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slm

ID: 1518439588 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 171 (168)
Sequences: 971 (573.9)
Seq/Len: 5.780
Nf(neff/√len): 44.3

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: 5.780).

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
118_D121_K3.1211.00
47_G86_P2.7081.00
15_E89_K2.6681.00
11_D121_K2.6481.00
85_D88_E2.0511.00
153_A156_G2.0021.00
52_H81_H1.9551.00
48_K85_D1.8231.00
115_H123_V1.7451.00
104_V145_M1.7141.00
160_M164_I1.6731.00
41_R51_S1.6200.99
116_P123_V1.5730.99
27_N37_D1.4890.99
33_V163_V1.4700.99
38_V41_R1.4220.98
2_K49_L1.4000.98
78_V95_S1.3820.98
126_Q156_G1.3820.98
42_H50_H1.3740.98
94_K109_R1.3550.97
20_A106_V1.3450.97
48_K83_V1.3080.97
53_R82_S1.2940.96
76_T99_S1.2890.96
7_E125_T1.2790.96
46_S50_H1.2610.96
43_I85_D1.2520.95
156_G161_E1.2480.95
27_N33_V1.2460.95
34_V39_L1.2400.95
44_D50_H1.2360.95
90_T113_K1.2250.95
33_V55_L1.2170.94
50_H83_V1.2040.94
13_P16_T1.2020.94
117_Q121_K1.1950.94
137_L141_L1.1870.93
52_H79_Q1.1820.93
32_S148_T1.1780.93
52_H59_W1.1650.93
110_L160_M1.1600.92
27_N159_A1.1480.92
159_A164_I1.1380.91
59_W76_T1.1170.90
152_N155_K1.1170.90
110_L124_L1.1130.90
24_K153_A1.1110.90
21_A24_K1.1060.90
39_L43_I1.1050.90
59_W156_G1.1030.90
86_P152_N1.1010.90
110_L164_I1.0980.89
92_E109_R1.0950.89
113_K123_V1.0950.89
44_D48_K1.0940.89
16_T19_T1.0900.89
63_S66_K1.0890.89
145_M148_T1.0850.89
147_S151_S1.0800.88
102_N130_I1.0730.88
36_V126_Q1.0700.88
64_I140_Y1.0700.88
84_V91_M1.0620.87
7_E11_D1.0590.87
137_L154_S1.0560.87
57_T132_V1.0560.87
25_Y54_L1.0420.86
28_P162_W1.0380.86
147_S150_S1.0350.85
159_A163_V1.0340.85
68_L72_A1.0340.85
49_L54_L1.0300.85
13_P157_R1.0260.85
154_S158_E1.0260.85
41_R82_S1.0250.85
14_W89_K1.0240.85
11_D118_D1.0230.84
123_V141_L1.0220.84
10_F93_L1.0220.84
41_R54_L1.0160.84
92_E111_I1.0140.84
124_L157_R1.0070.83
48_K87_V1.0070.83
7_E18_T1.0050.83
23_Q67_S1.0030.83
21_A28_P1.0030.83
76_T145_M1.0020.83
24_K162_W1.0010.83
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  
4xhrA201000.061Contact Map
4xizA201000.064Contact Map
2mouA10.9006860.914Contact Map
2r55A20.88378.40.921Contact Map
2psoA30.871378.20.921Contact Map
1em2A10.88374.70.924Contact Map
3qszA20.853871.90.925Contact Map
2d4rA40.842167.20.928Contact Map
3p0lA40.84863.40.929Contact Map
4n0gC20.818749.20.935Contact 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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