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OPENSEQ.org

pglB_aln

ID: 1418615554 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 200 (185)
Sequences: 3824 (2921.7)
Seq/Len: 20.670
Nf(neff/√len): 214.8

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: 20.670).

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
7_R11_I3.6261.00
28_L91_L3.3481.00
35_N81_P2.8921.00
61_S86_L2.8351.00
45_E53_P2.8341.00
31_L82_F2.8221.00
158_W162_N2.7541.00
100_V135_I2.7471.00
43_I55_K2.7321.00
45_E55_K2.5041.00
85_K89_A2.4321.00
138_W142_N2.3021.00
18_L98_W2.2421.00
108_V136_T2.1161.00
170_K174_L2.0111.00
151_E154_S2.0071.00
9_I13_A2.0031.00
127_R161_D2.0021.00
48_G133_P1.9401.00
33_R38_S1.8691.00
138_W158_W1.7951.00
28_L86_L1.7611.00
29_I40_V1.7481.00
15_A101_L1.7341.00
90_S144_R1.7031.00
28_L59_F1.6691.00
108_V172_L1.6401.00
33_R40_V1.6391.00
131_M160_T1.6381.00
139_A152_K1.6221.00
14_S18_L1.6111.00
41_F57_V1.6051.00
10_D106_S1.6031.00
43_I57_V1.5991.00
32_I35_N1.5871.00
57_V99_N1.5861.00
13_A107_L1.5561.00
137_G140_Q1.4981.00
25_F59_F1.4931.00
47_P53_P1.4771.00
114_L117_Y1.4461.00
174_L178_K1.4371.00
17_G21_L1.4151.00
27_V31_L1.3950.99
82_F86_L1.3900.99
21_L25_F1.3670.99
6_K168_D1.3630.99
17_G97_L1.3490.99
32_I36_L1.3420.99
14_S101_L1.3300.99
17_G107_L1.3270.99
98_W102_K1.3230.99
6_K10_D1.3200.99
158_W167_L1.3180.99
11_I15_A1.3090.99
177_K181_I1.3050.99
143_G147_L1.3030.99
97_L107_L1.2980.99
113_L117_Y1.2970.99
90_S152_K1.2890.99
7_R14_S1.2720.99
39_P64_D1.2670.99
49_K132_K1.2660.99
53_P115_M1.2530.99
117_Y121_Y1.2450.98
137_G152_K1.2420.98
107_L172_L1.2300.98
113_L149_W1.2120.98
30_Y34_K1.1850.98
138_W171_I1.1850.98
179_V184_G1.1820.98
88_T182_K1.1790.98
128_R156_D1.1770.98
159_Y168_D1.1620.97
39_P60_R1.1550.97
44_R56_M1.1460.97
13_A17_G1.1380.97
11_I14_S1.1370.97
165_F169_M1.1300.97
127_R130_E1.1290.97
19_I22_S1.1160.96
172_L176_V1.1150.96
113_L139_A1.1050.96
114_L121_Y1.0880.96
33_R36_L1.0780.95
18_L22_S1.0780.95
140_Q156_D1.0750.95
15_A19_I1.0720.95
138_W167_L1.0460.94
57_V102_K1.0440.94
94_L97_L1.0410.94
115_M119_P1.0410.94
11_I101_L1.0380.94
142_N174_L1.0170.93
113_L118_L1.0160.93
128_R152_K1.0090.93
51_G129_H1.0030.93
148_S151_E1.0000.92
138_W155_C1.0000.92
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: (06Sep14)
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  
3hinA20.3955.50.969Contact Map
2k44A10.1352.60.973Contact Map
4ezcA30.2952.30.974Contact Map
3wguG20.17520.975Contact Map
4k84A20.4220.975Contact Map
2clyA20.0951.90.975Contact Map
2yjtD10.4651.70.976Contact Map
8tfvA10.1051.70.976Contact Map
2bzwB10.1351.60.976Contact Map
1xqoA10.521.60.976Contact 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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