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OPENSEQ.org
cIp_3_40_cIV_A_40
Genes: A B A+B
Length: 674 558 1190
Sequences: 1916 3242 781
Seq/Len: 2.84 5.81 0.66
MirrorTree (Pazo et al. 2001) 0.16
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 0.01 0.01
10 0.01 0.01 0.01
20 0.01 0.02 0.03
100 0.03 0.03 0.12
∞ 0.09 0.06 0.63
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
7_I 490_S 1.12 0.34 0.00
467_L 495_I 1.00 0.26 0.00
519_D 454_I 0.99 0.25 0.00
28_M 349_V 0.96 0.23 0.00
222_A 191_A 0.93 0.22 0.00
335_L 482_F 0.93 0.22 0.00
402_K 328_Y 0.91 0.21 0.00
425_A 294_I 0.90 0.20 0.00
553_L 426_A 0.90 0.20 0.00
380_T 295_S 0.88 0.19 0.00
545_A 270_I 0.88 0.19 0.00
55_V 510_T 0.88 0.19 0.00
292_N 447_L 0.87 0.19 0.00
171_V 188_V 0.86 0.18 0.00
21_T 463_Q 0.86 0.18 0.00
289_I 65_M 0.85 0.18 0.00
433_E 329_T 0.83 0.17 0.00
405_L 405_T 0.83 0.17 0.00
135_Y 185_A 0.83 0.17 0.00
460_V 380_L 0.82 0.16 0.00
263_V 504_I 0.82 0.16 0.00
171_V 46_S 0.80 0.15 0.00
510_N 371_T 0.80 0.15 0.00
525_I 87_W 0.80 0.15 0.00
551_S 286_G 0.80 0.15 0.00
460_V 426_A 0.80 0.15 0.00
71_K 290_I 0.80 0.15 0.00
177_M 417_S 0.80 0.15 0.00
518_I 507_V 0.79 0.15 0.00
428_S 348_A 0.79 0.15 0.00
248_K 549_R 0.79 0.15 0.00
160_S 25_S 0.79 0.15 0.00
433_E 504_I 0.78 0.14 0.00
545_A 370_K 0.78 0.14 0.00
63_A 266_L 0.78 0.14 0.00
406_V 495_I 0.77 0.14 0.00
10_D 247_M 0.77 0.14 0.00
279_L 378_G 0.76 0.14 0.00
23_I 95_G 0.76 0.13 0.00
88_S 427_G 0.75 0.13 0.00
282_Q 487_N 0.75 0.13 0.00
297_P 293_V 0.75 0.13 0.00
298_A 290_I 0.75 0.13 0.00
221_T 44_L 0.75 0.13 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
4005 0.82 cIp_3_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4004 0.66 cIp_3_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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