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CrvA after CC

ID: 1513199725 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 197 (196)
Sequences: 382 (321.5)
Seq/Len: 1.949
Nf(neff/√len): 23.0

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: 1.949).

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
145_N163_H4.2671.00
80_N98_V3.1631.00
135_S152_T2.8291.00
88_Q153_P2.0060.99
70_S87_M1.9370.99
158_L181_V1.8730.98
140_D152_T1.7960.97
169_K172_Y1.7670.97
74_R88_Q1.7050.96
158_L163_H1.6340.95
93_A98_V1.6060.94
135_S153_P1.5620.93
135_S150_G1.5540.93
139_N169_K1.5440.92
144_I163_H1.5300.92
152_T169_K1.4990.91
142_V154_V1.4920.90
74_R87_M1.4790.90
182_N185_D1.4740.90
139_N152_T1.4500.89
161_G181_V1.3870.86
140_D169_K1.3550.84
141_S168_S1.3450.83
77_F85_T1.3260.82
76_G83_Y1.3170.81
142_V167_V1.2680.78
187_V191_L1.2660.78
95_P115_E1.2600.77
103_L131_V1.2540.77
142_V150_G1.2520.76
78_E83_Y1.2520.76
150_G153_P1.2500.76
145_N181_V1.2460.76
158_L161_G1.2270.74
70_S135_S1.2050.73
166_T176_N1.1880.71
75_S79_G1.1860.71
138_Y142_V1.1750.70
143_T166_T1.1620.69
18_T26_N1.1590.68
101_C169_K1.1580.68
146_G149_Y1.1530.68
101_C104_L1.1500.67
137_Q140_D1.1470.67
72_M77_F1.1460.67
152_T167_V1.1360.66
86_Q93_A1.1350.66
141_S148_N1.1140.64
131_V161_G1.1060.63
137_Q169_K1.1040.63
95_P142_V1.0970.62
137_Q152_T1.0890.61
138_Y159_P1.0840.61
167_V175_Y1.0840.61
145_N161_G1.0770.60
164_Q176_N1.0730.60
5_S25_A1.0670.59
78_E85_T1.0670.59
2_R49_T1.0670.59
81_N135_S1.0660.59
101_C156_L1.0630.58
29_Q52_A1.0600.58
143_T165_V1.0580.58
72_M75_S1.0520.57
79_G104_L1.0500.57
149_Y157_V1.0490.57
90_Q176_N1.0470.57
79_G102_K1.0440.56
105_N158_L1.0420.56
179_I188_W1.0420.56
145_N149_Y1.0300.55
17_T25_A1.0290.55
119_A163_H1.0240.54
6_V43_N1.0190.54
103_L136_D1.0180.54
83_Y111_C1.0110.53
167_V170_E1.0090.53
39_T45_I1.0070.52
13_T28_G1.0030.52
91_L166_T1.0020.52
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  
4u3sB1068.40.924Contact Map
1h8lA10.928944.40.934Contact Map
3cmgA10.6853340.938Contact Map
3mn8A40.9289320.939Contact Map
4jklA20.649728.60.941Contact Map
2nsmA10.893426.90.942Contact Map
3fn9A40.680223.10.943Contact Map
3lpfA20.715722.10.944Contact Map
3iduA20.5279190.945Contact Map
4q1zA10.4213190.945Contact 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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