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OPENSEQ.org
cIp_4_4_cIV_3_4
Genes: A B A+B
Length: 463 261 655
Sequences: 3147 2963 426
Seq/Len: 6.8 11.35 0.65
MirrorTree (Pazo et al. 2001) 0.24
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 0.01
2 0.01 0.00 0.02
5 0.02 0.00 0.03
10 0.02 0.00 0.05
20 0.03 0.00 0.09
100 0.05 0.00 0.17
∞ 0.11 0.01 0.59
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
412_V 254_V 1.27 0.46 0.00
339_Q 123_P 1.24 0.43 0.00
353_P 65_S 1.22 0.42 0.00
106_V 84_I 1.16 0.36 0.00
418_R 168_L 1.15 0.36 0.00
434_G 47_L 1.08 0.31 0.00
155_V 131_L 1.08 0.31 0.00
295_G 194_G 1.03 0.28 0.00
318_V 213_T 1.02 0.27 0.00
450_I 43_L 1.01 0.27 0.00
102_S 111_Q 1.00 0.26 0.00
220_A 63_R 1.00 0.26 0.00
197_M 110_P 1.00 0.25 0.00
350_K 210_I 1.00 0.25 0.00
348_L 136_V 0.98 0.24 0.00
386_T 147_A 0.97 0.24 0.00
347_C 176_L 0.97 0.24 0.00
187_V 153_E 0.94 0.22 0.00
163_P 142_V 0.91 0.20 0.00
444_L 192_I 0.91 0.20 0.00
159_L 45_L 0.89 0.20 0.00
98_V 27_M 0.89 0.20 0.00
188_T 110_P 0.89 0.19 0.00
101_L 194_G 0.88 0.19 0.00
277_V 198_F 0.88 0.19 0.00
150_A 255_S 0.88 0.19 0.00
418_R 126_P 0.88 0.19 0.00
106_V 162_A 0.88 0.18 0.00
453_T 28_T 0.87 0.18 0.00
345_A 18_L 0.87 0.18 0.00
291_V 194_G 0.87 0.18 0.00
283_A 83_M 0.87 0.18 0.00
298_I 10_M 0.87 0.18 0.00
275_I 165_I 0.86 0.18 0.00
312_D 213_T 0.86 0.18 0.00
186_A 188_I 0.86 0.18 0.00
261_L 170_G 0.86 0.18 0.00
334_V 129_V 0.85 0.17 0.00
349_N 229_S 0.85 0.17 0.00
107_R 216_T 0.85 0.17 0.00
106_V 106_L 0.85 0.17 0.00
246_Q 213_T 0.85 0.17 0.00
363_V 164_L 0.84 0.17 0.00
144_M 198_F 0.84 0.17 0.00
82_L 219_F 0.84 0.17 0.00
295_G 150_S 0.84 0.17 0.00
454_Q 226_H 0.83 0.17 0.00
320_V 219_F 0.83 0.16 0.00
189_T 170_G 0.83 0.16 0.00
389_Y 160_I 0.83 0.16 0.00
225_A 101_F 0.83 0.16 0.00
399_A 20_G 0.82 0.16 0.00
227_I 52_L 0.82 0.16 0.00
345_A 170_G 0.82 0.16 0.00
425_K 105_S 0.81 0.16 0.00
82_L 54_M 0.81 0.16 0.00
429_F 66_T 0.81 0.16 0.00
320_V 239_A 0.81 0.15 0.00
440_K 161_Q 0.81 0.15 0.00
332_C 48_L 0.81 0.15 0.00
358_V 219_F 0.81 0.15 0.00
78_K 147_A 0.81 0.15 0.00
328_D 167_I 0.81 0.15 0.00
356_I 228_T 0.80 0.15 0.00
150_A 191_G 0.80 0.15 0.00
200_F 43_L 0.80 0.15 0.00
163_P 118_P 0.80 0.15 0.00
415_G 225_F 0.79 0.15 0.00
102_S 48_L 0.79 0.15 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
4312 0.57 cIp_4_20_cIV_3_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4311 0.48 cIp_4_4_cIV_3_4 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4309 0.65 cIp_4_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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