OPENSEQ.org
his2

ID: 1516928233 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 335 (283)
Sequences: 301 (229.7)
Seq/Len: 1.064
Nf(neff/√len): 13.7

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: 1.064).

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
25_Q29_L2.7531.00
35_C124_F2.2800.99
25_Q28_N2.2750.99
37_T124_F2.2270.98
20_D84_Y2.1740.98
176_L309_S2.1340.98
167_Y227_R2.1290.97
243_T290_V2.0520.97
260_C271_F2.0390.97
8_S19_L1.9840.96
230_Q266_H1.9700.96
77_A96_I1.9640.95
271_F300_L1.9550.95
27_V92_T1.9530.95
239_I263_V1.8770.94
257_K296_D1.8550.93
183_L254_Y1.8500.93
6_S34_Y1.8380.93
12_S15_G1.7950.92
84_Y92_T1.7930.92
183_L244_S1.7600.91
20_D83_R1.7450.90
126_V179_G1.7320.90
76_H79_E1.6450.86
247_R283_V1.6370.86
187_F284_G1.6100.85
229_L239_I1.5890.83
17_D280_V1.5600.82
244_S248_K1.5430.81
246_L253_P1.5160.79
73_F94_F1.4740.77
229_L259_L1.4720.76
297_V300_L1.4690.76
263_V268_G1.4340.74
128_S179_G1.4300.74
40_I101_E1.4250.73
27_V84_Y1.4170.73
164_Q230_Q1.4110.72
127_G182_D1.4000.71
78_Q81_K1.3970.71
138_D242_N1.3580.68
229_L232_I1.3540.68
102_S228_N1.3460.67
129_V177_V1.3280.65
244_S254_Y1.3250.65
183_L186_L1.3180.65
241_I273_L1.3070.64
23_V92_T1.3040.63
38_E177_V1.3040.63
101_E185_K1.2970.63
267_C270_R1.2940.62
10_D15_G1.2880.62
225_V259_L1.2770.61
14_H41_P1.2770.61
22_V98_M1.2670.60
182_D240_E1.2630.60
245_A254_Y1.2620.60
135_I247_R1.2570.59
226_V265_K1.2420.58
267_C277_A1.2410.58
12_S41_P1.2210.56
19_L80_I1.2160.55
77_A94_F1.2090.55
294_I300_L1.2050.54
244_S284_G1.2050.54
243_T285_V1.2020.54
42_R49_Y1.1950.53
264_K300_L1.1900.53
14_H244_S1.1800.52
33_T95_I1.1720.51
76_H80_I1.1680.51
26_V36_L1.1670.51
170_L228_N1.1570.50
241_I294_I1.1510.49
286_C289_K1.1470.49
10_D38_E1.1450.49
95_I122_L1.1450.49
262_L265_K1.1450.49
22_V275_D1.1440.49
27_V94_F1.1380.48
258_T262_L1.1350.48
136_P244_S1.1320.47
185_K252_E1.1300.47
42_R63_I1.1270.47
170_L178_V1.1260.47
14_H221_I1.1250.47
183_L245_A1.1160.46
41_P63_I1.1160.46
80_I84_Y1.1110.45
238_A272_V1.1050.45
242_N274_S1.1020.45
169_M178_V1.1010.45
167_Y228_N1.0970.44
236_G311_S1.0950.44
119_N271_F1.0950.44
27_V91_R1.0910.44
35_C177_V1.0900.43
40_I179_G1.0880.43
128_S138_D1.0880.43
35_C240_E1.0840.43
3_S274_S1.0790.42
124_F127_G1.0780.42
3_S238_A1.0770.42
101_E121_I1.0760.42
27_V83_R1.0730.42
20_D27_V1.0730.42
186_L245_A1.0720.42
5_H39_H1.0710.42
15_G41_P1.0710.42
233_D270_R1.0590.41
82_T85_A1.0570.40
229_L266_H1.0520.40
17_D63_I1.0520.40
257_K297_V1.0520.40
23_V27_V1.0510.40
23_V80_I1.0500.40
304_C311_S1.0490.40
100_I111_A1.0480.40
74_M120_D1.0420.39
82_T113_R1.0410.39
290_V300_L1.0410.39
36_L254_Y1.0410.39
31_F306_L1.0410.39
123_K260_C1.0380.39
171_I235_Y1.0380.39
113_R292_K1.0360.39
34_Y144_W1.0330.38
103_C262_L1.0320.38
128_S278_H1.0310.38
156_K264_K1.0310.38
247_R254_Y1.0290.38
102_S169_M1.0280.38
3_S275_D1.0250.38
14_H284_G1.0250.38
46_K270_R1.0190.37
43_I229_L1.0180.37
129_V310_Q1.0170.37
19_L40_I1.0120.36
122_L287_Y1.0080.36
4_H33_T1.0050.36
26_V127_G1.0020.36
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  
4gc3A10.77011000.564Contact Map
3dcpA30.78511000.584Contact Map
2yxoA20.78811000.584Contact Map
3b0xA10.70451000.684Contact Map
2w9mA20.68361000.691Contact Map
1m65A10.67461000.694Contact Map
3qy7A10.72241000.696Contact Map
2wjeA10.70151000.702Contact Map
2anuA60.6091000.74Contact Map
1v77A10.579199.90.748Contact 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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