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OPENSEQ.org
cIp_2_40_cIV_A_40
Genes: A B A+B
Length: 239 558 781
Sequences: 528 3242 158
Seq/Len: 2.21 5.81 0.2
MirrorTree (Pazo et al. 2001) 0.15
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 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.02 0.00
100 0.00 0.03 0.02
∞ 0.00 0.06 0.20
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
109_L 507_V 1.50 0.32 0.00
42_V 53_M 1.30 0.22 0.00
63_D 454_I 1.29 0.22 0.00
53_L 95_G 1.26 0.21 0.00
175_P 294_I 1.18 0.18 0.00
179_P 359_I 1.13 0.16 0.00
81_M 313_A 1.12 0.16 0.00
91_A 314_A 1.10 0.15 0.00
172_G 209_A 1.09 0.15 0.00
93_I 479_P 1.08 0.15 0.00
175_P 454_I 1.06 0.14 0.00
194_A 497_F 1.04 0.13 0.00
149_I 209_A 1.03 0.13 0.00
95_I 290_I 1.02 0.13 0.00
194_A 302_I 1.02 0.13 0.00
21_E 241_A 1.01 0.12 0.00
68_P 502_F 1.00 0.12 0.00
196_A 302_I 1.00 0.12 0.00
82_F 198_I 0.99 0.12 0.00
54_S 266_L 0.98 0.12 0.00
164_A 45_I 0.97 0.12 0.00
73_L 504_I 0.97 0.12 0.00
14_E 346_T 0.97 0.12 0.00
53_L 371_T 0.97 0.12 0.00
149_I 533_T 0.96 0.11 0.00
108_D 147_A 0.95 0.11 0.00
16_T 204_F 0.95 0.11 0.00
158_T 141_G 0.93 0.11 0.00
80_F 329_T 0.93 0.11 0.00
127_D 314_A 0.92 0.10 0.00
11_D 19_F 0.92 0.10 0.00
160_E 321_V 0.91 0.10 0.00
7_P 454_I 0.91 0.10 0.00
63_D 267_Y 0.91 0.10 0.00
32_E 33_I 0.91 0.10 0.00
98_T 49_F 0.91 0.10 0.00
33_G 498_A 0.90 0.10 0.00
28_T 493_A 0.89 0.10 0.00
45_R 58_Q 0.89 0.10 0.00
162_L 172_T 0.89 0.10 0.00
181_N 549_R 0.89 0.10 0.00
72_A 185_A 0.88 0.10 0.00
59_E 34_L 0.88 0.10 0.00
91_A 445_G 0.87 0.09 0.00
165_L 293_V 0.87 0.09 0.00
142_T 257_D 0.87 0.09 0.00
82_F 302_I 0.87 0.09 0.00
159_V 44_L 0.87 0.09 0.00
68_P 39_A 0.86 0.09 0.00
82_F 293_V 0.86 0.09 0.00
109_L 508_F 0.86 0.09 0.00
54_S 265_V 0.86 0.09 0.00
202_E 87_W 0.86 0.09 0.00
21_E 41_I 0.86 0.09 0.00
102_M 267_Y 0.85 0.09 0.00
154_Y 490_S 0.85 0.09 0.00
77_T 372_P 0.85 0.09 0.00
126_A 512_F 0.85 0.09 0.00
34_R 328_Y 0.84 0.09 0.00
44_W 341_M 0.84 0.09 0.00
125_S 353_I 0.84 0.09 0.00
208_V 90_M 0.84 0.09 0.00
45_R 428_V 0.83 0.09 0.00
159_V 524_N 0.83 0.09 0.00
147_A 221_A 0.83 0.09 0.00
186_A 360_A 0.83 0.09 0.00
170_A 301_P 0.83 0.09 0.00
117_I 396_A 0.82 0.08 0.00
179_P 214_L 0.82 0.08 0.00
111_R 194_I 0.81 0.08 0.00
110_I 299_K 0.81 0.08 0.00
17_P 37_F 0.81 0.08 0.00
12_S 543_F 0.81 0.08 0.00
68_P 409_V 0.81 0.08 0.00
127_D 226_I 0.81 0.08 0.00
154_Y 151_A 0.80 0.08 0.00
39_I 185_A 0.80 0.08 0.00
12_S 102_V 0.80 0.08 0.00
106_A 487_N 0.80 0.08 0.00
109_L 130_L 0.80 0.08 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
4029 0.2 cIp_2_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4028 0.4 cIp_2_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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