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cdc42

ID: 1501026965 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 191 (172)
Sequences: 25639 (15807.4)
Seq/Len: 149.064
Nf(neff/√len): 1205.3

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: 149.064).

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_N3.2641.00
22_S162_Q2.8591.00
113_V168_V2.7741.00
19_L81_C2.3541.00
155_V171_E2.3281.00
84_V114_G2.2771.00
81_C115_T2.2731.00
79_L113_V2.0521.00
153_K171_E2.0421.00
77_V172_A2.0081.00
7_V75_T1.9731.00
84_V117_I1.9471.00
82_F154_Y1.9441.00
98_V102_T1.9231.00
171_E175_A1.8831.00
117_I163_K1.8601.00
171_E174_L1.8571.00
8_V20_L1.7961.00
87_P141_T1.7941.00
113_V157_C1.7711.00
139_P143_E1.7341.00
80_V93_V1.7121.00
145_L149_L1.6911.00
86_S89_S1.6611.00
45_M50_P1.6611.00
142_A146_A1.6571.00
19_L165_L1.5921.00
82_F114_G1.5281.00
114_G156_E1.5181.00
4_I176_A1.5071.00
157_C168_V1.4901.00
143_E147_R1.4701.00
77_V176_A1.4201.00
53_L173_I1.4151.00
83_S86_S1.4010.99
115_T159_A1.3950.99
111_L155_V1.3910.99
138_T141_T1.3730.99
144_K148_D1.3500.99
100_E103_H1.3280.99
21_I25_T1.3150.99
102_T110_F1.3080.99
164_G167_N1.2990.99
92_N96_K1.2940.99
175_A178_E1.2870.99
139_P156_E1.2700.99
79_L172_A1.2570.99
153_K175_A1.2540.99
142_A154_Y1.2460.98
135_K138_T1.2430.98
18_C159_A1.2380.98
43_T50_P1.2270.98
43_T52_T1.2220.98
99_P103_H1.2210.98
5_K54_G1.2200.98
83_S116_Q1.2020.98
85_V119_L1.1940.98
28_F160_L1.1810.98
166_K170_D1.1760.98
142_A145_L1.1640.97
111_L171_E1.1590.97
145_L148_D1.1520.97
134_Q138_T1.1420.97
149_L152_V1.1380.97
111_L168_V1.1240.97
144_K147_R1.1230.97
90_F94_K1.1200.96
136_P140_E1.1190.96
143_E146_A1.1140.96
6_C77_V1.1140.96
118_D158_S1.1060.96
75_T78_F1.0950.96
65_D68_R1.0840.96
78_F101_I1.0700.95
46_I49_E1.0690.95
146_A149_L1.0660.95
17_T57_D1.0650.95
99_P102_T1.0620.95
64_Y68_R1.0500.94
8_V79_L1.0490.94
109_P175_A1.0480.94
90_F93_V1.0480.94
141_T144_K1.0480.94
72_Y100_E1.0450.94
22_S26_N1.0420.94
98_V149_L1.0240.93
117_I156_E1.0200.93
94_K148_D1.0170.93
32_Y35_T1.0130.93
138_T142_A1.0120.93
87_P91_E1.0090.93
80_V98_V1.0080.93
45_M48_G1.0040.93
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  
1m7bA10.93191000.239Contact Map
2j0vA40.92671000.239Contact Map
2q3hA10.89531000.24Contact Map
1mh1A10.94761000.244Contact Map
2atxA20.93721000.253Contact Map
3regA20.89531000.256Contact Map
4mitA40.93721000.257Contact Map
2iwrA10.86911000.261Contact Map
3bwdD10.81681000.262Contact Map
3q3jB10.90581000.267Contact 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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