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cIV_C_60_cI_N_20_8_human
Genes: A B A+B
Length: 261 347 603
Sequences: 2363 18904 2674
Seq/Len: 9.05 54.48 4.43
MirrorTree (Pazo et al. 2001) 0.49
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 0.53 0.49
2 0.00 0.58 1.97
5 0.00 0.62 3.64
10 0.00 0.65 3.79
20 0.00 0.65 3.83
100 0.00 0.65 3.93
∞ 0.00 0.65 4.40
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
174_T 273_N 1.04 0.80 0.03
65_S 196_Y 0.98 0.74 0.03
250_L 55_A 0.93 0.68 0.02
8_Y 148_S 0.92 0.67 0.02
61_V 273_N 0.88 0.62 0.02
121_I 196_Y 0.86 0.59 0.02
153_E 166_S 0.85 0.58 0.02
62_T 222_N 0.84 0.56 0.02
8_Y 224_S 0.83 0.56 0.02
72_T 284_T 0.82 0.53 0.02
35_F 54_E 0.81 0.52 0.02
135_S 301_S 0.80 0.51 0.02
8_Y 70_L 0.79 0.50 0.02
62_T 19_I 0.79 0.49 0.02
30_G 189_W 0.78 0.49 0.02
101_F 270_F 0.78 0.48 0.01
168_L 310_N 0.78 0.48 0.01
206_L 86_M 0.77 0.47 0.01
253_Y 156_T 0.77 0.47 0.01
92_L 189_W 0.77 0.47 0.01
139_A 244_I 0.77 0.46 0.01
61_V 100_M 0.75 0.44 0.01
136_V 206_T 0.75 0.44 0.01
109_T 96_L 0.75 0.44 0.01
139_A 331_A 0.75 0.44 0.01
185_P 271_T 0.75 0.44 0.01
111_Q 158_S 0.74 0.43 0.01
65_S 149_L 0.74 0.43 0.01
253_Y 127_G 0.74 0.43 0.01
253_Y 83_Q 0.73 0.42 0.01
168_L 96_L 0.73 0.42 0.01
238_A 168_G 0.73 0.42 0.01
12_K 75_L 0.73 0.42 0.01
47_L 70_L 0.72 0.40 0.01
6_H 23_S 0.72 0.40 0.01
224_M 281_I 0.72 0.40 0.01
256_I 70_L 0.72 0.40 0.01
100_A 277_I 0.72 0.40 0.01
217_I 344_L 0.71 0.39 0.01
143_S 166_S 0.71 0.39 0.01
253_Y 236_K 0.71 0.39 0.01
25_L 165_G 0.71 0.39 0.01
143_S 164_A 0.71 0.38 0.01
225_F 266_I 0.70 0.38 0.01
144_I 93_Y 0.70 0.38 0.01
154_N 324_P 0.70 0.38 0.01
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.65 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
4561 3.97 cIV_C_40_cI_N_20_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.89 Done - Shared
4560 4.43 cIV_C_60_cI_N_20_8_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4559 3.96 cIV_C_60_cI_N_40_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.89 Done - Shared
4558 3.29 cIV_C_60_cI_N_40_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.80 Done - Shared
4557 2.14 cIV_C_60_cI_N_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.69 Done - Shared
4555 1.79 cIV_C_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4554 1.79 cIV_C_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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