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OPENSEQ.org

reduced_algn_FAMILY

ID: 1412957031 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 277 (277)
Sequences: 939 (720.4)
Seq/Len: 3.390
Nf(neff/√len): 43.3

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: 3.390).

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
179_A183_F1.8921.00
64_F271_R1.7410.99
264_L270_V1.7010.99
261_W265_F1.6650.99
260_A263_L1.6450.98
52_I133_F1.6450.98
32_H36_V1.6070.98
253_D260_A1.5750.98
76_E79_K1.5680.98
104_T267_S1.5190.97
154_S157_N1.5100.97
113_I120_G1.4660.96
64_F107_A1.4340.95
49_A153_D1.4280.95
9_I70_F1.4220.95
52_I56_L1.4130.95
7_I11_Q1.3970.94
77_K80_E1.3890.94
9_I16_L1.3500.93
22_Y262_T1.3320.92
190_L210_E1.3110.91
34_A80_E1.3070.91
77_K154_S1.2900.91
75_L79_K1.2840.90
52_I221_T1.2800.90
77_K81_P1.2730.90
40_F260_A1.2680.90
24_L67_L1.2470.88
87_P267_S1.2350.88
111_F115_V1.2290.88
79_K197_V1.2260.87
74_I154_S1.2200.87
252_I256_I1.2090.86
265_F271_R1.2090.86
209_A258_P1.2060.86
32_H35_N1.2010.86
33_K81_P1.1990.86
81_P154_S1.1960.86
133_F179_A1.1920.85
32_H75_L1.1890.85
1_M8_Y1.1890.85
144_V148_S1.1880.85
264_L268_T1.1740.84
70_F171_S1.1730.84
153_D157_N1.1690.84
75_L78_F1.1680.84
56_L91_V1.1610.83
24_L260_A1.1600.83
72_E150_A1.1590.83
75_L157_N1.1570.83
80_E154_S1.1540.83
75_L80_E1.1540.83
76_E154_S1.1520.82
59_F63_R1.1520.82
126_R222_V1.1500.82
172_S254_I1.1430.82
35_N76_E1.1360.81
60_L135_I1.1340.81
63_R175_F1.1330.81
34_A79_K1.1290.81
67_L70_F1.1260.80
11_Q18_T1.1250.80
198_L201_L1.1230.80
108_A223_F1.1220.80
13_C59_F1.1160.80
128_F141_W1.1150.80
205_K258_P1.1130.79
68_G191_T1.1120.79
176_A181_V1.1100.79
10_F14_Y1.1020.78
184_G259_Q1.1010.78
65_V249_T1.1010.78
149_Y234_L1.1000.78
229_F251_A1.1000.78
47_C263_L1.0980.78
179_A204_R1.0970.78
56_L121_I1.0920.78
252_I260_A1.0910.77
34_A74_I1.0910.77
45_T85_M1.0900.77
263_L271_R1.0900.77
135_I142_F1.0880.77
36_V213_L1.0870.77
50_L77_K1.0860.77
77_K156_G1.0860.77
23_A189_F1.0840.77
22_Y142_F1.0830.77
40_F94_Y1.0830.77
267_S270_V1.0810.77
226_I251_A1.0800.76
182_F272_R1.0780.76
74_I152_L1.0760.76
256_I260_A1.0750.76
175_F182_F1.0730.76
49_A76_E1.0730.76
231_Q234_L1.0720.76
93_S107_A1.0700.76
233_I238_I1.0690.75
101_V176_A1.0680.75
177_A258_P1.0670.75
22_Y241_K1.0650.75
92_A229_F1.0640.75
143_M176_A1.0620.75
24_L55_F1.0610.75
58_H243_I1.0600.75
140_M262_T1.0600.75
35_N81_P1.0570.74
48_A156_G1.0560.74
53_T193_G1.0540.74
44_Y220_M1.0530.74
49_A156_G1.0520.74
125_R227_Y1.0520.74
84_W88_Y1.0480.73
43_L274_T1.0480.73
69_F72_E1.0450.73
128_F207_G1.0450.73
63_R269_T1.0450.73
120_G123_H1.0450.73
74_I80_E1.0440.73
77_K155_E1.0440.73
125_R136_P1.0420.73
80_E155_E1.0410.73
56_L196_I1.0390.72
188_L223_F1.0390.72
34_A156_G1.0350.72
181_V185_L1.0340.72
43_L224_T1.0310.72
207_G255_F1.0270.71
65_V105_L1.0250.71
123_H175_F1.0250.71
185_L189_F1.0240.71
34_A50_L1.0220.71
16_L250_F1.0220.71
127_V130_I1.0220.71
214_I220_M1.0220.71
25_N172_S1.0190.70
13_C186_L1.0180.70
36_V49_A1.0170.70
6_G181_V1.0160.70
114_V158_G1.0160.70
56_L141_W1.0140.70
32_H77_K1.0130.70
101_V255_F1.0120.70
93_S194_M1.0100.69
59_F128_F1.0100.69
255_F260_A1.0090.69
247_F250_F1.0080.69
86_M218_I1.0070.69
65_V159_G1.0070.69
152_L155_E1.0060.69
175_F276_R1.0060.69
274_T277_I1.0040.69
45_T189_F1.0040.69
34_A154_S1.0030.69
64_F260_A1.0020.69
246_Q254_I1.0010.68
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: (06Sep14)
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  
2z73A20.953197.60.746Contact Map
4pxzA10.902597.50.747Contact Map
4ea3A20.949597.50.747Contact Map
3emlA10.949597.50.751Contact Map
4ldeA10.93597.50.751Contact Map
3uonA10.949597.40.752Contact Map
4eiyA10.953197.40.752Contact Map
3pblA20.927897.40.752Contact Map
4n6hA10.949597.40.753Contact Map
4mqsA10.920697.40.755Contact 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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