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mak3

ID: 1514415605 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 176 (155)
Sequences: 21126 (15176.6)
Seq/Len: 136.297
Nf(neff/√len): 1219.0

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: 136.297).

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
6_K51_V3.4451.00
104_I135_F2.7281.00
104_I156_L2.6551.00
65_I103_A2.4671.00
6_K15_Q2.4461.00
97_K133_M2.4261.00
25_A87_E2.3561.00
97_K132_G2.2581.00
9_D14_E2.1471.00
102_I105_D2.1381.00
62_I90_Y2.1201.00
117_L130_Y2.0961.00
49_I61_P2.0511.00
114_E155_I2.0081.00
50_A95_I1.9721.00
138_M155_I1.8751.00
131_E137_R1.8611.00
63_G86_V1.8531.00
102_I106_K1.8351.00
127_L131_E1.8301.00
48_Y102_I1.8231.00
101_E133_M1.7911.00
67_C103_A1.7911.00
137_R140_R1.7841.00
104_I115_I1.7721.00
106_K109_R1.7641.00
52_D62_I1.6911.00
128_N131_E1.6611.00
90_Y93_H1.6281.00
25_A88_S1.6241.00
18_S21_K1.5991.00
137_R152_F1.5611.00
18_S61_P1.4901.00
97_K101_E1.4831.00
100_V133_M1.4561.00
51_V61_P1.4411.00
17_A33_I1.4251.00
60_I87_E1.4111.00
87_E90_Y1.3950.99
60_I89_T1.3930.99
127_L137_R1.3760.99
12_N15_Q1.3590.99
126_A130_Y1.3550.99
79_G112_C1.3530.99
78_R114_E1.3510.99
67_C107_M1.3350.99
127_L154_L1.3320.99
106_K110_E1.2950.99
96_A129_L1.2910.99
86_V95_I1.2660.99
7_P106_K1.2590.99
65_I99_L1.2540.99
4_V51_V1.2480.99
21_K25_A1.2400.98
60_I90_Y1.2290.98
52_D90_Y1.2170.98
33_I37_R1.1990.98
20_K24_D1.1870.98
18_S60_I1.1790.98
121_V150_D1.1590.97
140_R150_D1.1390.97
105_D109_R1.1370.97
107_M115_I1.1340.97
51_V59_N1.1310.97
47_T66_V1.1290.97
48_Y106_K1.1220.97
108_Q156_L1.1060.96
115_I135_F1.1060.96
137_R154_L1.1030.96
8_L19_I1.1000.96
94_G97_K1.0980.96
98_K101_E1.0770.95
98_K102_I1.0680.95
100_V130_Y1.0600.95
22_L85_A1.0530.95
52_D93_H1.0480.94
52_D60_I1.0460.94
15_Q51_V1.0400.94
140_R152_F1.0380.94
129_L133_M1.0340.94
114_E157_P1.0200.93
119_T127_L1.0100.93
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  
4pv6C160.85899.80.298Contact Map
4kvxA20.846699.80.312Contact Map
2j8mA20.89299.80.317Contact Map
4r3lA10.846699.80.319Contact Map
2ob0A30.920599.80.321Contact Map
2reeA20.869399.80.333Contact Map
1tiqA20.880799.80.336Contact Map
2r7hA20.840999.80.339Contact Map
3kkwA10.835299.80.341Contact Map
3dr6A30.897799.80.342Contact 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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