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OPENSEQ.org
cIp_3_4_cIV_B_4
Genes: A B A+B
Length: 674 298 924
Sequences: 1936 3243 724
Seq/Len: 2.87 10.88 0.78
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 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.01
10 0.01 0.01 0.01
20 0.01 0.01 0.02
100 0.03 0.03 0.11
∞ 0.09 0.06 0.74
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
599_G 241_Y 1.33 0.56 0.00
188_I 201_V 1.10 0.36 0.00
79_G 241_Y 1.02 0.30 0.00
376_Q 76_I 1.00 0.29 0.00
72_D 57_A 0.99 0.28 0.00
282_Q 199_V 0.98 0.27 0.00
567_A 54_S 0.97 0.27 0.00
518_I 54_S 0.95 0.25 0.00
508_V 141_L 0.93 0.24 0.00
335_L 199_V 0.93 0.24 0.00
233_I 145_A 0.92 0.23 0.00
28_M 268_Y 0.91 0.23 0.00
296_R 196_G 0.90 0.22 0.00
445_V 254_A 0.90 0.22 0.00
255_I 88_R 0.89 0.22 0.00
399_K 237_Q 0.89 0.21 0.00
16_V 263_V 0.88 0.21 0.00
151_V 73_A 0.88 0.21 0.00
584_L 106_I 0.87 0.21 0.00
365_R 241_Y 0.87 0.20 0.00
377_L 199_V 0.86 0.20 0.00
575_K 108_V 0.86 0.20 0.00
7_I 241_Y 0.84 0.19 0.00
393_I 197_K 0.83 0.19 0.00
602_R 76_I 0.83 0.18 0.00
604_L 143_I 0.82 0.18 0.00
5_R 121_I 0.80 0.17 0.00
304_L 145_A 0.80 0.17 0.00
562_Q 271_W 0.80 0.17 0.00
305_E 240_V 0.78 0.16 0.00
268_I 118_L 0.78 0.16 0.00
14_I 161_V 0.78 0.16 0.00
188_I 138_D 0.78 0.16 0.00
62_P 146_I 0.77 0.16 0.00
429_L 199_V 0.77 0.16 0.00
96_E 77_F 0.77 0.15 0.00
284_L 163_F 0.77 0.15 0.00
367_E 31_D 0.77 0.15 0.00
319_L 214_I 0.77 0.15 0.00
274_F 193_V 0.76 0.15 0.00
171_V 81_L 0.75 0.15 0.00
22_L 119_V 0.75 0.14 0.00
507_V 195_V 0.75 0.14 0.00
445_V 116_L 0.75 0.14 0.00
395_K 113_V 0.74 0.14 0.00
146_N 132_S 0.74 0.14 0.00
510_N 199_V 0.74 0.14 0.00
371_D 263_V 0.74 0.14 0.00
510_N 41_K 0.74 0.14 0.00
33_V 84_I 0.74 0.14 0.00
72_D 238_E 0.74 0.14 0.00
336_V 86_I 0.73 0.14 0.00
502_I 143_I 0.73 0.14 0.00
524_V 30_Q 0.73 0.14 0.00
83_E 145_A 0.73 0.14 0.00
33_V 221_Q 0.73 0.14 0.00
286_R 228_I 0.73 0.14 0.00
335_L 273_A 0.73 0.14 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
4011 0.7 cIp_3_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4010 0.78 cIp_3_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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