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acra

ID: 1492011366 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 397 (361)
Sequences: 16217 (11544.8)
Seq/Len: 44.922
Nf(neff/√len): 607.6

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: 44.922).

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
78_K95_Q3.4461.00
92_S175_K3.3341.00
88_E181_S3.0691.00
327_G333_E2.9681.00
322_T334_T2.8871.00
123_Q127_N2.7891.00
335_R357_D2.7741.00
338_V351_E2.6951.00
44_T358_R2.6551.00
109_K168_R2.5921.00
258_G278_A2.5641.00
95_Q175_K2.5591.00
325_V335_R2.5011.00
61_S215_D2.4721.00
47_T355_A2.2941.00
105_Y164_V2.2931.00
130_Q134_G2.2761.00
98_P102_Q2.2661.00
261_E279_I2.2651.00
88_E91_V2.1751.00
80_N95_Q2.1261.00
129_Y138_I2.1201.00
92_S177_T2.0821.00
80_N92_S2.0631.00
89_A181_S2.0501.00
133_L143_Y2.0461.00
130_Q147_L2.0361.00
354_K357_D2.0251.00
71_Q173_Y2.0211.00
47_T304_N2.0141.00
310_Q347_W1.9941.00
140_K144_D1.9741.00
333_E369_P1.9511.00
216_V295_A1.9491.00
307_L346_K1.9461.00
126_V130_Q1.9271.00
340_S348_L1.9051.00
60_T214_V1.8811.00
126_V143_Y1.8651.00
338_V350_T1.8541.00
102_Q171_L1.8501.00
326_V373_V1.8421.00
129_Y146_A1.8401.00
76_I189_V1.8201.00
245_S257_D1.8171.00
185_G207_Q1.8161.00
178_S206_V1.7821.00
86_D183_R1.7761.00
216_V278_A1.7721.00
133_L140_K1.7601.00
332_V360_V1.7521.00
53_T296_R1.7521.00
116_Q161_K1.7271.00
45_V356_G1.7261.00
165_E168_R1.7211.00
45_V306_I1.7131.00
82_K85_S1.7091.00
48_E307_L1.7041.00
76_I94_Y1.7031.00
147_L151_Q1.7021.00
340_S350_T1.6991.00
213_Y277_R1.6651.00
123_Q154_N1.6511.00
106_D109_K1.6511.00
49_P303_P1.6491.00
244_V278_A1.6431.00
337_I349_V1.6341.00
64_R208_Q1.6231.00
325_V357_D1.6211.00
215_D275_T1.6141.00
112_L157_V1.6131.00
48_E346_K1.6121.00
102_Q106_D1.6071.00
331_K372_Q1.5921.00
308_V359_V1.5791.00
158_T161_K1.5691.00
323_V337_I1.5651.00
55_E296_R1.5581.00
245_S296_R1.5501.00
105_Y168_R1.5491.00
142_E145_Q1.5431.00
114_K156_A1.5321.00
74_G96_I1.5301.00
184_I204_A1.5231.00
42_V375_A1.5211.00
245_S255_P1.5171.00
65_I205_T1.5111.00
105_Y109_K1.4841.00
107_S163_A1.4691.00
121_I125_T1.4621.00
339_A347_W1.4521.00
93_L204_A1.4521.00
39_A374_K1.4471.00
214_V293_V1.4461.00
217_T275_T1.4361.00
55_E294_R1.4351.00
77_L97_D1.4081.00
306_I355_A1.4020.99
101_Y174_T1.3990.99
164_V168_R1.3980.99
98_P174_T1.3970.99
127_N130_Q1.3820.99
113_A116_Q1.3790.99
219_S222_D1.3730.99
42_V358_R1.3710.99
151_Q154_N1.3710.99
119_A150_A1.3670.99
259_T279_I1.3650.99
320_D336_P1.3520.99
42_V326_V1.3440.99
150_A154_N1.3400.99
60_T212_I1.3400.99
112_L164_V1.3330.99
243_K257_D1.3270.99
109_K164_V1.3160.99
126_V150_A1.3060.99
131_K135_T1.3010.99
260_L278_A1.2980.99
78_K191_E1.2970.99
168_R172_A1.2920.99
76_I195_V1.2900.99
92_S95_Q1.2890.99
316_T334_T1.2810.99
302_N348_L1.2620.99
104_T170_N1.2580.99
49_P304_N1.2430.98
120_N123_Q1.2400.98
81_F91_V1.2340.98
125_T129_Y1.2330.98
310_Q345_D1.2290.98
267_V274_I1.2280.98
41_G362_S1.2250.98
77_L95_Q1.2180.98
67_E202_A1.2160.98
43_V361_I1.2000.98
83_E186_K1.1970.98
211_P279_I1.1960.98
161_K165_E1.1960.98
231_A257_D1.1950.98
22_L25_C1.1940.98
254_F286_T1.1900.98
67_E205_T1.1900.98
222_D225_R1.1870.98
214_V295_A1.1790.98
127_N131_K1.1760.98
143_Y147_L1.1750.98
94_Y204_A1.1710.98
341_Q348_L1.1680.97
262_F277_R1.1640.97
103_A169_I1.1620.97
63_Y211_P1.1610.97
166_T170_N1.1580.97
208_Q211_P1.1550.97
128_R144_D1.1530.97
247_I296_R1.1510.97
105_Y171_L1.1440.97
44_T356_G1.1420.97
104_T166_T1.1400.97
120_N124_L1.1390.97
123_Q150_A1.1370.97
71_Q75_I1.1320.97
106_D165_E1.1230.97
125_T145_Q1.1180.96
259_T281_P1.1170.96
94_Y203_L1.1120.96
81_F204_A1.1050.96
305_A348_L1.1010.96
126_V147_L1.0840.96
72_V101_Y1.0830.96
195_V203_L1.0820.96
246_L280_F1.0730.95
215_D277_R1.0700.95
178_S181_S1.0700.95
187_S204_A1.0690.95
112_L116_Q1.0680.95
119_A123_Q1.0670.95
130_Q143_Y1.0650.95
157_V161_K1.0640.95
310_Q342_A1.0580.95
81_F184_I1.0580.95
141_Q145_Q1.0490.94
66_A180_I1.0450.94
94_Y187_S1.0440.94
60_T287_L1.0380.94
79_R191_E1.0340.94
187_S190_T1.0300.94
111_D163_A1.0270.94
59_R272_G1.0260.94
94_Y176_V1.0240.93
109_K113_A1.0160.93
51_Q298_E1.0140.93
105_Y167_A1.0000.92
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  
1vf7A130.63221000.308Contact Map
4dk0A10.77081000.315Contact Map
3lnnA20.82871000.326Contact Map
3fppA20.62971000.342Contact Map
4l8jA10.79091000.347Contact Map
3ne5B20.79351000.37Contact Map
4kkuA40.66751000.389Contact Map
2f1mA40.59191000.444Contact Map
4tkoB10.58691000.523Contact Map
2k32A10.289799.80.724Contact 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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