OPENSEQ.org
knl1_extra

ID: 1517333265 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 159 (135)
Sequences: 372 (265.7)
Seq/Len: 2.756
Nf(neff/√len): 22.9

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: 2.756).

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
23_R26_T2.5161.00
148_W151_W2.0661.00
79_L102_E2.0421.00
148_W152_K1.5790.96
105_E115_F1.5490.96
18_T26_T1.5250.95
118_F149_Y1.5230.95
88_D151_W1.4860.95
27_V60_E1.4720.94
103_A106_E1.4130.92
88_D91_A1.4130.92
36_A59_D1.4030.92
11_I94_Q1.3300.89
7_Q62_A1.3110.88
107_A153_L1.2850.87
92_Y155_W1.2740.86
27_V32_L1.2640.86
90_T132_Q1.2530.85
2_I140_N1.2520.85
13_F81_L1.2510.85
84_A88_D1.2430.84
6_F155_W1.2420.84
30_G117_E1.2380.84
65_L68_F1.2370.84
84_A151_W1.2310.83
141_M152_K1.2300.83
18_T23_R1.2280.83
6_F118_F1.2220.83
111_T154_Q1.2120.82
111_T155_W1.2020.81
82_Y155_W1.1900.80
96_C126_Q1.1770.79
1_S153_L1.1760.79
5_F137_K1.1680.79
34_P70_V1.1650.78
147_Q158_Q1.1630.78
89_L137_K1.1570.78
92_Y96_C1.1520.77
93_I115_F1.1380.76
8_M119_A1.1120.74
115_F121_V1.1100.74
114_L145_K1.1100.74
117_E125_E1.1060.73
26_T110_V1.1030.73
87_R158_Q1.1030.73
9_T121_V1.1000.73
94_Q140_N1.0980.72
130_I134_K1.0920.72
79_L144_A1.0910.72
85_V137_K1.0890.72
154_Q158_Q1.0850.71
11_I77_P1.0840.71
118_F126_Q1.0820.71
86_A97_K1.0780.70
64_P129_L1.0780.70
31_Q157_E1.0770.70
9_T115_F1.0710.70
116_K144_A1.0630.69
77_P80_D1.0620.69
143_T154_Q1.0390.66
118_F140_N1.0380.66
16_E152_K1.0350.66
22_P26_T1.0270.65
116_K119_A1.0260.65
60_E116_K1.0240.65
9_T14_M1.0200.64
144_A147_Q1.0170.64
2_I156_V1.0150.64
19_M23_R1.0070.63
17_L144_A1.0050.63
111_T142_G1.0040.62
60_E143_T1.0000.62
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  
4bt9A20.5668.90.94Contact Map
2ve7C20.6737.90.941Contact Map
1gl2D10.34597.20.942Contact Map
3viqB20.44036.70.943Contact Map
4eveA10.65416.30.944Contact Map
1gmjA40.40255.20.946Contact Map
4a1nA10.45915.10.946Contact Map
1o5hA20.748450.946Contact Map
4j2cA20.59124.90.946Contact Map
1fyhA20.46544.80.947Contact 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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