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OPENSEQ.org

Mcd 160-548

ID: 1485518404 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 389 (371)
Sequences: 19812 (10594.2)
Seq/Len: 53.402
Nf(neff/√len): 550.0

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: 53.402).

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 > 50% 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
147_E227_R4.0281.00
23_R45_A3.6491.00
151_H225_G3.6281.00
301_E339_A3.5071.00
104_D108_A2.9911.00
113_K118_E2.8651.00
203_M224_D2.8391.00
17_R76_E2.8181.00
273_Q277_E2.6751.00
265_Q306_R2.5851.00
294_K343_N2.5101.00
183_S233_L2.5011.00
153_N222_G2.4881.00
30_G35_D2.4441.00
66_S69_S2.3041.00
44_E48_E2.1811.00
143_K230_A2.1731.00
18_R22_E2.1521.00
275_A347_I2.1471.00
355_L360_S2.1291.00
79_R269_E2.0821.00
284_A287_E2.0741.00
104_D107_K2.0461.00
203_M222_G2.0431.00
166_M189_K2.0261.00
267_A341_A2.0131.00
268_L302_I1.9931.00
75_E306_R1.9611.00
170_A185_F1.9451.00
45_A48_E1.9431.00
144_D227_R1.9131.00
264_A302_I1.9101.00
149_V225_G1.9021.00
265_Q269_E1.8941.00
113_K119_I1.8791.00
298_M340_A1.8591.00
76_E79_R1.8351.00
153_N220_E1.8201.00
108_A112_P1.7971.00
305_A333_G1.7901.00
283_K287_E1.7281.00
160_A219_Y1.7101.00
148_W185_F1.7091.00
103_T106_Q1.6891.00
339_A343_N1.6871.00
122_T166_M1.6801.00
144_D149_V1.6591.00
240_Q243_K1.6581.00
360_S364_C1.6401.00
205_G222_G1.6381.00
266_N270_V1.6321.00
229_K232_N1.6031.00
279_K284_A1.6011.00
127_E154_K1.6001.00
68_A314_W1.5941.00
58_E64_G1.5881.00
149_V227_R1.5881.00
14_D18_R1.5851.00
144_D147_E1.5831.00
351_N357_Y1.5721.00
291_V347_I1.5681.00
11_M14_D1.5581.00
275_A291_V1.5451.00
335_R376_A1.5411.00
20_A80_G1.5411.00
6_D9_L1.5311.00
270_V273_Q1.5291.00
112_P116_S1.5141.00
311_H315_E1.5111.00
75_E265_Q1.5061.00
57_P99_L1.5051.00
209_E355_L1.5011.00
270_V358_Q1.4681.00
271_G344_A1.4651.00
151_H224_D1.4571.00
236_G240_Q1.4531.00
338_W370_N1.4491.00
13_R76_E1.4441.00
314_W318_H1.4431.00
264_A340_A1.4361.00
266_N362_I1.4311.00
79_R265_Q1.4261.00
16_F51_V1.4201.00
11_M15_Q1.4131.00
124_V157_I1.4111.00
261_I302_I1.4050.99
78_S85_G1.4010.99
280_Q288_F1.3990.99
188_E232_N1.3950.99
342_D367_R1.3950.99
304_V332_L1.3940.99
60_F107_K1.3910.99
75_E310_Y1.3880.99
302_I340_A1.3870.99
45_A49_M1.3840.99
272_M276_E1.3700.99
142_V151_H1.3630.99
146_D230_A1.3600.99
44_E47_A1.3580.99
290_R293_G1.3400.99
228_V232_N1.3370.99
101_G247_Q1.3340.99
344_A359_I1.3170.99
105_A109_A1.3050.99
327_G379_Q1.3040.99
161_A219_Y1.2940.99
315_E325_E1.2930.99
298_M343_N1.2920.99
113_K116_S1.2900.99
198_F226_F1.2890.99
338_W342_D1.2790.99
337_A366_A1.2770.99
114_L121_P1.2710.99
31_W215_G1.2600.99
147_E230_A1.2550.99
148_W230_A1.2480.99
19_F45_A1.2440.98
270_V348_H1.2430.98
107_K111_L1.2330.98
81_Y84_V1.2300.98
109_A113_K1.2270.98
338_W363_L1.2210.98
283_K288_F1.2190.98
301_E336_V1.2180.98
54_L73_V1.2170.98
301_E343_N1.2160.98
124_V223_F1.2110.98
263_V337_A1.2100.98
299_A303_M1.2000.98
16_F20_A1.1970.98
109_A231_E1.1940.98
40_M44_E1.1940.98
205_G220_E1.1930.98
272_M295_L1.1920.98
197_P226_F1.1910.98
94_A121_P1.1810.98
335_R339_A1.1770.98
71_V313_A1.1770.98
297_M343_N1.1770.98
305_A336_V1.1720.98
150_V170_A1.1710.98
258_A309_T1.1700.97
335_R380_A1.1680.97
150_V185_F1.1650.97
169_L184_M1.1640.97
276_E286_I1.1640.97
303_M311_H1.1610.97
189_K198_F1.1600.97
261_I309_T1.1540.97
260_A369_L1.1520.97
146_D227_R1.1500.97
71_V258_A1.1500.97
56_I115_A1.1470.97
297_M380_A1.1460.97
47_A52_F1.1410.97
27_H30_G1.1390.97
13_R72_V1.1360.97
172_T183_S1.1350.97
141_A185_F1.1350.97
342_D370_N1.1320.97
17_R21_D1.1300.97
102_G106_Q1.1300.97
168_L187_A1.1270.97
312_S329_A1.1210.97
143_K238_E1.1200.96
10_E13_R1.1120.96
10_E14_D1.1060.96
341_A366_A1.1050.96
268_L272_M1.1030.96
227_R230_A1.1030.96
16_F73_V1.1010.96
142_V149_V1.0950.96
41_E44_E1.0940.96
230_A233_L1.0890.96
193_T196_D1.0890.96
9_L69_S1.0880.96
168_L223_F1.0880.96
331_L380_A1.0790.95
275_A285_L1.0700.95
67_K317_D1.0700.95
126_T156_W1.0680.95
65_L69_S1.0680.95
140_R151_H1.0650.95
129_N138_R1.0630.95
271_G347_I1.0620.95
193_T232_N1.0540.95
105_A231_E1.0480.94
148_W172_T1.0470.94
267_A362_I1.0440.94
311_H314_W1.0440.94
297_M301_E1.0430.94
7_E11_M1.0360.94
263_V366_A1.0320.94
15_Q18_R1.0310.94
15_Q49_M1.0300.94
119_I165_V1.0280.94
30_G34_R1.0280.94
9_L66_S1.0230.93
100_C247_Q1.0200.93
20_A77_L1.0180.93
124_V166_M1.0130.93
142_V173_D1.0080.93
119_I164_H1.0070.93
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  
2d29A20.97431000.046Contact Map
3owaA40.9641000.048Contact Map
2jifA40.96921000.051Contact Map
2z1qA20.96141000.052Contact Map
1ivhA40.97431000.053Contact Map
4l1fA20.97171000.054Contact Map
3r7kA40.96661000.055Contact Map
4m9aA40.9641000.056Contact Map
4u83A40.9461000.056Contact Map
3pfdA40.94861000.056Contact 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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