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TEST

ID: 1504611876 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 480 (443)
Sequences: 2361 (1820.4)
Seq/Len: 5.330
Nf(neff/√len): 86.5

Jackhmmer Results: (2016_04)
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: 5.330).

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
247_E373_G3.4001.00
378_S405_H3.0651.00
262_D403_M2.7261.00
256_E287_H2.6931.00
167_V178_M2.5941.00
260_A290_I2.5731.00
378_S382_G2.2531.00
339_M379_L2.2161.00
343_M376_A2.1361.00
254_G339_M2.0571.00
228_E289_K2.0161.00
213_L225_F2.0031.00
167_V176_Y1.9901.00
332_W383_L1.9591.00
412_V415_H1.9541.00
247_E407_F1.8751.00
387_D390_Q1.8031.00
236_F278_E1.7511.00
106_V110_L1.7101.00
281_M291_T1.6961.00
415_H420_K1.6771.00
48_R51_P1.6751.00
251_R410_G1.6721.00
151_E168_K1.6671.00
178_M226_V1.5650.99
42_P46_D1.5640.99
105_T109_G1.5630.99
275_L338_V1.5320.99
44_D48_R1.5190.99
32_D35_F1.5080.99
69_R73_F1.4870.99
43_Q47_Q1.4710.98
64_K67_R1.4650.98
103_I107_A1.4470.98
73_F76_R1.4400.98
379_L402_I1.4340.98
207_H263_Y1.4320.98
150_F215_Y1.4300.98
72_T76_R1.4030.98
262_D266_S1.4030.98
68_P72_T1.3870.98
82_T86_R1.3870.98
276_K312_T1.3860.98
60_C65_T1.3800.97
38_Y41_R1.3750.97
258_V402_I1.3730.97
385_K390_Q1.3630.97
100_T104_Q1.3550.97
94_E98_E1.3520.97
234_E278_E1.3480.97
107_A111_K1.3460.97
60_C68_P1.3420.97
151_E170_K1.3340.97
272_Y338_V1.3310.97
66_E69_R1.3230.96
122_S125_P1.3220.96
250_A339_M1.3190.96
112_K115_E1.3180.96
67_R72_T1.3160.96
81_T85_E1.3130.96
155_L158_K1.3090.96
35_F38_Y1.3020.96
36_I39_K1.2970.96
83_V86_R1.2920.96
41_R44_D1.2910.96
111_K114_E1.2860.96
155_L165_I1.2850.96
63_M66_E1.2780.95
42_P47_Q1.2760.95
82_T85_E1.2760.95
254_G335_L1.2710.95
34_T38_Y1.2640.95
68_P71_N1.2600.95
85_E88_F1.2600.95
65_T68_P1.2590.95
108_D112_K1.2570.95
41_R45_V1.2550.95
311_G348_P1.2530.95
102_A106_V1.2510.95
60_C63_M1.2470.95
84_I87_T1.2470.95
183_K218_Q1.2450.95
108_D111_K1.2450.95
70_P73_F1.2440.95
326_Y330_V1.2420.94
105_T110_L1.2400.94
344_C372_L1.2390.94
64_K68_P1.2370.94
54_N57_V1.2350.94
92_T98_E1.2280.94
117_E121_R1.2220.94
42_P45_V1.2210.94
351_N356_K1.2210.94
47_Q51_P1.2170.94
86_R90_V1.2090.93
81_T84_I1.2040.93
297_K306_M1.2030.93
108_D113_Q1.2030.93
39_K42_P1.2020.93
34_T37_G1.2010.93
56_S59_Q1.2000.93
85_E89_H1.1980.93
104_Q108_D1.1970.93
30_K33_G1.1940.93
71_N75_I1.1940.93
400_K404_Q1.1890.93
45_V49_E1.1870.93
110_L113_Q1.1830.92
62_L65_T1.1830.92
94_E97_E1.1810.92
50_A53_N1.1770.92
68_P73_F1.1760.92
48_R52_L1.1750.92
86_R89_H1.1730.92
69_R72_T1.1700.92
87_T91_E1.1680.92
66_E70_P1.1680.92
92_T95_E1.1680.92
206_R212_A1.1630.91
35_F39_K1.1610.91
166_L175_Y1.1610.91
261_L335_L1.1580.91
109_G113_Q1.1550.91
337_V347_L1.1540.91
51_P54_N1.1500.91
392_L402_I1.1490.91
88_F92_T1.1460.91
40_E44_D1.1440.91
87_T90_V1.1440.91
67_R71_N1.1380.90
108_D114_E1.1370.90
80_W85_E1.1350.90
101_T107_A1.1320.90
253_Y288_I1.1300.90
104_Q107_A1.1300.90
84_I88_F1.1290.90
382_G392_L1.1290.90
65_T70_P1.1250.90
97_E100_T1.1220.89
277_L315_Y1.1200.89
364_E386_K1.1150.89
55_F58_A1.1150.89
37_G41_R1.1140.89
80_W83_V1.1110.89
40_E43_Q1.1110.89
273_R326_Y1.1110.89
111_K115_E1.1110.89
106_V112_K1.1080.89
332_W399_A1.1050.88
47_Q50_A1.1030.88
36_I40_E1.1030.88
49_E53_N1.1010.88
37_G40_E1.0980.88
61_Q64_K1.0970.88
44_D49_E1.0940.88
165_I180_I1.0940.88
96_R99_W1.0890.88
33_G36_I1.0890.88
110_L114_E1.0840.87
57_V62_L1.0840.87
35_F40_E1.0820.87
62_L66_E1.0800.87
434_D438_F1.0780.87
155_L163_K1.0780.87
99_W103_I1.0740.87
74_I77_C1.0710.86
113_Q117_E1.0700.86
52_L56_S1.0690.86
46_D50_A1.0680.86
56_S60_C1.0640.86
102_A107_A1.0640.86
53_N61_Q1.0640.86
99_W105_T1.0630.86
39_K53_N1.0630.86
166_L229_Y1.0620.86
69_R75_I1.0620.86
93_P98_E1.0610.86
61_Q67_R1.0600.86
93_P96_R1.0590.85
125_P128_N1.0570.85
54_N58_A1.0540.85
44_D47_Q1.0490.85
105_T111_K1.0470.85
379_L392_L1.0450.84
43_Q46_D1.0450.84
101_T108_D1.0430.84
122_S126_S1.0420.84
36_I43_Q1.0400.84
447_I450_T1.0380.84
49_E52_L1.0360.84
333_W349_F1.0360.84
98_E109_G1.0350.84
57_V60_C1.0340.84
98_E103_I1.0340.84
103_I106_V1.0320.83
79_Q87_T1.0310.83
39_K44_D1.0310.83
97_E105_T1.0270.83
123_G127_D1.0250.83
66_E74_I1.0250.83
67_R70_P1.0220.83
101_T104_Q1.0210.83
169_E172_T1.0200.82
79_Q83_V1.0200.82
31_N39_K1.0190.82
94_E102_A1.0190.82
118_M122_S1.0190.82
191_E194_H1.0180.82
232_G286_G1.0170.82
99_W102_A1.0170.82
379_L405_H1.0160.82
276_K279_N1.0160.82
107_A113_Q1.0160.82
70_P74_I1.0150.82
51_P55_F1.0150.82
383_L392_L1.0140.82
61_Q65_T1.0130.82
258_V335_L1.0130.82
72_T75_I1.0090.81
219_T224_C1.0080.81
44_D52_L1.0070.81
39_K45_V1.0040.81
102_A105_T1.0040.81
79_Q82_T1.0030.81
128_N131_A1.0030.81
70_P75_I1.0000.81
101_T106_V1.0000.81
100_T103_I1.0000.81
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: (06Aug15)
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  
4gv1A10.68541000.31Contact Map
4ejnA10.78331000.329Contact Map
4lqsA10.73121000.335Contact Map
4dc2A10.67291000.338Contact Map
2i0eA20.67291000.342Contact Map
3pfqA10.73751000.342Contact Map
4aw2A10.78541000.344Contact Map
2r5tA10.58961000.346Contact Map
3txoA10.65621000.347Contact Map
1xjdA10.57921000.35Contact 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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