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OPENSEQ.org
cIp_3_4_cIV_3_4
Genes: A B A+B
Length: 727 261 947
Sequences: 1951 2963 424
Seq/Len: 2.68 11.35 0.45
MirrorTree (Pazo et al. 2001) 0.11
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.01
10 0.01 0.00 0.01
20 0.01 0.00 0.02
100 0.03 0.00 0.07
∞ 0.09 0.01 0.43
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
102_I 31_L 1.22 0.33 0.00
36_V 258_W 1.15 0.28 0.00
96_V 136_V 1.14 0.28 0.00
466_L 116_W 1.07 0.24 0.00
320_E 164_L 1.05 0.23 0.00
318_S 175_L 1.04 0.22 0.00
206_V 23_S 1.01 0.21 0.00
402_L 108_P 1.00 0.20 0.00
102_I 21_A 0.99 0.20 0.00
335_G 154_N 0.98 0.19 0.00
259_S 53_T 0.97 0.19 0.00
346_V 95_A 0.96 0.18 0.00
543_K 129_V 0.95 0.18 0.00
32_I 23_S 0.95 0.18 0.00
153_F 18_L 0.94 0.17 0.00
36_V 20_G 0.94 0.17 0.00
41_V 26_L 0.93 0.17 0.00
97_M 195_S 0.91 0.16 0.00
251_I 23_S 0.90 0.16 0.00
630_A 192_I 0.90 0.16 0.00
35_F 198_F 0.90 0.16 0.00
49_V 27_M 0.89 0.15 0.00
39_Q 210_I 0.89 0.15 0.00
101_N 47_L 0.89 0.15 0.00
82_I 219_F 0.89 0.15 0.00
206_V 206_L 0.88 0.15 0.00
251_I 35_F 0.88 0.15 0.00
259_S 196_T 0.88 0.15 0.00
250_S 176_L 0.88 0.15 0.00
622_I 100_A 0.87 0.15 0.00
324_S 175_L 0.87 0.15 0.00
617_R 21_A 0.86 0.14 0.00
646_L 167_I 0.85 0.14 0.00
318_S 216_T 0.85 0.14 0.00
81_E 195_S 0.85 0.14 0.00
82_I 45_L 0.85 0.14 0.00
405_T 100_A 0.84 0.14 0.00
457_S 22_L 0.84 0.13 0.00
622_I 174_T 0.83 0.13 0.00
102_I 55_Y 0.83 0.13 0.00
432_I 51_T 0.83 0.13 0.00
641_Q 175_L 0.82 0.13 0.00
331_Q 50_N 0.82 0.13 0.00
545_L 198_F 0.82 0.13 0.00
58_M 224_M 0.82 0.13 0.00
153_F 84_I 0.81 0.13 0.00
496_I 126_P 0.81 0.13 0.00
31_L 189_S 0.81 0.12 0.00
251_I 206_L 0.81 0.12 0.00
143_S 225_F 0.81 0.12 0.00
418_I 165_I 0.81 0.12 0.00
400_V 209_I 0.80 0.12 0.00
588_A 50_N 0.80 0.12 0.00
337_D 230_K 0.80 0.12 0.00
84_K 191_G 0.80 0.12 0.00
333_F 21_A 0.80 0.12 0.00
614_G 136_V 0.79 0.12 0.00
684_L 10_M 0.79 0.12 0.00
535_E 19_T 0.79 0.12 0.00
336_K 164_L 0.79 0.12 0.00
328_G 140_S 0.79 0.12 0.00
593_S 167_I 0.79 0.12 0.00
496_I 26_L 0.78 0.12 0.00
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
4189 0.45 cIp_3_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4188 0.37 cIp_3_40_cIV_3_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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