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T4_Jack

ID: 1500497499 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 164 (148)
Sequences: 1167 (906.5)
Seq/Len: 7.885
Nf(neff/√len): 74.5

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: 7.885).

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
125_R128_E3.4841.00
31_H70_D3.4801.00
93_A97_A3.4441.00
142_T146_A2.9631.00
146_A149_V2.5821.00
92_D95_R2.4131.00
13_L63_A2.3691.00
10_D148_R2.1091.00
8_R64_E2.0881.00
117_S132_N2.0391.00
77_G108_E2.0041.00
105_Q142_T1.9661.00
19_K25_Y1.9111.00
24_Y32_L1.8971.00
120_M132_N1.8721.00
132_N135_K1.8471.00
13_L29_I1.8251.00
31_H104_F1.8241.00
144_N148_R1.8021.00
58_I66_L1.7561.00
28_G63_A1.7291.00
29_I63_A1.6971.00
120_M125_R1.6891.00
142_T149_V1.6761.00
74_A103_V1.6211.00
58_I63_A1.6181.00
8_R29_I1.6091.00
143_P146_A1.6051.00
103_V111_V1.5591.00
120_M128_E1.5321.00
15_L63_A1.5061.00
142_T148_R1.4600.99
149_V152_T1.4470.99
27_I58_I1.3870.99
116_N132_N1.3860.99
70_D104_F1.3620.99
102_M106_M1.3600.99
95_R126_W1.3420.99
13_L60_K1.3180.98
74_A78_I1.2940.98
91_L121_L1.2830.98
59_T62_E1.2780.98
151_T154_R1.2740.98
18_Y26_T1.2700.98
29_I67_F1.2590.98
138_W141_Q1.2530.98
60_K63_A1.2310.97
111_V118_L1.2260.97
17_I27_I1.2230.97
93_A96_R1.2200.97
28_G58_I1.2140.97
143_P148_R1.1930.96
143_P149_V1.1910.96
17_I25_Y1.1780.96
87_V91_L1.1710.96
121_L126_W1.1530.96
149_V153_F1.1450.95
148_R152_T1.1370.95
128_E132_N1.1360.95
29_I104_F1.1280.95
19_K23_G1.1270.95
15_L58_I1.1260.95
116_N119_R1.1230.95
87_V122_Q1.1060.94
105_Q143_P1.1060.94
33_L36_S1.1040.94
60_K64_E1.0940.94
76_R80_R1.0900.93
16_K57_V1.0830.93
96_R100_I1.0730.93
133_L153_F1.0700.93
6_M10_D1.0640.92
29_I64_E1.0560.92
116_N120_M1.0530.92
143_P147_K1.0520.92
106_M111_V1.0440.91
17_I55_N1.0250.90
6_M101_N1.0240.90
74_A104_F1.0210.90
10_D101_N1.0190.90
25_Y54_T1.0060.89
19_K24_Y1.0050.89
134_A139_Y1.0010.89
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  
1swyA111000.122Contact Map
4httA201000.135Contact Map
4e97A211000.137Contact Map
4epiA111000.138Contact Map
4zwjA401000.152Contact Map
2qb0B20.98781000.154Contact Map
4yx7C201000.164Contact Map
1wthA111000.169Contact Map
4xesA101000.196Contact Map
4iapA20.99391000.221Contact 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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