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OPENSEQ.org
cIV_B_10_cI_A_20_Pdenitr
Genes: A B A+B
Length: 252 121 346
Sequences: 4618 4481 2816
Seq/Len: 18.33 37.03 8.14
MirrorTree (Pazo et al. 2001) 0.71
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 0.16
2 0.00 0.00 0.31
5 0.00 0.00 4.98
10 0.01 0.00 5.38
20 0.01 0.00 5.55
100 0.02 0.01 5.73
∞ 0.04 0.02 7.55
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
46_T 117_A 1.06 0.92 0.07
92_I 66_V 1.06 0.92 0.07
76_P 84_A 1.02 0.90 0.06
23_A 79_F 0.96 0.86 0.05
54_L 119_E 0.91 0.82 0.04
137_L 67_S 0.89 0.80 0.04
17_G 68_I 0.88 0.79 0.04
47_I 26_I 0.84 0.75 0.03
114_I 37_P 0.84 0.75 0.03
164_V 53_D 0.84 0.74 0.03
51_L 81_F 0.83 0.74 0.03
52_L 83_W 0.82 0.73 0.03
160_N 119_E 0.82 0.73 0.03
239_Y 39_P 0.82 0.72 0.03
111_D 102_L 0.81 0.70 0.03
106_M 67_S 0.80 0.70 0.03
230_V 121_A 0.80 0.69 0.03
19_N 53_D 0.79 0.67 0.03
169_K 117_A 0.77 0.66 0.03
67_V 14_F 0.77 0.65 0.03
243_L 17_M 0.76 0.64 0.03
237_E 16_G 0.76 0.64 0.03
141_K 117_A 0.76 0.64 0.03
162_V 68_I 0.76 0.64 0.03
44_A 62_R 0.75 0.63 0.03
131_G 95_F 0.75 0.62 0.03
112_L 94_A 0.74 0.61 0.02
200_A 72_I 0.74 0.61 0.02
21_Q 105_L 0.73 0.60 0.02
177_T 72_I 0.73 0.60 0.02
92_I 115_K 0.73 0.59 0.02
239_Y 44_A 0.73 0.59 0.02
58_V 100_V 0.73 0.58 0.02
27_L 13_V 0.73 0.58 0.02
162_V 83_W 0.72 0.58 0.02
228_P 49_F 0.71 0.57 0.02
231_V 37_P 0.71 0.56 0.02
180_I 30_A 0.71 0.56 0.02
239_Y 6_Q 0.71 0.56 0.02
55_I 85_V 0.71 0.56 0.02
238_K 95_F 0.71 0.56 0.02
244_A 45_Y 0.71 0.56 0.02
187_A 121_A 0.71 0.56 0.02
103_S 117_A 0.70 0.55 0.02
42_I 117_A 0.70 0.55 0.02
56_C 77_V 0.70 0.55 0.02
66_P 107_V 0.70 0.54 0.02
23_A 69_L 0.70 0.54 0.02
170_V 102_L 0.69 0.53 0.02
155_L 68_I 0.69 0.53 0.02
54_L 19_S 0.69 0.53 0.02
180_I 78_A 0.69 0.53 0.02
195_V 115_K 0.69 0.52 0.02
83_L 20_A 0.69 0.52 0.02
205_S 119_E 0.68 0.51 0.02
114_I 94_A 0.68 0.50 0.02
49_V 105_L 0.67 0.50 0.02
146_D 55_A 0.67 0.50 0.02
139_L 115_K 0.67 0.50 0.02
42_I 83_W 0.67 0.49 0.02
190_V 25_L 0.67 0.49 0.02
117_I 91_S 0.67 0.49 0.02
48_F 72_I 0.67 0.49 0.02
225_A 60_D 0.67 0.49 0.02
77_I 27_L 0.67 0.49 0.02
204_F 79_F 0.66 0.48 0.02
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
3230 8.06 cIV_B_4_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3229 8.65 cIV_B_20_cI_A_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3228 8.14 cIV_B_10_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3227 8.15 cIV_B_20_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3226 0.91 cIV_B_40_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3225 8.81 cIV_B_2_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3224 1.06 cIV_B_2_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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