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Hp_ParB

ID: 1515167329 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 240 (223)
Sequences: 5128 (3325.6)
Seq/Len: 22.996
Nf(neff/√len): 222.7

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: 22.996).

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
35_E101_T4.3651.00
42_M81_R3.9111.00
138_K142_E3.3681.00
61_A96_L3.0561.00
178_A204_L3.0091.00
206_S210_Q2.9641.00
84_L91_L2.9601.00
207_I217_T2.7131.00
135_R176_Q2.5911.00
41_V84_L2.5061.00
40_E81_R2.3931.00
37_G40_E2.3781.00
148_Q163_A2.3501.00
69_L94_S2.3361.00
73_V102_I2.3181.00
158_S161_H2.2921.00
36_L104_A2.2421.00
58_E96_L2.1901.00
75_V104_A2.0831.00
177_N181_E2.0771.00
109_I117_V2.0581.00
57_L96_L2.0341.00
54_E96_L1.9821.00
131_L176_Q1.9711.00
76_V83_H1.9701.00
56_S126_E1.9271.00
110_E113_K1.9121.00
139_E143_S1.9081.00
58_E62_Q1.9061.00
94_S99_M1.8381.00
69_L103_K1.8251.00
57_L61_A1.8161.00
212_L220_L1.8131.00
91_L95_K1.7531.00
172_S200_Q1.7471.00
141_L151_L1.7251.00
38_I91_L1.7231.00
73_V84_L1.7161.00
36_L75_V1.6951.00
42_M83_H1.6861.00
86_A121_E1.6741.00
203_I220_L1.6721.00
54_E58_E1.6591.00
133_L165_I1.6261.00
216_Q219_D1.6231.00
41_V75_V1.6181.00
179_L189_A1.6161.00
37_G101_T1.6121.00
150_E153_K1.6051.00
48_P118_A1.5931.00
62_Q65_K1.5671.00
165_I186_S1.5621.00
135_R180_L1.5531.00
188_H214_V1.5521.00
76_V114_M1.5501.00
53_S56_S1.5491.00
206_S220_L1.5181.00
88_E92_R1.4801.00
94_S97_A1.4501.00
191_V217_T1.4381.00
64_I69_L1.4201.00
73_V104_A1.4191.00
129_N180_L1.4131.00
149_E153_K1.3960.99
137_Y155_V1.3870.99
175_V204_L1.3630.99
205_N209_G1.3250.99
76_V111_Q1.3250.99
174_K201_E1.3210.99
160_A163_A1.2970.99
116_E154_I1.2940.99
178_A208_I1.2670.99
173_S177_N1.2640.99
204_L208_I1.2510.99
133_L157_K1.2440.98
64_I94_S1.2420.98
199_K202_L1.2370.98
44_N114_M1.2360.98
177_N180_L1.2350.98
67_H113_K1.2320.98
178_A183_K1.2230.98
58_E61_A1.2230.98
56_S59_E1.2120.98
175_V200_Q1.1980.98
151_L162_V1.1960.98
35_E103_K1.1900.98
70_L74_L1.1850.98
137_Y151_L1.1680.97
85_I109_I1.1650.97
121_E125_R1.1470.97
40_E80_G1.1320.97
63_S120_I1.1270.97
94_S102_I1.1120.96
38_I94_S1.1080.96
61_A97_A1.1070.96
44_N83_H1.1060.96
67_H116_E1.1020.96
77_S80_G1.0960.96
161_H165_I1.0960.96
60_L89_R1.0670.95
52_F88_E1.0580.95
196_D199_K1.0330.94
44_N118_A1.0250.93
203_I224_F1.0200.93
137_Y157_K1.0180.93
34_V106_V1.0170.93
157_K161_H1.0160.93
141_L148_Q1.0120.93
69_L102_I1.0090.93
149_E159_R1.0060.93
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  
4umkA401000.192Contact Map
1vz0A80.81000.234Contact Map
1r71A40.458399.90.577Contact Map
1vk1A10.766799.80.634Contact Map
1yzsA10.470899.80.641Contact Map
1xw3A10.42599.80.644Contact Map
3mkyB20.441799.60.715Contact Map
1zx4A20.479297.90.849Contact Map
2hwjA60.72597.30.866Contact Map
2w7nA20.492.10.905Contact 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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