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OPENSEQ.org

hp1

ID: 1401911873 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 355 (354)
Sequences: 487 (345.8)
Seq/Len: 1.376
Nf(neff/√len): 18.4

HHblits Results: (2013_03)
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: 1.376).

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
130_L172_A2.5481.00
168_N184_H2.5401.00
181_T226_I2.3971.00
208_Y213_V2.3160.99
115_H134_H2.2500.99
53_E224_N2.0720.98
52_S67_S2.0640.98
53_E270_N2.0120.98
53_E269_D2.0090.98
268_V282_V1.9960.98
271_I280_L1.9150.97
64_F85_I1.8980.96
168_N269_D1.7190.93
168_N224_N1.6480.91
168_N332_T1.6260.90
180_G206_V1.6190.90
128_Y145_K1.6020.89
224_N270_N1.5900.89
227_N271_I1.5840.88
274_D277_T1.5820.88
156_L299_P1.5690.88
235_V351_L1.5610.87
53_E115_H1.5490.87
53_E168_N1.5230.86
302_S331_S1.5030.85
67_S86_L1.5020.85
66_S114_P1.4970.84
58_L64_F1.4850.84
116_G269_D1.4400.81
7_L10_L1.4360.81
281_W320_V1.4340.81
33_E36_P1.4190.80
53_E116_G1.3930.78
63_A195_E1.3860.77
114_P131_V1.3840.77
179_Y250_K1.3380.74
127_M148_E1.3340.73
131_V146_F1.3270.73
287_N290_K1.3250.73
51_G114_P1.3140.72
266_T284_C1.3090.71
115_H270_N1.3060.71
132_V170_I1.3010.71
83_G114_P1.2950.70
168_N183_D1.2920.70
245_I307_I1.2840.69
140_T158_T1.2830.69
63_A230_P1.2820.69
3_K12_M1.2810.69
143_L339_G1.2790.69
179_Y202_W1.2780.69
205_V226_I1.2750.69
9_L17_F1.2700.68
274_D279_D1.2660.68
7_L11_G1.2640.68
174_G232_G1.2610.67
12_M15_A1.2610.67
18_R28_L1.2500.66
71_Y74_I1.2500.66
52_S344_G1.2450.66
205_V223_A1.2340.65
7_L12_M1.2340.65
10_L13_G1.2330.65
215_V223_A1.2320.65
180_G344_G1.2210.64
247_V257_T1.2200.64
50_T283_G1.2180.63
350_A353_C1.2150.63
4_L9_L1.2150.63
115_H225_G1.2140.63
99_E341_L1.2120.63
115_H222_F1.2060.62
174_G245_I1.1990.62
220_F226_I1.1940.61
236_Y284_C1.1930.61
225_G270_N1.1930.61
198_L231_D1.1920.61
54_D118_S1.1890.61
215_V218_E1.1890.61
8_T14_L1.1840.60
179_Y229_S1.1830.60
232_G341_L1.1780.60
191_L195_E1.1760.59
11_G14_L1.1750.59
20_H24_Y1.1720.59
164_L167_L1.1690.59
176_E185_Y1.1690.59
115_H224_N1.1680.59
42_C353_C1.1680.59
51_G169_D1.1660.58
52_S345_T1.1630.58
177_H207_Y1.1600.58
281_W318_T1.1570.57
19_N23_S1.1470.56
4_L22_S1.1430.56
55_M335_S1.1390.56
167_L180_G1.1390.56
64_F129_L1.1380.56
236_Y247_V1.1380.56
111_S135_P1.1350.55
226_I237_I1.1310.55
139_S167_L1.1260.54
26_T30_A1.1240.54
247_V262_L1.1210.54
236_Y245_I1.1180.54
10_L14_L1.1180.54
5_I17_F1.1170.53
3_K24_Y1.1140.53
54_D272_S1.1140.53
118_S346_V1.1140.53
133_N142_E1.1100.53
63_A335_S1.1090.53
179_Y291_I1.1080.53
6_A22_S1.1040.52
3_K9_L1.1040.52
173_V179_Y1.1020.52
233_K342_L1.1000.52
100_L283_G1.0990.52
84_K283_G1.0980.52
49_E63_A1.0940.51
223_A250_K1.0920.51
226_I235_V1.0910.51
281_W336_V1.0900.51
12_M22_S1.0850.50
20_H28_L1.0770.49
5_I12_M1.0710.49
16_L20_H1.0700.49
155_H169_D1.0630.48
266_T315_P1.0610.48
168_N270_N1.0610.48
99_E343_I1.0600.48
64_F187_L1.0580.48
13_G22_S1.0560.47
175_P253_N1.0550.47
186_F260_K1.0540.47
223_A274_D1.0530.47
6_A24_Y1.0530.47
10_L17_F1.0510.47
142_E155_H1.0510.47
134_H144_F1.0510.47
274_D350_A1.0460.46
118_S301_A1.0440.46
3_K7_L1.0420.46
14_L17_F1.0410.46
18_R21_Q1.0410.46
3_K10_L1.0390.46
249_E257_T1.0380.46
116_G224_N1.0370.45
51_G115_H1.0350.45
9_L33_E1.0350.45
222_F240_L1.0320.45
63_A342_L1.0310.45
169_D346_V1.0280.45
181_T348_H1.0280.45
180_G345_T1.0280.45
158_T167_L1.0270.44
213_V286_P1.0250.44
181_T332_T1.0210.44
185_Y195_E1.0150.43
6_A21_Q1.0140.43
63_A90_L1.0140.43
67_S166_N1.0140.43
16_L23_S1.0130.43
31_L38_E1.0130.43
88_M259_L1.0100.43
3_K6_A1.0090.43
11_G24_Y1.0070.42
25_Q31_L1.0060.42
47_G96_T1.0060.42
143_L262_L1.0040.42
10_L21_Q1.0030.42
115_H344_G1.0030.42
133_N166_N1.0020.42
183_D320_V1.0010.42
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: (29May14)
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  
3sreA10.92681000.541Contact Map
2fp8A20.79151000.681Contact Map
2p4oA10.774699.80.774Contact Map
1pjxA10.791599.70.782Contact Map
3dr2A20.899.70.787Contact Map
2qe8A20.774699.70.793Contact Map
3q6kA20.828299.70.797Contact Map
2dg1A60.819799.60.8Contact Map
2g8sA20.791599.60.801Contact Map
3a9gA10.76999.60.802Contact 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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