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T0808 150-418 cov50 -force run

ID: 1405033968 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 269 (264)
Sequences: 181 (159)
Seq/Len: 0.686
Nf(neff/√len): 9.8

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: 0.686).

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
120_N144_A2.1540.95
77_N80_E2.0240.92
66_L109_Q2.0050.91
71_S106_S1.9440.90
42_Y171_F1.7770.83
204_T252_C1.7730.83
210_H246_M1.7680.83
70_W104_E1.7490.82
101_F104_E1.6610.77
214_A222_Y1.5530.70
103_N106_S1.5320.68
90_L156_F1.5260.68
126_M140_A1.5210.67
51_G107_G1.5140.67
202_R252_C1.4760.64
52_Y173_E1.4470.62
254_P257_K1.4430.61
24_E127_Q1.4120.59
70_W101_F1.3790.56
70_W102_G1.3620.55
248_T254_P1.3540.54
5_W223_Q1.3390.53
260_E264_E1.3380.53
253_K258_E1.3370.53
128_I165_Y1.3260.52
188_F234_L1.3250.52
46_A66_L1.3190.51
139_T155_S1.3170.51
25_W141_Y1.3050.50
31_T121_T1.3000.50
257_K262_D1.3000.50
25_W167_R1.2930.49
255_T265_A1.2830.48
29_E104_E1.2800.48
14_L186_V1.2790.48
44_M47_G1.2760.48
58_N140_A1.2620.47
179_Q237_G1.2450.45
93_G96_V1.2380.45
255_T264_E1.2350.44
47_G175_F1.2280.44
260_E265_A1.2130.42
44_M156_F1.2120.42
70_W116_W1.2100.42
243_S255_T1.2050.42
8_R224_G1.2010.41
55_M65_I1.1950.41
101_F107_G1.1940.41
122_Y142_F1.1930.41
195_S199_K1.1850.40
193_A257_K1.1840.40
40_H43_Y1.1820.40
5_W87_I1.1810.40
63_R116_W1.1690.39
31_T119_G1.1670.39
84_D88_K1.1560.38
215_S246_M1.1480.37
71_S101_F1.1480.37
252_C256_G1.1470.37
262_D265_A1.1400.37
231_R247_G1.1370.36
70_W103_N1.1330.36
220_L243_S1.1280.36
83_D260_E1.1200.35
231_R243_S1.1170.35
69_V116_W1.1170.35
128_I164_W1.1170.35
138_Y156_F1.1150.35
83_D86_K1.1140.35
105_G171_F1.1130.35
253_K264_E1.1120.34
66_L111_Y1.1100.34
55_M63_R1.1060.34
207_T215_S1.1040.34
244_V253_K1.1040.34
112_L172_L1.1030.34
251_Y265_A1.0980.33
51_G69_V1.0970.33
107_G110_S1.0940.33
205_D251_Y1.0930.33
156_F218_V1.0920.33
79_K83_D1.0910.33
245_P249_K1.0900.33
71_S103_N1.0890.33
29_E37_E1.0890.33
134_G263_W1.0890.33
71_S158_R1.0880.33
257_K260_E1.0880.33
247_G255_T1.0850.32
254_P264_E1.0810.32
71_S78_P1.0760.32
241_N246_M1.0720.31
213_T250_F1.0710.31
59_S101_F1.0710.31
243_S249_K1.0710.31
244_V255_T1.0700.31
9_G240_F1.0680.31
106_S139_T1.0640.31
210_H223_Q1.0590.31
44_M51_G1.0580.30
37_E40_H1.0580.30
248_T257_K1.0580.30
204_T256_G1.0560.30
231_R244_V1.0550.30
141_Y150_W1.0510.30
249_K264_E1.0500.30
47_G65_I1.0440.29
136_T171_F1.0390.29
242_E247_G1.0340.29
37_E47_G1.0300.29
79_K253_K1.0290.28
245_P248_T1.0290.28
29_E70_W1.0280.28
5_W251_Y1.0240.28
228_K264_E1.0210.28
3_D210_H1.0200.28
122_Y159_P1.0170.28
17_A258_E1.0170.28
109_Q174_N1.0140.27
4_Y250_F1.0140.27
95_D170_S1.0130.27
57_Y70_W1.0110.27
255_T260_E1.0090.27
249_K255_T1.0090.27
104_E116_W1.0080.27
84_D87_I1.0040.27
124_F142_F1.0040.27
47_G75_T1.0030.27
202_R232_F1.0020.27
47_G150_W1.0010.27
55_M67_F1.0010.27
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  
1yo8A10.516725.40.964Contact Map
4h62V10.02976.60.972Contact Map
2ww6A30.092960.973Contact Map
2zwsA10.21563.80.975Contact Map
3owtC10.04093.10.976Contact Map
3uzeC20.04092.90.977Contact Map
4oy6A10.29372.60.977Contact Map
3fbyA30.58362.40.978Contact Map
2d10E40.05952.40.978Contact Map
2d11E40.0522.40.978Contact 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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