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rac1

ID: 1501027031 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 192 (171)
Sequences: 26450 (16156.2)
Seq/Len: 154.678
Nf(neff/√len): 1235.5

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: 154.678).

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
11_D92_N3.2221.00
22_S162_Q2.8201.00
113_V168_V2.7161.00
84_L114_G2.3521.00
19_L81_C2.3491.00
155_L171_E2.3141.00
81_C115_T2.2491.00
79_L113_V2.0741.00
77_V172_A2.0161.00
7_V75_T1.9841.00
153_K171_E1.9701.00
84_L117_L1.9531.00
82_F154_Y1.9301.00
171_E175_A1.9071.00
87_P141_Q1.8951.00
98_Y102_R1.8691.00
171_E174_R1.8221.00
117_L163_R1.8221.00
139_Y143_L1.7991.00
8_V20_L1.7751.00
113_V157_C1.7191.00
80_I93_V1.6881.00
45_M50_P1.6611.00
43_N52_N1.6581.00
19_L165_L1.6181.00
145_M149_I1.6101.00
86_S89_S1.6081.00
142_G146_A1.5611.00
114_G156_E1.5531.00
82_F114_G1.5531.00
4_I176_V1.5011.00
143_L147_K1.4941.00
77_V176_V1.4841.00
157_C168_V1.4821.00
111_I155_L1.4411.00
83_S86_S1.4181.00
100_E103_H1.3890.99
136_P140_P1.3590.99
115_T159_A1.3550.99
138_T141_Q1.3500.99
144_A148_E1.3370.99
53_L173_I1.3280.99
92_N96_K1.3120.99
43_N50_P1.2930.99
164_G167_T1.2830.99
175_A178_C1.2770.99
142_G154_Y1.2760.99
21_I25_T1.2680.99
18_C159_A1.2560.99
102_R110_I1.2490.99
79_L172_A1.2450.98
153_K175_A1.2420.98
85_V119_L1.2250.98
83_S116_K1.1900.98
99_P103_H1.1770.98
166_K170_D1.1700.97
90_F94_R1.1550.97
64_Y68_R1.1450.97
120_R123_K1.1450.97
28_F160_L1.1330.97
6_C77_V1.1230.97
139_Y156_E1.1200.96
111_I168_V1.1180.96
109_P175_A1.1140.96
61_Q64_Y1.1100.96
145_M148_E1.1050.96
111_I171_E1.0950.96
96_K100_E1.0940.96
144_A147_K1.0900.96
141_Q144_A1.0750.95
118_D158_S1.0740.95
143_L146_A1.0640.95
135_T138_T1.0620.95
99_P102_R1.0580.95
75_T78_F1.0540.95
64_Y67_L1.0530.95
142_G145_M1.0530.95
5_K54_G1.0500.94
65_D68_R1.0480.94
19_L159_A1.0470.94
72_Y100_E1.0410.94
117_L156_E1.0390.94
137_I141_Q1.0380.94
82_F142_G1.0370.94
78_F101_V1.0350.94
8_V79_L1.0310.94
87_P91_E1.0240.93
146_A149_I1.0210.93
80_I98_Y1.0160.93
17_T57_D1.0110.93
167_T170_D1.0050.93
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  
2j0vA40.92711000.248Contact Map
1m7bA10.92711000.249Contact Map
2q3hA10.89061000.252Contact Map
1mh1A10.94271000.253Contact Map
2atxA20.93231000.263Contact Map
4mitA40.93231000.266Contact Map
3regA20.89061000.267Contact Map
3oesA10.81771000.27Contact Map
3bwdD10.81251000.274Contact Map
2iwrA10.86461000.276Contact 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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