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OPENSEQ.org
cIV_A_40_cI_J_40_Pdenitr
Genes: A B A+B
Length: 538 200 715
Sequences: 3263 733 435
Seq/Len: 6.07 3.67 0.61
MirrorTree (Pazo et al. 2001) 0.01
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 0.00 0.00 0.02
5 0.01 0.00 0.08
10 0.01 0.00 0.16
20 0.01 0.00 0.21
100 0.02 0.00 0.25
∞ 0.06 0.00 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
411_G 30_V 1.37 0.52 0.00
436_M 150_A 1.31 0.47 0.00
100_M 16_A 1.26 0.43 0.00
114_L 76_D 1.19 0.38 0.00
172_V 98_V 1.14 0.34 0.00
79_G 161_A 1.14 0.34 0.00
481_F 83_K 1.11 0.32 0.00
412_V 21_V 1.11 0.32 0.00
21_F 23_G 1.09 0.30 0.00
483_S 21_V 1.09 0.30 0.00
462_Y 141_D 1.08 0.30 0.00
438_I 94_L 1.07 0.29 0.00
378_S 114_S 1.06 0.29 0.00
26_V 152_L 1.05 0.28 0.00
347_W 66_V 1.04 0.27 0.00
181_A 41_A 1.03 0.27 0.00
369_V 88_R 1.02 0.26 0.00
489_G 76_D 0.99 0.24 0.00
193_A 166_M 0.97 0.23 0.00
490_I 177_V 0.97 0.23 0.00
7_F 139_L 0.97 0.23 0.00
278_I 89_Y 0.96 0.22 0.00
353_F 167_R 0.96 0.22 0.00
23_A 64_V 0.96 0.22 0.00
411_G 140_Y 0.96 0.22 0.00
196_M 104_L 0.95 0.22 0.00
155_S 23_G 0.95 0.22 0.00
429_G 16_A 0.95 0.22 0.00
175_A 34_I 0.95 0.22 0.00
172_V 103_Q 0.95 0.22 0.00
501_V 150_A 0.95 0.21 0.00
172_V 132_T 0.94 0.21 0.00
414_Y 76_D 0.94 0.21 0.00
381_P 35_L 0.94 0.21 0.00
364_L 92_L 0.94 0.21 0.00
381_P 66_V 0.93 0.21 0.00
301_I 152_L 0.93 0.20 0.00
326_L 29_S 0.93 0.20 0.00
533_R 43_L 0.92 0.20 0.00
519_P 12_S 0.92 0.20 0.00
442_L 48_G 0.92 0.20 0.00
201_V 10_A 0.91 0.20 0.00
428_A 166_M 0.91 0.20 0.00
442_L 139_L 0.91 0.20 0.00
23_A 56_L 0.91 0.20 0.00
107_P 17_G 0.91 0.20 0.00
209_F 53_A 0.91 0.19 0.00
12_H 56_L 0.90 0.19 0.00
208_V 146_M 0.90 0.19 0.00
475_I 94_L 0.90 0.19 0.00
176_S 31_L 0.89 0.18 0.00
280_T 53_A 0.88 0.18 0.00
7_F 102_A 0.88 0.18 0.00
207_S 55_L 0.88 0.18 0.00
411_G 153_V 0.88 0.18 0.00
333_V 11_I 0.87 0.18 0.00
276_H 44_F 0.87 0.18 0.00
264_Y 70_F 0.87 0.18 0.00
188_F 32_W 0.86 0.17 0.00
182_I 66_V 0.86 0.17 0.00
127_A 11_I 0.86 0.17 0.00
436_M 76_D 0.86 0.17 0.00
365_F 138_V 0.86 0.17 0.00
238_Q 15_V 0.86 0.17 0.00
274_I 98_V 0.86 0.17 0.00
472_I 159_I 0.86 0.17 0.00
278_I 98_V 0.85 0.17 0.00
532_K 189_M 0.84 0.16 0.00
359_W 77_V 0.84 0.16 0.00
462_Y 102_A 0.84 0.16 0.00
37_M 146_M 0.84 0.16 0.00
9_S 176_N 0.84 0.16 0.00
30_S 10_A 0.84 0.16 0.00
420_S 34_I 0.84 0.16 0.00
39_M 157_A 0.84 0.16 0.00
384_R 49_A 0.84 0.16 0.00
411_G 78_D 0.84 0.16 0.00
339_V 191_L 0.83 0.16 0.00
394_A 27_V 0.83 0.16 0.00
189_L 14_C 0.83 0.16 0.00
20_L 107_A 0.83 0.16 0.00
193_A 22_I 0.83 0.16 0.00
100_M 14_C 0.83 0.16 0.00
172_V 96_I 0.83 0.16 0.00
278_I 30_V 0.83 0.16 0.00
181_A 176_N 0.82 0.15 0.00
178_I 21_V 0.82 0.15 0.00
485_L 143_Y 0.82 0.15 0.00
79_G 169_R 0.82 0.15 0.00
26_V 54_M 0.82 0.15 0.00
12_H 147_F 0.82 0.15 0.00
146_V 193_D 0.81 0.15 0.00
411_G 192_K 0.81 0.15 0.00
273_I 170_K 0.81 0.15 0.00
28_L 192_K 0.81 0.15 0.00
316_M 13_A 0.81 0.15 0.00
124_C 21_V 0.81 0.15 0.00
251_Y 41_A 0.81 0.15 0.00
298_A 172_V 0.81 0.15 0.00
308_A 28_H 0.81 0.15 0.00
72_N 155_L 0.81 0.15 0.00
474_S 139_L 0.81 0.15 0.00
436_M 52_V 0.80 0.15 0.00
378_S 17_G 0.80 0.15 0.00
39_M 52_V 0.80 0.15 0.00
236_G 148_Q 0.80 0.15 0.00
42_Q 36_A 0.80 0.15 0.00
372_V 151_G 0.80 0.15 0.00
316_M 161_A 0.80 0.14 0.00
175_A 81_E 0.80 0.14 0.00
217_L 162_I 0.79 0.14 0.00
439_G 29_S 0.79 0.14 0.00
170_V 173_K 0.79 0.14 0.00
37_M 95_V 0.79 0.14 0.00
466_F 138_V 0.79 0.14 0.00
163_M 196_P 0.78 0.14 0.00
274_I 18_F 0.78 0.14 0.00
479_I 51_F 0.78 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
3468 3.07 cIV_A_4_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.58 Done - Shared
3385 1.55 cIV_A_6_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3384 3.98 cIV_A_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
3380 3.97 cIV_A_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
3378 3.98 cIV_A_10_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3377 3.07 cIV_A_10_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.42 Done - Shared
3372 3.08 cIV_A_6_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.67 Done - Shared
3370 3.98 cIV_A_6_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3369 3.99 cIV_A_6_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
3368 0.61 cIV_A_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3367 4 cIV_A_4_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
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