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OPENSEQ.org
cIp_4_40_cIV_B_40
Genes: A B A+B
Length: 412 298 669
Sequences: 1283 2549 596
Seq/Len: 3.11 8.55 0.89
MirrorTree (Pazo et al. 2001) 0.59
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 0.00 0.00 0.03
10 0.00 0.01 0.05
20 0.01 0.01 0.08
100 0.01 0.02 0.13
∞ 0.03 0.06 0.84
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
52_I 205_A 1.34 0.61 0.00
265_I 240_V 1.28 0.56 0.00
349_V 211_A 1.26 0.54 0.00
265_I 116_L 1.22 0.51 0.00
389_R 195_V 1.18 0.47 0.00
281_M 158_N 1.17 0.46 0.00
53_V 121_I 1.12 0.41 0.00
77_L 199_V 1.11 0.40 0.00
45_V 203_V 1.02 0.33 0.00
109_V 193_V 1.00 0.32 0.00
211_E 100_F 1.00 0.32 0.00
338_F 201_V 0.99 0.31 0.00
309_R 229_A 0.94 0.27 0.00
399_I 82_L 0.93 0.26 0.00
361_V 90_N 0.93 0.26 0.00
302_P 209_I 0.93 0.26 0.00
101_A 239_G 0.92 0.26 0.00
245_L 76_I 0.92 0.26 0.00
242_G 203_V 0.92 0.26 0.00
389_R 272_L 0.92 0.26 0.00
222_I 264_S 0.92 0.25 0.00
136_T 143_I 0.91 0.25 0.00
240_V 53_S 0.91 0.25 0.00
228_A 112_L 0.90 0.24 0.00
122_S 241_Y 0.89 0.24 0.00
396_V 246_S 0.88 0.23 0.00
252_S 63_L 0.87 0.23 0.00
262_D 264_S 0.87 0.23 0.00
233_W 76_I 0.86 0.22 0.00
202_V 145_A 0.86 0.22 0.00
114_A 101_T 0.86 0.21 0.00
361_V 121_I 0.85 0.21 0.00
141_V 264_S 0.85 0.21 0.00
406_V 243_G 0.84 0.20 0.00
306_V 265_Q 0.83 0.20 0.00
109_V 272_L 0.82 0.20 0.00
172_A 106_I 0.82 0.19 0.00
289_K 121_I 0.81 0.19 0.00
351_A 103_N 0.81 0.19 0.00
104_R 39_I 0.81 0.19 0.00
400_I 134_E 0.81 0.19 0.00
224_I 76_I 0.80 0.18 0.00
264_Q 196_G 0.80 0.18 0.00
402_T 103_N 0.80 0.18 0.00
110_I 54_S 0.80 0.18 0.00
215_F 235_V 0.79 0.18 0.00
316_R 66_F 0.79 0.18 0.00
53_V 246_S 0.79 0.18 0.00
228_A 191_V 0.79 0.18 0.00
53_V 70_I 0.78 0.17 0.00
260_E 119_V 0.78 0.17 0.00
358_V 117_I 0.77 0.17 0.00
101_A 74_V 0.77 0.17 0.00
410_V 84_I 0.77 0.17 0.00
286_E 234_S 0.77 0.17 0.00
393_L 37_P 0.77 0.17 0.00
349_V 193_V 0.76 0.16 0.00
53_V 169_E 0.76 0.16 0.00
405_I 268_Y 0.76 0.16 0.00
374_R 221_Q 0.76 0.16 0.00
271_G 271_W 0.76 0.16 0.00
342_A 34_G 0.76 0.16 0.00
289_K 36_L 0.75 0.16 0.00
326_S 138_D 0.75 0.16 0.00
281_M 76_I 0.75 0.16 0.00
213_R 118_L 0.75 0.16 0.00
202_V 195_V 0.75 0.16 0.00
73_S 54_S 0.74 0.15 0.00
120_L 76_I 0.74 0.15 0.00
112_R 116_L 0.74 0.15 0.00
167_A 104_T 0.74 0.15 0.00
296_Q 115_V 0.74 0.15 0.00
374_R 224_V 0.73 0.15 0.00
398_A 103_N 0.73 0.15 0.00
48_L 237_Q 0.73 0.15 0.00
65_R 125_S 0.73 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
4002 0.89 cIp_4_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4001 1.23 cIp_4_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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