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OPENSEQ.org

b1

ID: 1452520454 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 651 (405)
Sequences: 2198 (1715.4)
Seq/Len: 5.427
Nf(neff/√len): 85.2

Jackhmmer Results: (2015_08)
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: 5.427).

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
280_G283_I3.0281.00
283_I296_S2.4741.00
280_G296_S2.4481.00
268_V272_T2.1821.00
210_N214_N2.1251.00
266_G271_S1.9481.00
296_S300_T1.6661.00
268_V271_S1.6360.99
258_F262_S1.6320.99
240_Q245_P1.5380.99
141_A147_Q1.5130.99
283_I287_C1.4910.99
227_N255_D1.4900.99
293_A296_S1.4740.99
280_G287_C1.4650.98
266_G272_T1.3460.97
224_P239_S1.3450.97
134_H137_K1.3270.97
143_A147_Q1.3240.97
146_E149_L1.3200.97
141_A149_L1.3070.96
287_C296_S1.2870.96
133_R136_M1.2810.96
388_H392_D1.2780.96
139_K146_E1.2450.95
250_A253_V1.2450.95
224_P252_T1.2430.95
141_A146_E1.2350.94
141_A144_F1.2190.94
357_E360_F1.2180.94
143_A146_E1.2170.94
146_E150_K1.2070.93
140_E143_A1.2030.93
147_Q150_K1.1980.93
146_E155_E1.1970.93
150_K155_E1.1960.93
273_H277_P1.1930.93
247_P258_F1.1890.93
125_H134_H1.1840.93
112_E115_R1.1800.92
118_K121_Q1.1770.92
129_V135_Y1.1760.92
139_K147_Q1.1760.92
283_I293_A1.1750.92
139_K151_Q1.1720.92
267_C272_T1.1650.92
138_R144_F1.1640.92
137_K140_E1.1620.92
358_D361_E1.1580.92
138_R146_E1.1570.91
135_Y139_K1.1550.91
134_H138_R1.1530.91
101_K106_E1.1510.91
139_K144_F1.1490.91
132_D136_M1.1440.91
135_Y143_A1.1430.91
244_P247_P1.1420.91
131_E137_K1.1420.91
220_P223_P1.1390.91
139_K148_L1.1380.91
240_Q243_A1.1380.91
129_V132_D1.1350.90
129_V136_M1.1300.90
339_T344_S1.1270.90
139_K143_A1.1240.90
116_A121_Q1.1200.90
110_S119_Y1.1180.90
114_L118_K1.1160.89
109_F117_Q1.1160.89
237_A240_Q1.1130.89
141_A145_E1.1110.89
97_Y100_E1.1110.89
220_P232_A1.1100.89
96_M103_I1.1100.89
133_R138_R1.1090.89
138_R141_A1.1090.89
139_K149_L1.1080.89
112_E116_A1.1060.89
149_L153_M1.1050.89
126_E135_Y1.1050.89
128_W136_M1.1040.89
116_A120_N1.1030.89
111_F119_Y1.1030.89
128_W132_D1.1030.89
133_R143_A1.0990.88
111_F117_Q1.0980.88
150_K157_H1.0950.88
126_E129_V1.0940.88
117_Q120_N1.0940.88
240_Q244_P1.0940.88
95_V105_G1.0920.88
133_R137_K1.0910.88
283_I300_T1.0910.88
127_Q137_K1.0910.88
128_W135_Y1.0870.88
129_V137_K1.0870.88
138_R143_A1.0870.88
130_N134_H1.0870.88
365_Q370_S1.0860.88
110_S118_K1.0860.88
99_K102_L1.0860.88
116_A122_R1.0860.88
338_P342_D1.0850.88
144_F150_K1.0800.87
127_Q132_D1.0800.87
108_E122_R1.0790.87
124_K137_K1.0740.87
128_W133_R1.0740.87
112_E118_K1.0740.87
128_W141_A1.0730.87
359_A362_A1.0690.87
128_W134_H1.0670.86
138_R150_K1.0670.86
104_R108_E1.0660.86
125_H133_R1.0650.86
96_M100_E1.0650.86
114_L121_Q1.0640.86
280_G293_A1.0630.86
229_I257_M1.0620.86
98_C101_K1.0610.86
116_A119_Y1.0590.86
135_Y145_E1.0590.86
128_W131_E1.0560.86
131_E134_H1.0550.86
133_R145_E1.0520.85
137_K144_F1.0520.85
128_W137_K1.0510.85
97_Y101_K1.0500.85
117_Q121_Q1.0470.85
93_Q105_G1.0460.85
100_E113_E1.0450.85
123_R127_Q1.0440.85
160_L164_V1.0420.85
138_R156_L1.0410.85
131_E136_M1.0410.85
106_E115_R1.0400.84
95_V103_I1.0400.84
146_E159_K1.0400.84
234_V259_A1.0370.84
145_E150_K1.0360.84
148_L160_L1.0360.84
88_K91_V1.0320.84
149_L154_D1.0300.84
280_G300_T1.0300.84
234_V237_A1.0300.84
115_R123_R1.0290.84
270_K273_H1.0280.83
95_V99_K1.0270.83
97_Y105_G1.0260.83
127_Q134_H1.0250.83
93_Q98_C1.0250.83
149_L155_E1.0240.83
121_Q127_Q1.0230.83
99_K110_S1.0230.83
127_Q135_Y1.0230.83
135_Y147_Q1.0210.83
127_Q136_M1.0200.83
141_A148_L1.0200.83
147_Q151_Q1.0200.83
367_N370_S1.0190.83
140_E144_F1.0170.83
132_D146_E1.0150.82
98_C112_E1.0150.82
407_P410_A1.0150.82
92_E96_M1.0140.82
123_R136_M1.0140.82
96_M104_R1.0140.82
146_E161_H1.0130.82
246_V259_A1.0130.82
141_A152_K1.0120.82
135_Y146_E1.0120.82
104_R114_L1.0120.82
390_F393_G1.0120.82
133_R140_E1.0110.82
98_C115_R1.0110.82
136_M145_E1.0110.82
90_D94_V1.0090.82
395_K401_P1.0090.82
163_V167_S1.0090.82
95_V98_C1.0080.82
133_R141_A1.0070.82
223_P239_S1.0060.82
109_F116_A1.0060.82
266_G269_N1.0050.82
147_Q159_K1.0030.81
105_G108_E1.0020.81
152_K165_E1.0020.81
104_R109_F1.0020.81
96_M107_S1.0010.81
119_Y133_R1.0010.81
144_F151_Q1.0000.81
233_L262_S1.0000.81
125_H129_V1.0000.81
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  
2n25A1099.80.814Contact Map
2dlqA10.182899.80.82Contact Map
1wjpA10.162899.80.82Contact Map
2dmiA10.165999.80.82Contact Map
2lt7A10.202899.80.82Contact Map
1ubdC10.16999.80.823Contact Map
2ee8A10.162899.80.824Contact Map
2jp9A10.170599.80.824Contact Map
2dmdA10.147599.80.825Contact Map
2yt9A10.142999.80.825Contact 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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