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T4_HH

ID: 1500497483 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 164 (158)
Sequences: 606 (474.2)
Seq/Len: 3.835
Nf(neff/√len): 37.7

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: 3.835).

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
31_H70_D3.7591.00
125_R128_E3.0771.00
105_Q142_T2.5001.00
92_D95_R2.4991.00
93_A97_A2.4831.00
117_S132_N2.4141.00
105_Q143_P2.2531.00
8_R29_I2.2361.00
13_L63_A2.0461.00
10_D148_R2.0231.00
59_T62_E2.0131.00
77_G108_E2.0101.00
18_Y26_T1.9451.00
134_A139_Y1.8561.00
13_L29_I1.7940.99
28_G63_A1.7420.99
8_R64_E1.7290.99
133_L153_F1.7220.99
31_H104_F1.7170.99
6_M101_N1.7000.99
29_I63_A1.6700.99
24_Y32_L1.6360.99
70_D104_F1.6240.99
103_V111_V1.6180.99
116_N132_N1.5940.98
120_M128_E1.5010.97
60_K63_A1.4610.97
29_I60_K1.4470.97
4_F68_N1.4460.96
58_I66_L1.4420.96
58_I63_A1.4390.96
19_K25_Y1.4360.96
7_L101_N1.4300.96
29_I67_F1.3950.95
146_A149_V1.3600.95
26_T105_Q1.3300.94
10_D101_N1.3220.93
127_D131_V1.3220.93
8_R60_K1.3210.93
7_L29_I1.3040.93
128_E132_N1.3000.93
132_N137_R1.3000.93
17_I25_Y1.2960.93
17_I27_I1.2940.92
98_A153_F1.2580.91
15_L63_A1.2380.90
17_I55_N1.2370.90
16_K57_V1.2370.90
74_A103_V1.2330.90
17_I56_G1.2270.90
117_S133_L1.1720.86
139_Y150_I1.1560.85
120_M125_R1.1550.85
136_S141_Q1.1550.85
91_L121_L1.1440.85
98_A149_V1.1330.84
102_M106_M1.1270.83
134_A150_I1.1150.83
102_M110_G1.1050.82
105_Q149_V1.1020.82
151_T154_R1.0900.81
92_D156_G1.0830.80
72_D75_V1.0760.79
27_I58_I1.0700.79
20_D23_G1.0600.78
31_H66_L1.0480.77
62_E65_K1.0440.76
90_S124_K1.0390.76
144_N148_R1.0350.76
147_K151_T1.0350.76
6_M10_D1.0280.75
88_Y96_R1.0200.74
117_S120_M1.0180.74
44_S47_D1.0140.73
93_A129_A1.0130.73
6_M97_A1.0120.73
15_L58_I1.0110.73
106_M145_R1.0000.72
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  
4epiA111000.113Contact Map
2qb0B20.98171000.132Contact Map
1swyA10.99391000.138Contact Map
4e97A20.99391000.141Contact Map
4zwjA401000.146Contact Map
4httA201000.152Contact Map
4xesA101000.159Contact Map
4yx7C201000.163Contact Map
1wthA10.99391000.179Contact Map
4iapA20.99391000.207Contact 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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