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1an0

ID: 1506711061 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 188 (170)
Sequences: 38465 (20728.7)
Seq/Len: 226.265
Nf(neff/√len): 1589.8

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: 226.265).

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
21_S161_Q3.2731.00
154_V170_E3.0811.00
10_D91_N2.8191.00
83_V113_G2.7831.00
18_L80_C2.4741.00
78_L112_V2.4711.00
80_C114_T2.4621.00
170_E173_L2.3171.00
112_V167_V2.3161.00
170_E174_A2.1521.00
152_K170_E2.1481.00
112_V156_C2.1001.00
116_I155_E2.0721.00
113_G155_E1.9661.00
6_V74_T1.9111.00
17_C158_A1.8591.00
116_I162_K1.8401.00
97_V109_F1.7961.00
114_T158_A1.7641.00
78_L171_A1.7441.00
83_V116_I1.7391.00
7_V19_L1.7361.00
79_V97_V1.7151.00
76_V171_A1.6881.00
81_F111_L1.6881.00
4_K53_G1.6841.00
81_F153_Y1.6671.00
163_G166_N1.6641.00
142_E146_R1.6331.00
3_I175_A1.6091.00
156_C167_V1.5541.00
18_L167_V1.5501.00
52_L172_I1.5441.00
110_L154_V1.5391.00
78_L110_L1.5281.00
18_L164_L1.5101.00
84_V118_L1.4871.00
138_P142_E1.4861.00
143_K147_D1.4771.00
42_T51_T1.4671.00
110_L170_E1.4501.00
21_S164_L1.3810.99
82_S115_Q1.3720.99
7_V78_L1.3720.99
76_V110_L1.3570.99
50_Y172_I1.2860.99
81_F113_G1.2830.99
97_V101_T1.2820.99
82_S85_S1.2690.99
141_A145_A1.2420.98
86_P140_T1.2320.98
165_K169_D1.2210.98
79_V92_V1.2140.98
5_C76_V1.2040.98
22_Y168_F1.2020.98
44_M49_P1.1920.98
20_I28_P1.1810.98
137_T140_T1.1800.98
166_N169_D1.1790.98
113_G153_Y1.1700.97
98_P102_H1.1670.97
174_A177_E1.1410.97
2_T53_G1.1340.97
85_S88_S1.1270.97
108_P174_A1.1260.97
144_L148_L1.1170.96
164_L168_F1.1160.96
18_L22_Y1.1030.96
152_K174_A1.1000.96
172_I176_L1.0840.96
78_L167_V1.0810.95
112_V154_V1.0710.95
168_F171_A1.0710.95
117_D157_S1.0670.95
18_L158_A1.0670.95
169_D173_L1.0600.95
166_N170_E1.0590.95
115_Q118_L1.0400.94
77_F107_T1.0350.94
4_K9_G1.0300.94
99_E102_H1.0300.94
56_D59_G1.0270.94
143_K146_R1.0160.93
87_S90_E1.0130.93
4_K55_F1.0110.93
83_V119_R1.0030.93
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  
1mh1A10.95741000.18Contact Map
1m7bA10.94681000.184Contact Map
2atxA20.94681000.19Contact Map
2j0vA40.94151000.192Contact Map
3regA20.90431000.192Contact Map
2q3hA10.90961000.194Contact Map
4mitA40.94681000.195Contact Map
3bwdD10.82981000.201Contact Map
2j1lA10.82981000.213Contact Map
2wkqA10.94151000.215Contact 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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