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T0827 212-369 -force run

ID: 1406136844 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 158 (157)
Sequences: 94 (65.4)
Seq/Len: 0.599
Nf(neff/√len): 5.2

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: 0.599).

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
95_A108_V1.7520.79
43_A47_S1.5770.67
58_A90_G1.5170.63
101_T139_A1.4490.58
39_R92_E1.4280.56
96_I148_V1.3950.53
85_I107_C1.3690.51
98_C150_R1.3420.49
58_A105_R1.3340.49
147_T151_Y1.3190.47
31_L95_A1.3130.47
124_G137_Y1.2780.44
15_A137_Y1.2620.43
102_G143_D1.2500.42
38_Q111_L1.2360.41
37_R132_R1.2330.41
31_L39_R1.2330.41
98_C101_T1.2270.40
88_D95_A1.2220.40
99_K149_L1.2210.40
111_L128_P1.2190.39
4_E139_A1.2180.39
2_S7_Q1.2100.39
115_L151_Y1.2040.38
5_I9_A1.2020.38
59_G108_V1.2020.38
78_K98_C1.2000.38
10_V14_F1.1970.38
99_K139_A1.1960.38
41_R82_G1.1940.37
103_L108_V1.1890.37
101_T130_L1.1890.37
92_E147_T1.1870.37
31_L149_L1.1850.37
58_A108_V1.1780.36
62_G93_P1.1770.36
88_D152_W1.1770.36
149_L153_N1.1670.35
74_L113_R1.1510.34
125_A137_Y1.1510.34
113_R137_Y1.1500.34
68_A152_W1.1500.34
86_F150_R1.1470.34
31_L36_R1.1420.34
85_I110_Q1.1400.33
111_L129_N1.1390.33
47_S137_Y1.1330.33
31_L37_R1.1330.33
58_A95_A1.1320.33
94_L138_D1.1250.32
77_L150_R1.1250.32
29_K56_V1.1240.32
95_A138_D1.1220.32
2_S96_I1.1130.32
7_Q143_D1.1120.32
5_I121_D1.1110.31
90_G95_A1.1100.31
30_A143_D1.1020.31
53_D81_T1.1010.31
4_E155_S1.0970.30
103_L146_Q1.0960.30
74_L150_R1.0920.30
52_L70_E1.0910.30
68_A124_G1.0910.30
14_F101_T1.0820.29
15_A19_A1.0780.29
59_G71_I1.0770.29
115_L120_V1.0690.29
72_S84_K1.0690.29
2_S10_V1.0640.28
83_A98_C1.0630.28
118_Q157_T1.0600.28
2_S11_G1.0550.28
18_S75_S1.0540.28
88_D92_E1.0520.27
79_P85_I1.0500.27
95_A105_R1.0490.27
33_F98_C1.0490.27
13_V20_E1.0490.27
101_T150_R1.0470.27
137_Y142_V1.0450.27
41_R60_E1.0450.27
96_I112_W1.0420.27
31_L92_E1.0360.26
20_E24_D1.0350.26
67_I103_L1.0330.26
57_A110_Q1.0310.26
63_F138_D1.0290.26
34_I71_I1.0280.26
4_E157_T1.0230.26
59_G66_E1.0210.26
58_A92_E1.0130.25
93_P104_P1.0100.25
10_V107_C1.0050.25
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  
3pxpA30.708968.20.915Contact Map
3op9A10.639248.30.925Contact Map
1b0nA10.613944.60.926Contact Map
3qwgA20.46243.90.927Contact Map
3ivpA40.670936.20.93Contact Map
4o8bA10.5823360.93Contact Map
4jcyA20.53829.70.933Contact Map
2ppxA10.360828.50.934Contact Map
2of5A70.411426.60.935Contact Map
2o71A10.411426.60.935Contact 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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