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ssh333

ID: 1506516855 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 136 (136)
Sequences: 634 (448.7)
Seq/Len: 4.662
Nf(neff/√len): 38.5

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: 4.662).

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
108_T120_I3.6781.00
47_V50_R2.9741.00
109_N120_I2.5781.00
69_Q85_F2.2661.00
124_D127_L1.9711.00
1_M4_T1.9291.00
1_M5_K1.8631.00
88_S91_M1.8441.00
76_A85_F1.8271.00
104_L107_D1.7461.00
112_A120_I1.6700.99
97_C101_L1.5800.99
109_N112_A1.5490.99
130_R133_G1.5380.99
7_T10_K1.5340.99
103_G107_D1.4780.98
53_R70_R1.4600.98
15_K18_R1.4120.97
7_T12_T1.3990.97
92_A95_E1.3420.96
64_R69_Q1.3390.96
122_P134_E1.3220.95
40_H47_V1.3090.95
103_G134_E1.3030.95
129_R133_G1.2690.94
2_A5_K1.2630.94
41_R45_G1.2610.94
26_A29_S1.2590.94
65_K69_Q1.2580.94
52_I56_Q1.2530.93
128_A132_R1.2530.93
90_V99_A1.2470.93
64_R67_P1.2320.93
26_A30_A1.2210.92
119_T124_D1.2200.92
107_D128_A1.2100.92
77_Q82_D1.1920.91
128_A133_G1.1860.91
123_K127_L1.1770.90
89_A98_E1.1720.90
76_A83_L1.1290.88
76_A82_D1.1230.87
67_P74_E1.1170.87
51_E56_Q1.1150.87
78_D83_L1.1140.87
111_C126_Q1.1070.86
56_Q62_L1.1060.86
104_L128_A1.1040.86
90_V100_Y1.0900.85
113_I116_K1.0900.85
20_Q23_T1.0870.85
66_L69_Q1.0850.85
111_C131_I1.0780.84
34_G37_K1.0720.84
129_R132_R1.0660.83
68_F94_Q1.0590.83
114_H117_R1.0460.82
72_V76_A1.0430.81
69_Q134_E1.0390.81
1_M6_Q1.0390.81
111_C121_M1.0270.80
100_Y103_G1.0240.80
26_A31_P1.0210.79
119_T127_L1.0170.79
88_S97_C1.0170.79
69_Q103_G1.0120.78
16_A19_K1.0110.78
102_V106_E1.0110.78
5_K8_A1.0090.78
13_G16_A1.0070.78
65_K87_S1.0060.78
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  
1tzyC20.72061000.084Contact Map
3r45A10.56621000.161Contact Map
3nquA10.54411000.169Contact Map
2yfvA10.51000.184Contact Map
2l5aA10.55151000.358Contact Map
2hueB10.55151000.409Contact Map
3nqjA10.54411000.416Contact Map
2ly8A10.492699.90.53Contact Map
4jjnB20.632499.90.548Contact Map
1tafB10.514799.70.626Contact 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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