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OPENSEQ.org
2zzm
ID: 1490183013 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 336 (331)
Sequences: 887 (543.2)
Seq/Len: 2.680
Nf(neff/√len): 29.9
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: 2.680).

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
170_W234_K2.4871.00
12_G38_L2.4461.00
281_V285_G2.4141.00
318_K326_I2.3611.00
200_V259_G2.2881.00
201_D265_N2.2141.00
160_T171_V2.1661.00
227_H230_E2.1451.00
167_Y211_I2.1101.00
171_V231_L2.1031.00
236_I245_I2.0621.00
125_Y153_A1.9970.99
203_F273_F1.9770.99
159_L231_L1.9730.99
197_D261_R1.8930.99
202_M252_V1.8680.99
168_R238_L1.8460.99
182_L265_N1.7820.99
229_I247_P1.7600.98
169_L212_A1.7400.98
158_T174_A1.7320.98
11_H14_Q1.7260.98
210_S221_A1.7200.98
253_R275_D1.7060.98
236_I247_P1.7040.98
98_D180_P1.7040.98
163_K168_R1.6990.98
117_R150_E1.6870.98
124_A129_P1.6780.98
121_G153_A1.6770.98
181_R208_P1.6180.97
201_D318_K1.6030.97
261_R288_H1.5910.96
134_F149_L1.5610.96
207_G232_L1.5470.96
288_H330_D1.5430.96
229_I233_K1.5350.95
199_V219_I1.5240.95
177_Y182_L1.5220.95
201_D326_I1.5210.95
265_N326_I1.5130.95
98_D181_R1.4960.95
26_N29_Y1.4930.94
177_Y181_R1.4920.94
177_Y265_N1.4860.94
261_R330_D1.4830.94
16_R20_I1.4790.94
230_E234_K1.4790.94
310_E332_K1.4770.94
234_K237_K1.4460.93
223_D265_N1.4210.92
208_P265_N1.4080.92
171_V176_V1.4050.92
175_K227_H1.3960.91
34_E39_Y1.3880.91
176_V231_L1.3820.91
204_A232_L1.3810.91
265_N318_K1.3740.91
201_D232_L1.3710.90
104_V128_I1.3580.90
201_D223_D1.3440.89
185_E188_R1.3430.89
186_R228_A1.3420.89
136_R292_I1.3390.89
103_L160_T1.3370.89
218_K246_I1.3300.89
317_V326_I1.3290.89
182_L326_I1.3250.88
121_G133_V1.3240.88
187_A191_K1.3230.88
8_N11_H1.3210.88
144_F224_I1.3130.88
162_H178_F1.3110.88
213_C263_I1.3070.87
181_R265_N1.3010.87
262_V281_V1.3010.87
214_K245_I1.2980.87
177_Y267_P1.2960.87
182_L318_K1.2960.87
172_D175_K1.2950.87
286_V312_L1.2850.86
181_R290_Y1.2820.86
169_L211_I1.2780.86
177_Y208_P1.2770.86
135_R150_E1.2740.86
182_L223_D1.2710.85
141_K148_E1.2690.85
158_T172_D1.2680.85
182_L267_P1.2680.85
233_K237_K1.2610.85
182_L208_P1.2550.84
121_G152_L1.2500.84
226_P249_L1.2380.83
167_Y215_N1.2360.83
200_V222_I1.2360.83
86_K116_I1.2340.83
192_K313_E1.2330.83
147_R318_K1.2290.83
159_L170_W1.2290.83
143_E224_I1.2270.83
266_L270_A1.2110.81
31_I40_L1.2110.81
161_I168_R1.2050.81
319_S326_I1.2040.81
151_H158_T1.1980.80
201_D317_V1.1980.80
181_R267_P1.1940.80
264_M277_A1.1830.79
319_S325_Y1.1760.79
202_M264_M1.1730.78
288_H328_A1.1720.78
177_Y183_G1.1680.78
227_H231_L1.1490.76
182_L201_D1.1490.76
197_D260_N1.1380.75
181_R266_L1.1370.75
133_V153_A1.1350.75
311_V331_F1.1340.75
165_N187_A1.1330.75
161_I170_W1.1310.75
214_K264_M1.1300.75
204_A223_D1.1270.74
223_D229_I1.1210.74
268_K292_I1.1180.74
177_Y290_Y1.1170.74
13_E16_R1.1160.73
228_A290_Y1.1150.73
264_M270_A1.1090.73
102_D131_K1.1080.73
13_E17_R1.1020.72
169_L177_Y1.0990.72
189_I193_V1.0910.71
86_K89_D1.0870.71
253_R272_K1.0850.70
265_N290_Y1.0840.70
177_Y270_A1.0800.70
221_A232_L1.0770.70
198_V259_G1.0760.69
25_L40_L1.0730.69
285_G328_A1.0720.69
250_S255_V1.0650.68
292_I320_Y1.0630.68
199_V236_I1.0620.68
316_I325_Y1.0620.68
6_K37_Y1.0590.68
134_F173_I1.0590.68
182_L290_Y1.0460.66
223_D318_K1.0460.66
94_S162_H1.0420.66
105_I173_I1.0420.66
9_K36_N1.0410.66
190_M213_C1.0400.66
177_Y326_I1.0390.66
188_R328_A1.0350.65
147_R182_L1.0320.65
147_R326_I1.0290.64
326_I330_D1.0290.64
208_P267_P1.0260.64
212_A232_L1.0250.64
100_V180_P1.0250.64
102_D157_R1.0230.64
125_Y129_P1.0220.64
211_I241_L1.0220.64
265_N292_I1.0210.64
286_V332_K1.0190.63
28_D35_G1.0180.63
208_P326_I1.0160.63
14_Q37_Y1.0120.63
208_P290_Y1.0120.63
237_K242_E1.0110.62
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  
2yx1A20.95241000.451Contact Map
3k6rA10.7441000.589Contact Map
3a27A10.61311000.629Contact Map
3vseA40.928699.90.764Contact Map
2b78A10.913799.90.767Contact Map
2as0A20.967399.90.767Contact Map
3v97A20.87899.90.773Contact Map
4dmgA20.907799.90.773Contact Map
1wxxA40.916799.90.78Contact Map
3c0kA20.922699.90.781Contact 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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