GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0825

ID: 1404798805 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 205 (205)
Sequences: 3668 (3170.2)
Seq/Len: 17.893
Nf(neff/√len): 221.4

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: 17.893).

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
66_V100_S2.1681.00
148_V182_S1.9501.00
123_H141_S1.8941.00
67_K78_T1.8751.00
82_H100_S1.8621.00
25_V59_S1.8391.00
99_A139_I1.8271.00
41_H59_S1.7541.00
108_K119_T1.7361.00
164_H182_S1.7121.00
56_T97_T1.7101.00
17_A50_F1.6901.00
107_V141_S1.6761.00
140_A173_F1.6751.00
75_L116_L1.6671.00
26_K37_T1.6341.00
55_Q96_Q1.6131.00
149_K160_T1.6051.00
17_A57_I1.5951.00
157_L198_L1.5691.00
140_A180_I1.5371.00
116_L157_L1.5171.00
88_G101_A1.5161.00
34_L75_L1.5011.00
137_Q178_Q1.4981.00
99_A132_F1.4951.00
74_Q115_Q1.4931.00
190_K201_T1.4911.00
77_Q118_Q1.4821.00
131_A172_A1.4711.00
156_Q197_Q1.4491.00
129_G142_A1.4321.00
33_Q74_Q1.4311.00
58_A91_F1.4281.00
52_P95_G1.4101.00
138_T179_T1.3930.99
96_Q137_Q1.3910.99
15_T56_T1.3870.99
50_F91_F1.3530.99
11_P54_G1.3490.99
111_N152_N1.3490.99
90_A131_A1.3490.99
121_T162_T1.3330.99
58_A98_I1.3250.99
152_N193_N1.3190.99
49_A90_A1.3170.99
8_A49_A1.3150.99
97_T138_T1.3090.99
34_L116_L1.3010.99
75_L157_L1.3000.99
118_Q159_Q1.2990.99
6_G19_A1.2940.99
80_T121_T1.2820.99
67_K75_L1.2800.99
36_Q118_Q1.2770.99
36_Q77_Q1.2740.99
91_F132_F1.2740.99
170_G183_A1.2690.99
128_W144_D1.2540.99
143_S147_T1.2540.99
75_L198_L1.2460.98
70_N111_N1.2440.98
14_Q55_Q1.2350.98
31_N113_N1.2240.98
56_T138_T1.2020.98
33_Q156_Q1.2020.98
34_L157_L1.2000.98
29_N70_N1.1990.98
77_Q159_Q1.1940.98
111_N193_N1.1840.98
87_W103_D1.1830.98
56_T179_T1.1830.98
15_T97_T1.1820.98
9_F50_F1.1820.98
47_G60_A1.1810.98
30_R71_R1.1750.98
159_Q200_Q1.1750.98
33_Q197_Q1.1740.98
18_S22_D1.1700.97
34_L198_L1.1670.97
71_R112_R1.1620.97
46_W62_D1.1570.97
117_L158_L1.1570.97
164_H184_S1.1490.97
74_Q156_Q1.1480.97
115_Q156_Q1.1370.97
82_H102_S1.1300.97
123_H143_S1.1280.97
112_R153_R1.1220.97
82_H86_V1.1210.97
115_Q197_Q1.1130.96
61_S65_T1.1100.96
97_T179_T1.1070.96
72_N195_N1.1040.96
14_Q96_Q1.1010.96
162_T203_T1.1000.96
123_H127_V1.0980.96
74_Q197_Q1.0980.96
116_L198_L1.0960.96
102_S106_T1.0950.96
123_H145_D1.0940.96
20_S24_T1.0940.96
41_H45_V1.0910.96
35_L117_L1.0900.96
132_F173_F1.0900.96
58_A89_V1.0890.96
5_W21_D1.0770.95
76_L117_L1.0770.95
55_Q137_Q1.0750.95
39_T80_T1.0730.95
15_T27_L1.0730.95
134_P177_G1.0690.95
71_R153_R1.0630.95
158_L199_L1.0630.95
128_W169_W1.0570.95
82_H104_D1.0560.95
124_S165_S1.0560.95
15_T138_T1.0520.95
117_L199_L1.0470.94
77_Q200_Q1.0400.94
55_Q178_Q1.0380.94
50_F132_F1.0360.94
184_S188_T1.0350.94
30_R194_R1.0290.94
87_W128_W1.0260.94
26_K34_L1.0250.93
14_Q137_Q1.0140.93
9_F30_R1.0110.93
76_L158_L1.0080.93
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: (05Jul14)
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  
1nr0A10.99511000.221Contact Map
1vyhC1011000.222Contact Map
2ymuA211000.223Contact Map
3sfzA10.97561000.23Contact Map
3w15A10.98541000.238Contact Map
3f3fA40.99511000.242Contact Map
4lg9A111000.258Contact Map
3mkqA311000.262Contact Map
3j65q10.99511000.268Contact Map
3zwlB20.99511000.27Contact 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 0.0253 seconds.