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OPENSEQ.org
cIp_6_4_cIV_1_4
Genes: A B A+B
Length: 213 513 688
Sequences: 415 4454 200
Seq/Len: 1.95 8.68 0.29
MirrorTree (Pazo et al. 2001) 0.21
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 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.02 0.00
10 0.01 0.03 0.00
20 0.01 0.03 0.02
100 0.01 0.05 0.06
∞ 0.01 0.08 0.28
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
178_I 332_M 1.35 0.32 0.00
56_P 501_P 1.22 0.24 0.00
65_A 282_F 1.12 0.20 0.00
180_I 335_S 1.06 0.17 0.00
104_D 107_P 1.05 0.17 0.00
193_G 238_F 1.02 0.16 0.00
72_N 104_L 1.00 0.15 0.00
178_I 124_T 0.98 0.15 0.00
126_L 456_V 0.98 0.15 0.00
193_G 272_G 0.98 0.14 0.00
178_I 143_V 0.97 0.14 0.00
199_R 130_P 0.96 0.14 0.00
152_S 264_K 0.95 0.14 0.00
180_I 183_L 0.94 0.14 0.00
63_V 164_F 0.94 0.13 0.00
198_Q 295_V 0.94 0.13 0.00
52_V 463_T 0.93 0.13 0.00
180_I 419_I 0.93 0.13 0.00
194_I 479_K 0.93 0.13 0.00
201_I 281_G 0.92 0.13 0.00
180_I 442_D 0.92 0.13 0.00
110_F 183_L 0.91 0.12 0.00
70_L 118_V 0.91 0.12 0.00
120_M 276_A 0.90 0.12 0.00
199_R 204_A 0.89 0.12 0.00
201_I 406_D 0.89 0.12 0.00
68_D 110_L 0.89 0.12 0.00
201_I 367_L 0.88 0.12 0.00
51_A 359_A 0.88 0.12 0.00
69_D 110_L 0.88 0.12 0.00
119_V 331_N 0.88 0.12 0.00
63_V 7_L 0.87 0.12 0.00
191_L 345_I 0.87 0.11 0.00
180_I 459_F 0.87 0.11 0.00
79_L 353_L 0.87 0.11 0.00
91_V 382_S 0.87 0.11 0.00
79_L 453_L 0.86 0.11 0.00
68_D 460_I 0.86 0.11 0.00
113_S 434_S 0.85 0.11 0.00
160_Y 276_A 0.85 0.11 0.00
176_V 305_F 0.85 0.11 0.00
194_I 459_F 0.84 0.11 0.00
146_Y 160_G 0.84 0.11 0.00
152_S 257_I 0.84 0.11 0.00
106_F 36_L 0.84 0.11 0.00
60_G 410_A 0.84 0.11 0.00
178_I 173_P 0.84 0.10 0.00
99_P 332_M 0.84 0.10 0.00
145_R 444_P 0.83 0.10 0.00
65_A 477_A 0.83 0.10 0.00
119_V 180_Q 0.83 0.10 0.00
142_P 310_M 0.83 0.10 0.00
194_I 169_I 0.83 0.10 0.00
72_N 507_E 0.82 0.10 0.00
145_R 404_T 0.82 0.10 0.00
109_V 66_I 0.82 0.10 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
4328 0.29 cIp_6_4_cIV_1_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4327 0.22 cIp_6_40_cIV_1_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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