OPENSEQ.org
YjhB_MembraneProt

ID: 1517362718 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 405 (373)
Sequences: 60956 (36601.9)
Seq/Len: 163.421
Nf(neff/√len): 1895.2

HHblits Results: (2016_02)
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: 163.421).

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
101_T105_M4.4891.00
89_I116_G4.0681.00
96_L109_C4.0601.00
98_G173_F3.7161.00
62_A111_F3.3051.00
86_A119_G3.2661.00
91_S179_V3.1971.00
138_S276_D3.1721.00
79_R130_E3.0931.00
93_G109_C3.0351.00
335_F343_G3.0311.00
102_N105_M2.9561.00
136_L139_K2.9161.00
70_F119_G2.9131.00
104_Y108_V2.8931.00
132_W140_A2.5451.00
93_G112_I2.4801.00
93_G116_G2.4761.00
75_D341_G2.4451.00
249_N252_V2.4101.00
133_P136_L2.3771.00
58_V111_F2.3761.00
103_L107_A2.2711.00
72_A76_K2.2561.00
280_V333_D2.2271.00
48_T51_Q2.2071.00
66_G115_L2.1921.00
336_P339_L2.1801.00
80_K84_M2.1481.00
74_A123_C2.0821.00
13_Q136_L2.0461.00
166_Y170_N2.0341.00
73_M82_M2.0311.00
97_S109_C2.0101.00
100_A105_M2.0061.00
51_Q103_L1.9711.00
100_A109_C1.9321.00
97_S106_L1.8751.00
58_V107_A1.8651.00
95_G176_L1.8401.00
273_F277_K1.8301.00
21_W147_G1.7951.00
105_M109_C1.7581.00
78_G81_P1.7511.00
55_I106_L1.7431.00
167_G170_N1.7291.00
40_I43_A1.7191.00
47_I103_L1.7091.00
279_G282_K1.6771.00
66_G118_S1.6771.00
66_G69_F1.6331.00
23_G83_M1.6261.00
73_M77_Y1.6141.00
270_F273_F1.6071.00
128_A144_L1.5861.00
130_E340_R1.5811.00
104_Y107_A1.5511.00
93_G113_V1.5431.00
272_G276_D1.5351.00
28_G148_F1.5091.00
77_Y81_P1.5051.00
75_D342_L1.4991.00
81_P85_W1.4731.00
281_K285_V1.4711.00
47_I51_Q1.4621.00
77_Y82_M1.4551.00
207_L211_R1.4501.00
96_L99_I1.4471.00
134_K137_Q1.4301.00
42_K52_A1.4221.00
71_G75_D1.4111.00
139_K276_D1.4101.00
16_A131_S1.4050.99
282_K285_V1.4050.99
40_I44_D1.3800.99
162_F170_N1.3800.99
50_I367_G1.3760.99
274_V278_I1.3640.99
199_K202_D1.3570.99
38_L52_A1.3530.99
84_M186_R1.3500.99
139_K273_F1.3470.99
62_A114_G1.3440.99
86_A116_G1.3420.99
244_A253_I1.3280.99
81_P84_M1.3250.99
139_K143_F1.3200.99
184_W188_S1.3180.99
62_A66_G1.3180.99
364_Y368_Y1.3160.99
14_R18_F1.3160.99
354_G358_A1.3080.99
149_S264_T1.2990.99
173_F177_L1.2920.99
78_G82_M1.2890.99
279_G283_A1.2610.99
92_V96_L1.2610.99
49_D367_G1.2600.99
95_G99_I1.2570.99
74_A341_G1.2560.99
79_R191_E1.2530.99
74_A79_R1.2450.98
267_G270_F1.2440.98
12_P15_K1.2370.98
84_M88_F1.2360.98
99_I173_F1.2300.98
108_V112_I1.2270.98
170_N173_F1.2270.98
75_D79_R1.2210.98
89_I93_G1.2150.98
94_T175_G1.2090.98
85_W89_I1.2020.98
251_V255_T1.2010.98
30_D33_M1.1970.98
127_Y189_A1.1970.98
71_G341_G1.1950.98
61_I356_M1.1910.98
137_Q333_D1.1910.98
263_G267_G1.1890.98
332_Y344_T1.1840.98
244_A250_T1.1830.98
129_V137_Q1.1810.98
363_T367_G1.1670.97
98_G169_R1.1640.97
59_A117_M1.1610.97
44_D169_R1.1600.97
25_V154_I1.1600.97
69_F72_A1.1580.97
266_T269_I1.1560.97
17_L132_W1.1500.97
331_I347_I1.1460.97
88_F183_L1.1390.97
79_R126_T1.1380.97
242_Y246_N1.1340.97
252_V255_T1.1320.97
278_I283_A1.1270.97
248_V252_V1.1270.97
96_L105_M1.1240.97
289_I293_I1.1230.97
282_K286_V1.1210.97
23_G120_E1.1180.96
81_P191_E1.1100.96
54_L360_V1.1080.96
263_G314_F1.1050.96
84_M183_L1.1020.96
101_T104_Y1.0990.96
269_I273_F1.0950.96
351_G355_G1.0950.96
278_I282_K1.0940.96
55_I103_L1.0910.96
29_F155_A1.0910.96
127_Y131_S1.0800.95
57_T356_M1.0740.95
95_G173_F1.0730.95
105_M108_V1.0710.95
58_V62_A1.0680.95
146_S149_S1.0680.95
286_V289_I1.0660.95
30_D110_R1.0600.95
55_I107_A1.0590.95
25_V151_G1.0560.95
97_S172_F1.0560.95
129_V141_S1.0550.95
50_I360_V1.0480.94
146_S265_L1.0440.94
183_L187_K1.0400.94
157_Q258_T1.0380.94
98_G176_L1.0350.94
85_W88_F1.0330.94
27_D120_E1.0320.94
157_Q161_Q1.0320.94
82_M85_W1.0290.94
305_N308_L1.0270.94
53_T238_L1.0210.93
21_W143_F1.0150.93
91_S176_L1.0130.93
72_A342_L1.0120.93
138_S272_G1.0110.93
337_T340_R1.0090.93
126_T341_G1.0050.93
170_N174_I1.0020.92
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  
1pw4A10.97041000.243Contact Map
4j05A20.92591000.243Contact Map
4pypA10.94811000.255Contact Map
2gfpA20.91361000.272Contact Map
3wdoA10.96791000.275Contact Map
4ldsA20.94811000.284Contact Map
4gc0A10.97781000.287Contact Map
3o7qA10.93091000.292Contact Map
4zw9A101000.296Contact Map
2cfqA10.9581000.321Contact 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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