OPENSEQ.org
1e4c

ID: 1515876663 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 215 (209)
Sequences: 6644 (3523.1)
Seq/Len: 31.789
Nf(neff/√len): 243.7

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: 31.789).

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
59_D63_K4.7711.00
97_H183_T3.1261.00
179_Q183_T3.0631.00
37_G57_F2.8781.00
6_L32_V2.8461.00
162_V166_K2.8291.00
38_M78_M2.7121.00
9_Q165_E2.4571.00
97_H179_Q2.2401.00
39_L55_I2.1951.00
87_A160_C2.1631.00
100_A183_T2.0961.00
4_N8_R2.0681.00
149_A174_V2.0601.00
127_P153_Q2.0581.00
37_G65_E2.0311.00
11_I52_E2.0031.00
97_H182_L1.9421.00
8_R12_D1.9271.00
79_A138_E1.8931.00
34_Y39_L1.8671.00
96_V179_Q1.8551.00
91_V167_A1.8511.00
134_R138_E1.8051.00
89_A164_L1.7521.00
195_S198_E1.7441.00
51_T54_H1.7141.00
196_D200_A1.6911.00
88_N163_N1.6611.00
39_L57_F1.6531.00
79_A82_Q1.6351.00
163_N166_K1.5871.00
183_T186_A1.5861.00
79_A83_S1.5651.00
8_R52_E1.5541.00
94_H155_H1.5491.00
5_K9_Q1.5141.00
10_I30_V1.5051.00
58_I74_W1.4961.00
161_E166_K1.4771.00
61_N82_Q1.4761.00
15_L19_R1.4691.00
11_I15_L1.4591.00
3_R57_F1.4491.00
96_V100_A1.4291.00
157_L174_V1.4281.00
20_L172_H1.4161.00
105_N153_Q1.4151.00
13_T168_L1.4121.00
10_I55_I1.3880.99
93_N171_A1.3860.99
76_F140_V1.3790.99
31_S81_Y1.3790.99
92_H155_H1.3730.99
148_K170_L1.3600.99
159_A171_A1.3580.99
139_H142_L1.3570.99
97_H175_E1.3440.99
181_Y185_L1.3390.99
127_P142_L1.3200.99
16_E20_L1.3090.99
31_S90_V1.3070.99
32_V89_A1.3020.99
32_V164_L1.2960.99
101_V185_L1.2950.99
124_P147_R1.2920.99
84_R87_A1.2900.99
3_R7_A1.2900.99
106_R185_L1.2830.99
129_A139_H1.2770.99
144_L160_C1.2520.99
40_I71_Q1.2510.99
18_T48_E1.2240.98
83_S141_A1.2150.98
78_M82_Q1.2090.98
3_R39_L1.2090.98
157_L171_A1.1950.98
138_E142_L1.1870.98
152_L158_I1.1810.98
102_S151_L1.1590.97
45_I54_H1.1570.97
108_I178_A1.1530.97
98_C157_L1.1480.97
50_L54_H1.1460.97
76_F158_I1.1420.97
14_C30_V1.1240.97
99_T102_S1.1240.97
3_R6_L1.1140.96
182_L186_A1.1100.96
176_V179_Q1.0840.96
42_P45_I1.0810.95
17_M30_V1.0680.95
13_T164_L1.0630.95
17_M91_V1.0630.95
9_Q12_D1.0630.95
38_M74_W1.0590.95
16_E19_R1.0560.95
81_Y90_V1.0550.95
84_R160_C1.0520.95
6_L9_Q1.0500.94
194_L198_E1.0490.94
38_M60_G1.0490.94
149_A159_A1.0440.94
161_E170_L1.0400.94
123_I174_V1.0390.94
101_V181_Y1.0290.94
34_Y57_F1.0250.93
80_A87_A1.0230.93
175_E179_Q1.0210.93
3_R37_G1.0130.93
33_R88_N1.0070.93
5_K8_R1.0030.93
200_A204_E1.0020.92
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  
1e4cP10.95811000.044Contact Map
4c24A10.95351000.059Contact Map
2opiA20.93951000.109Contact Map
3ocrA20.98141000.113Contact Map
1k0wA60.93021000.129Contact Map
2v9lA10.98141000.137Contact Map
4m6rA40.93021000.14Contact Map
2fk5A20.86981000.146Contact Map
2z7bA10.98141000.156Contact Map
4xxfA10.94421000.16Contact 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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