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T0805

ID: 1401904884 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 214 (208)
Sequences: 2245 (1793)
Seq/Len: 10.793
Nf(neff/√len): 124.3

Jackhmmer Results: (2014_04_16)
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: 10.793).

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
34_E151_R3.0141.00
52_Q210_H2.6251.00
53_W140_A2.4551.00
29_R33_M2.3661.00
65_I170_V2.3041.00
29_R57_E2.2411.00
25_K191_Y2.2231.00
154_G192_T2.2111.00
169_K172_D2.1541.00
59_A63_K2.1441.00
7_V10_V2.0841.00
20_R188_P2.0761.00
145_C157_W1.9721.00
59_A62_K1.9651.00
205_A209_T1.9321.00
66_A76_Y1.8581.00
171_A183_Q1.8451.00
37_E40_L1.8381.00
153_L191_Y1.8151.00
28_P31_V1.7871.00
68_V173_V1.7851.00
141_V185_G1.7851.00
20_R156_C1.7681.00
149_R154_G1.7341.00
22_D25_K1.6971.00
166_G169_K1.6921.00
7_V11_L1.6851.00
33_M206_E1.6371.00
31_V153_L1.6281.00
6_S9_E1.6271.00
35_C148_L1.6121.00
64_A173_V1.6101.00
105_A108_M1.6041.00
145_C155_S1.5971.00
72_N75_G1.5661.00
61_K173_V1.5591.00
35_C144_F1.5521.00
94_M97_V1.5201.00
57_E212_N1.5151.00
60_A63_K1.5051.00
9_E13_T1.5041.00
112_P115_L1.4871.00
13_T149_R1.4771.00
61_K64_A1.4721.00
35_C189_I1.4641.00
27_V153_L1.4391.00
135_A159_T1.4331.00
5_L9_E1.3970.99
39_A144_F1.3880.99
38_L147_A1.3870.99
153_L189_I1.3860.99
120_K123_E1.3740.99
44_T51_W1.3710.99
119_L123_E1.3660.99
148_L189_I1.3460.99
73_A77_L1.2960.99
109_H113_V1.2930.99
141_V187_L1.2900.99
36_L55_F1.2860.99
12_T41_Q1.2860.99
33_M205_A1.2750.99
53_W208_V1.2740.99
40_L208_V1.2650.99
58_D61_K1.2590.99
130_G182_S1.2560.99
161_H186_L1.2540.99
137_L184_G1.2430.98
31_V151_R1.2420.98
75_G78_S1.2330.98
7_V150_S1.2310.98
104_L107_H1.2240.98
34_E38_L1.2230.98
148_L155_S1.2070.98
84_Y144_F1.1980.98
16_S156_C1.1970.98
45_G159_T1.1850.98
132_S159_T1.1830.98
117_P120_K1.1660.97
27_V31_V1.1640.97
38_L151_R1.1600.97
107_H110_R1.1420.97
32_L189_I1.1210.97
69_Y186_L1.1190.96
36_L209_T1.1110.96
61_K212_N1.1060.96
108_M111_A1.1050.96
78_S81_A1.0980.96
68_V169_K1.0890.96
19_K193_Q1.0660.95
139_P142_W1.0630.95
140_A208_V1.0630.95
131_V135_A1.0580.95
35_C153_L1.0550.95
72_N78_S1.0530.95
102_T107_H1.0460.94
93_R98_R1.0440.94
27_V32_L1.0370.94
26_P59_A1.0320.94
135_A138_F1.0290.94
44_T50_G1.0280.94
37_E205_A1.0210.93
177_P180_E1.0200.93
118_C123_E1.0140.93
102_T105_A1.0140.93
9_E12_T1.0030.93
75_G81_A1.0010.92
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: (29May14)
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  
3ge6A20.95331000.298Contact Map
3of4A30.93461000.302Contact Map
3gbhA40.94861000.303Contact Map
3gagA40.93931000.304Contact Map
2b67A40.89721000.306Contact Map
3gr3A20.92991000.306Contact Map
1vfrA20.92991000.306Contact Map
2h0uA10.86451000.307Contact Map
2hayA40.93461000.308Contact Map
1bkjA20.84111000.311Contact 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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