OPENSEQ.org
1JM7

ID: 1516190191 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 200 (185)
Sequences: 273 (185.4)
Seq/Len: 1.476
Nf(neff/√len): 13.6

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: 1.476).

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
149_C152_C2.2860.99
27_C44_C2.0130.98
128_C131_C1.9700.98
39_C44_C1.8530.96
34_P39_C1.8040.95
27_C39_C1.7880.95
24_C27_C1.7870.95
41_H61_C1.7150.94
187_S192_L1.7010.93
128_C144_C1.6830.93
188_K195_D1.6800.93
138_P146_H1.5850.90
44_C47_C1.5510.88
34_P44_C1.5320.87
24_C39_C1.5170.87
146_H162_P1.4900.85
27_C34_P1.4820.85
34_P41_H1.4800.85
128_C152_C1.4740.84
27_C47_C1.4610.84
40_D145_E1.4470.83
138_P162_P1.4290.82
192_L195_D1.4280.82
48_M143_G1.4170.81
128_C149_C1.4130.81
187_S190_R1.3780.79
40_D146_H1.3760.78
189_L192_L1.3730.78
109_R117_A1.3710.78
39_C47_C1.3390.76
41_H64_C1.3310.75
144_C149_C1.3280.75
42_I79_F1.2950.72
142_G146_H1.2890.72
16_N28_L1.2860.72
188_K191_N1.2850.71
22_L119_L1.2820.71
24_C44_C1.2750.71
190_R193_L1.2730.70
144_C152_C1.2670.70
47_C145_E1.2570.69
38_K47_C1.2520.69
138_P183_I1.2500.68
38_K141_L1.2450.68
141_L148_F1.2390.67
24_C34_P1.2380.67
47_C129_S1.2260.66
33_E75_E1.2200.66
131_C144_C1.2060.64
38_K129_S1.1990.64
191_N194_H1.1990.64
75_E83_V1.1680.61
164_C176_N1.1680.61
109_R112_W1.1630.60
36_S86_L1.1580.60
43_F148_F1.1550.59
113_A116_R1.1540.59
107_D111_A1.1400.58
187_S195_D1.1380.58
34_P161_C1.1370.58
190_R194_H1.1330.57
164_C171_Q1.1300.57
187_S194_H1.1280.57
140_C147_I1.1220.56
18_M115_S1.1170.56
12_Q190_R1.1150.55
12_Q187_S1.1120.55
16_N19_Q1.0900.53
190_R195_D1.0870.53
131_C152_C1.0760.51
80_S84_E1.0560.49
161_C164_C1.0510.49
135_L179_L1.0510.49
27_C152_C1.0490.49
33_E46_F1.0450.48
41_H44_C1.0420.48
12_Q193_L1.0370.47
31_I34_P1.0360.47
62_P72_S1.0350.47
109_R113_A1.0350.47
127_R153_V1.0320.47
137_E150_S1.0290.47
44_C152_C1.0280.46
12_Q195_D1.0260.46
40_D164_C1.0230.46
188_K192_L1.0220.46
135_L146_H1.0200.46
127_R137_E1.0160.45
189_L195_D1.0130.45
61_C64_C1.0110.45
131_C149_C1.0070.44
42_I76_S1.0070.44
114_H118_A1.0060.44
39_C164_C1.0020.44
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  
4wz3B10.8451000.504Contact Map
4cfgA20.07599.80.62Contact Map
4ap4A10.56599.80.653Contact Map
1jm7A10.51599.60.691Contact Map
4kblA20.7399.50.709Contact Map
2c2lA40.46599.50.71Contact Map
2kreA10.4699.50.717Contact Map
2kr4A10.42599.50.717Contact Map
1z6uA20.4699.50.718Contact Map
2f42A10.4699.50.72Contact 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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