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1R6C_X Clp protease subunit ClpA 2W9R_A Clp protease adaptor protein ClpS

Genes: A B A+B
Length: 143 108 241
Sequences: 5425 798 583
Seq/Len: 37.94 7.39 2.42
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 2.27
2 0.01 0.00 2.29
5 0.02 0.00 2.30
10 0.03 0.00 2.31
20 0.04 0.00 2.32
100 0.06 0.00 2.37
0.17 0.02 2.61
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!

GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution.
Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
83_S 79_E 1.35 0.88 0.25
139_S 102_T 1.29 0.84 0.21
112_I 29_K 1.21 0.79 0.17
132_L 29_K 1.14 0.72 0.14
119_Q 22_L 1.11 0.70 0.13
8_L 68_Q 1.07 0.66 0.11
20_H 79_E 1.06 0.65 0.11
53_A 61_L 1.03 0.61 0.10
31_L 101_C 1.00 0.58 0.09
123_L 53_Y 0.99 0.57 0.08
142_T 76_F 0.99 0.57 0.08
66_T 70_K 0.95 0.52 0.07
117_E 78_A 0.94 0.51 0.07
128_E 105_K 0.93 0.50 0.07
7_E 101_C 0.92 0.49 0.07
134_V 79_E 0.92 0.48 0.06
58_L 76_F 0.91 0.48 0.06
56_Q 93_R 0.91 0.48 0.06
138_I 61_L 0.91 0.48 0.06
28_E 62_M 0.89 0.45 0.06
136_N 99_L 0.86 0.42 0.05
53_A 12_Q 0.84 0.40 0.05
85_Q 73_C 0.84 0.39 0.05
98_S 59_T 0.84 0.39 0.05
86_R 82_E 0.84 0.39 0.05
19_E 12_Q 0.83 0.38 0.05
50_D 46_V 0.82 0.38 0.04
124_L 77_T 0.82 0.38 0.04
110_V 80_V 0.82 0.37 0.04
139_S 103_L 0.81 0.36 0.04
37_N 79_E 0.81 0.36 0.04
61_F 37_Y 0.80 0.35 0.04
112_I 76_F 0.80 0.35 0.04
55_R 80_V 0.79 0.34 0.04
92_V 45_D 0.79 0.34 0.04
127_H 78_A 0.78 0.33 0.04
132_L 103_L 0.78 0.33 0.04
117_E 65_V 0.78 0.33 0.04
105_G 38_T 0.78 0.33 0.04
129_V 15_E 0.77 0.32 0.04
44_L 41_E 0.77 0.32 0.04
25_M 78_A 0.77 0.32 0.04
117_E 23_K 0.77 0.32 0.04
40_A 85_V 0.76 0.31 0.04
56_Q 52_S 0.76 0.31 0.04
106_A 39_P 0.76 0.31 0.03
4_Q 103_L 0.76 0.31 0.03
128_E 78_A 0.76 0.31 0.03
37_N 16_E 0.75 0.30 0.03
107_N 97_H 0.75 0.30 0.03
139_S 41_E 0.75 0.30 0.03
45_E 61_L 0.75 0.30 0.03
33_A 59_T 0.75 0.30 0.03
9_S 31_I 0.74 0.29 0.03
59_E 27_M 0.74 0.29 0.03
1_M 88_V 0.74 0.29 0.03
42_E 65_V 0.74 0.29 0.03
74_E 32_L 0.74 0.29 0.03
25_M 33_V 0.73 0.28 0.03
34_L 67_Y 0.73 0.28 0.03
50_D 48_Q 0.73 0.28 0.03
36_S 50_F 0.72 0.27 0.03
72_S 94_E 0.72 0.27 0.03
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)

ID Seq/Len Name Options I_Prob Status
4117 2.42 1R6C_X Clp protease subunit ClpA 2W9R_A Clp protease adaptor protein ClpS Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.25 Done - Shared
4082 2.76 1R6C_X Clp protease subunit ClpA 2W9R_A Clp protease adaptor protein ClpS Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.73 Done - Shared

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