0770.95
56_A130_L1.0710.95
6_V135_A1.0700.95
96_N100_T1.0690.95
127_L131_G1.0660.95
3_A48_I1.0660.95
143_G147_Y1.0560.95
46_F71_H1.0520.95
142_R145_P1.0410.94
36_D82_L1.0400.94
136_A140_Q1.0390.94
11_H45_H1.0330.94
20_K23_E1.0310.94
35_F82_L1.0260.94
108_V112_D1.0240.93
66_G108_V1.0160.93
104_A107_D1.0120.93
97_V100_T1.0090.93
47_R51_D1.0090.93
141_L145_P1.0020.92
20_K30_E1.0010.92
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  
2p0nA20.857199.70.424Contact Map
3caxA10.975299.70.451Contact Map
2hmqA40.5901940.819Contact Map
4xpxA1093.40.823Contact Map
3agtA20.714392.70.828Contact Map
2mhrA10.621191.80.832Contact Map
3u9jA20.8571780.862Contact Map
3d5aX10.69579.80.92Contact Map
3zeyT10.26717.50.924Contact Map
2b3tB10.46585.40.928Contact 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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