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T0834 2-215 -force run

ID: 1406831374 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 214 (213)
Sequences: 61 (52.3)
Seq/Len: 0.286
Nf(neff/√len): 3.6

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: 0.286).

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
36_L88_S1.7840.59
57_Y122_L1.7330.56
47_E195_S1.6710.52
101_H209_N1.6280.49
31_F117_A1.6140.48
135_A210_I1.5860.46
31_F163_S1.5470.43
12_L190_A1.5420.43
184_L210_I1.5370.43
54_Q69_L1.5190.42
137_G174_I1.5060.41
36_L167_L1.4750.39
113_E156_S1.4600.38
24_I206_Q1.4570.38
13_F18_A1.4420.37
29_T36_L1.4300.36
112_A117_A1.4100.35
159_S163_S1.4080.35
13_F126_M1.3990.34
100_I127_H1.3940.34
135_A167_L1.3240.30
57_Y208_G1.3240.30
133_N145_N1.3190.30
76_P103_G1.3040.29
89_L101_H1.2960.28
30_D192_L1.2890.28
83_L162_G1.2720.27
38_P116_P1.2610.26
59_L173_D1.2600.26
134_A138_T1.2520.26
115_Y125_Y1.2520.26
79_F183_W1.2490.26
129_Q148_E1.2320.25
90_S206_Q1.2280.25
27_I121_N1.2250.25
121_N156_S1.2240.25
18_A126_M1.2230.25
73_I115_Y1.2220.24
60_A210_I1.2190.24
121_N213_D1.2120.24
90_S159_S1.2080.24
50_L80_T1.2060.24
150_A196_L1.2040.24
16_N61_Q1.1960.23
87_S166_D1.1700.22
106_T213_D1.1660.22
200_D213_D1.1600.22
30_D106_T1.1430.21
34_R162_G1.1400.21
187_A210_I1.1330.20
134_A170_R1.1290.20
28_Q151_I1.1260.20
60_A107_Y1.1110.19
34_R53_I1.1090.19
98_G162_G1.1090.19
154_L183_W1.1070.19
81_R134_A1.1060.19
66_K69_L1.1040.19
97_S175_Y1.0990.19
3_P50_L1.0950.19
51_K172_G1.0920.19
129_Q158_A1.0920.19
22_Y107_Y1.0900.19
50_L76_P1.0890.19
19_T90_S1.0880.18
147_G174_I1.0870.18
153_A193_S1.0860.18
148_E153_A1.0820.18
187_A197_L1.0820.18
109_F172_G1.0800.18
109_F137_G1.0790.18
154_L206_Q1.0750.18
159_S187_A1.0740.18
2_L110_R1.0730.18
17_S53_I1.0720.18
150_A177_L1.0710.18
113_E201_N1.0710.18
135_A184_L1.0690.18
71_P140_L1.0690.18
167_L199_A1.0670.18
162_G187_A1.0630.18
165_S188_N1.0630.18
135_A149_D1.0610.17
195_S198_S1.0560.17
64_T138_T1.0550.17
83_L159_S1.0550.17
172_G176_Y1.0520.17
71_P122_L1.0520.17
173_D204_F1.0510.17
115_Y177_L1.0500.17
55_L86_G1.0480.17
9_F122_L1.0430.17
79_F154_L1.0410.17
12_L193_S1.0410.17
82_S106_T1.0370.17
36_L132_P1.0360.16
50_L103_G1.0360.16
132_P200_D1.0360.16
82_S141_Y1.0340.16
107_Y173_D1.0340.16
137_G167_L1.0330.16
29_T129_Q1.0280.16
4_E85_K1.0280.16
14_D187_A1.0270.16
42_L45_T1.0270.16
99_L169_L1.0240.16
8_L58_K1.0230.16
40_S59_L1.0220.16
24_I85_K1.0200.16
155_V205_I1.0180.16
89_L107_Y1.0140.16
78_V103_G1.0130.16
19_T60_A1.0120.16
19_T55_L1.0110.16
9_F126_M1.0100.16
82_S194_Y1.0100.16
42_L146_M1.0050.15
15_Y165_S1.0030.15
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: (12Jul14)
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  
3f0iA20.51426.80.966Contact Map
3rdwA20.495318.20.968Contact Map
1pbuA10.644911.70.971Contact Map
3fz4A10.50479.50.972Contact Map
1y0nA10.17767.20.974Contact Map
1avoA70.2575.60.975Contact Map
3gkxA20.50935.50.975Contact Map
3hshA60.2575.40.975Contact Map
3d3aA10.26644.90.975Contact Map
3n3fA20.24774.90.976Contact 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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