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OPENSEQ.org
cIp_4_40_cIV_2_40
Genes: A B A+B
Length: 463 227 619
Sequences: 2150 4148 646
Seq/Len: 4.64 18.27 1.04
MirrorTree (Pazo et al. 2001) 0.42
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 0.04
10 0.01 0.00 0.06
20 0.02 0.00 0.09
100 0.03 0.01 0.18
∞ 0.09 0.02 0.94
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
160_N 183_T 1.25 0.58 0.00
246_Q 192_Y 1.16 0.49 0.00
106_V 97_I 1.09 0.43 0.00
180_L 99_S 1.08 0.42 0.00
106_V 191_V 1.06 0.40 0.00
305_T 23_F 1.05 0.39 0.00
162_R 144_L 1.04 0.39 0.00
353_P 146_I 0.97 0.33 0.00
443_M 219_F 0.97 0.33 0.00
448_V 143_V 0.95 0.31 0.00
192_L 168_L 0.92 0.29 0.00
440_K 146_I 0.92 0.29 0.00
281_E 97_I 0.90 0.27 0.00
82_L 100_I 0.90 0.27 0.00
449_A 58_A 0.89 0.26 0.00
277_V 219_F 0.88 0.25 0.00
82_L 221_M 0.87 0.25 0.00
360_D 180_N 0.87 0.25 0.00
98_V 154_I 0.87 0.24 0.00
154_A 190_G 0.84 0.23 0.00
242_D 43_F 0.84 0.23 0.00
412_V 97_I 0.83 0.22 0.00
429_F 147_E 0.83 0.22 0.00
173_L 147_E 0.82 0.22 0.00
194_L 211_L 0.82 0.21 0.00
161_I 140_N 0.81 0.21 0.00
170_I 97_I 0.81 0.21 0.00
225_A 61_M 0.80 0.20 0.00
277_V 9_L 0.80 0.20 0.00
339_Q 14_S 0.80 0.20 0.00
334_V 112_D 0.80 0.20 0.00
167_A 63_T 0.79 0.20 0.00
177_I 58_A 0.78 0.19 0.00
342_R 218_I 0.78 0.19 0.00
296_S 192_Y 0.77 0.19 0.00
167_A 100_I 0.77 0.19 0.00
341_L 41_A 0.77 0.19 0.00
318_V 30_I 0.77 0.19 0.00
323_R 150_I 0.76 0.18 0.00
318_V 212_E 0.76 0.18 0.00
444_L 225_F 0.76 0.18 0.00
279_T 215_P 0.76 0.18 0.00
409_V 218_I 0.75 0.17 0.00
338_R 97_I 0.75 0.17 0.00
447_V 76_I 0.75 0.17 0.00
188_T 205_S 0.75 0.17 0.00
411_L 87_T 0.75 0.17 0.00
158_L 219_F 0.74 0.17 0.00
345_A 68_L 0.74 0.17 0.00
344_I 63_T 0.74 0.17 0.00
356_I 154_I 0.74 0.17 0.00
279_T 75_L 0.73 0.16 0.00
281_E 37_L 0.73 0.16 0.00
339_Q 83_I 0.72 0.16 0.00
353_P 58_A 0.72 0.16 0.00
318_V 57_D 0.72 0.16 0.00
232_V 38_V 0.71 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
4507 1 cIp_4_80_cIV_2_60 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4506 0.43 cIp_4_80_cIV_2_60 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4505 0.16 cIp_4_80_cIV_2_80 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4294 1.04 cIp_4_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4293 1.46 cIp_4_4_cIV_2_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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