GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0823

ID: 1403033653 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 296 (281)
Sequences: 14089 (10330.8)
Seq/Len: 50.139
Nf(neff/√len): 616.3

HHblits Results: (2013_03)
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: 50.139).

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
94_R134_A3.2071.00
37_T261_E2.9811.00
28_A61_E2.7531.00
64_A101_S2.7461.00
93_K129_L2.7171.00
73_L102_L2.5221.00
229_P275_V2.5011.00
75_W105_L2.4511.00
90_D132_G2.4321.00
37_T41_N2.4301.00
228_T278_Q2.3521.00
272_P275_V2.1911.00
228_T275_V2.1731.00
5_P12_A2.0791.00
90_D128_D2.0391.00
75_W96_A2.0231.00
105_L135_L1.9451.00
109_L158_A1.9251.00
239_G269_R1.9151.00
93_K108_L1.8821.00
243_T276_C1.8741.00
95_S99_G1.8501.00
32_R62_A1.8281.00
232_S262_R1.8051.00
128_D132_G1.8041.00
177_Q181_N1.8041.00
4_R15_A1.7801.00
41_N264_A1.7551.00
128_D131_K1.7491.00
32_R65_S1.7291.00
109_L186_I1.7271.00
32_R61_E1.7251.00
38_A43_V1.7201.00
273_T277_A1.7101.00
127_Q131_K1.7061.00
231_W269_R1.7051.00
178_A185_V1.6991.00
17_T45_S1.6651.00
223_E227_N1.6621.00
184_A249_T1.6551.00
46_F59_A1.6521.00
257_R261_E1.6491.00
244_E280_E1.6381.00
224_F278_Q1.6371.00
74_T109_L1.6361.00
41_N261_E1.6341.00
104_Y136_R1.6251.00
93_K105_L1.6141.00
57_K99_G1.6031.00
27_R30_D1.5931.00
225_L236_I1.5821.00
52_A92_L1.5771.00
67_E70_L1.5521.00
77_L89_L1.5511.00
90_D125_G1.5501.00
86_P90_D1.5181.00
86_P128_D1.5021.00
11_V137_G1.4901.00
129_L135_L1.4851.00
32_R36_F1.4751.00
135_L138_L1.4711.00
34_L260_I1.4681.00
35_V62_A1.4491.00
254_A260_I1.4271.00
231_W235_D1.4241.00
37_T40_E1.4181.00
39_L71_L1.3900.99
232_S235_D1.3860.99
254_A259_E1.3640.99
94_R98_E1.3560.99
9_T137_G1.3400.99
11_V72_F1.3340.99
37_T257_R1.3310.99
137_G157_T1.3300.99
30_D33_A1.3190.99
261_E265_A1.3160.99
176_R180_Q1.3100.99
90_D94_R1.3040.99
239_G243_T1.3010.99
125_G128_D1.2990.99
57_K98_E1.2980.99
148_P180_Q1.2960.99
36_F40_E1.2940.99
77_L108_L1.2920.99
56_L96_A1.2870.99
91_A95_S1.2830.99
265_A268_E1.2800.99
148_P152_A1.2790.99
126_L138_L1.2780.99
260_I264_A1.2760.99
258_Q261_E1.2660.99
95_S98_E1.2650.99
161_S185_V1.2650.99
36_F62_A1.2590.99
68_R102_L1.2540.99
148_P177_Q1.2490.99
86_P125_G1.2460.98
173_H176_R1.2410.98
165_L279_I1.2350.98
222_Y233_A1.2320.98
72_F107_L1.2270.98
3_Y12_A1.2210.98
86_P124_S1.2170.98
222_Y279_I1.2120.98
86_P121_A1.2020.98
241_A250_V1.1870.98
130_Q154_D1.1840.98
68_R104_Y1.1800.98
179_S245_P1.1740.98
231_W236_I1.1720.98
130_Q157_T1.1690.97
277_A281_M1.1650.97
238_L266_V1.1640.97
236_I269_R1.1610.97
28_A32_R1.1580.97
107_L158_A1.1390.97
165_L237_C1.1360.97
228_T272_P1.1340.97
36_F65_S1.1330.97
229_P272_P1.1330.97
45_S186_I1.1230.97
239_G266_V1.1220.97
221_G224_F1.1130.96
100_L105_L1.1100.96
94_R132_G1.1040.96
57_K61_E1.1000.96
224_F227_N1.0910.96
61_E101_S1.0900.96
97_F134_A1.0890.96
60_G101_S1.0880.96
74_T186_I1.0810.95
148_P181_N1.0770.95
110_I126_L1.0740.95
278_Q281_M1.0730.95
14_S43_V1.0700.95
235_D262_R1.0660.95
122_F125_G1.0650.95
9_T157_T1.0600.95
235_D265_A1.0560.95
85_G88_T1.0550.95
168_G171_E1.0510.94
163_Y244_E1.0500.94
63_F71_L1.0460.94
14_S44_N1.0460.94
52_A88_T1.0450.94
29_N33_A1.0440.94
87_H91_A1.0370.94
127_Q130_Q1.0340.94
129_L132_G1.0330.94
258_Q262_R1.0300.94
242_L266_V1.0260.94
2_R15_A1.0190.93
178_A183_F1.0190.93
225_L229_P1.0190.93
129_L134_A1.0170.93
277_A280_E1.0170.93
140_V159_V1.0150.93
274_G277_A1.0150.93
33_A37_T1.0120.93
120_M149_G1.0100.93
44_N72_F1.0070.93
35_V46_F1.0060.93
244_E276_C1.0060.93
106_D136_R1.0050.93
45_S74_T1.0020.92
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: (14Jun14)
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  
1pyfA10.95611000.16Contact Map
1pz1A20.99321000.169Contact Map
3n2tA10.97971000.174Contact Map
3erpA20.92231000.176Contact Map
3v0sA10.86151000.176Contact Map
1ur3M10.92231000.181Contact Map
1ynpA20.94931000.184Contact Map
1lqaA20.96961000.185Contact Map
3lutA10.95951000.187Contact Map
3n6qA80.93241000.188Contact 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.

Page generated in 0.055 seconds.