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OPENSEQ.org
cIp_2_40_cytb_40_human
Genes: A B A+B
Length: 249 378 578
Sequences: 1028 4493 225
Seq/Len: 4.13 11.89 0.39
MirrorTree (Pazo et al. 2001) 0.88
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 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.02
∞ 0.00 0.00 0.36
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
204_I 320_L 1.57 0.54 0.00
137_T 204_G 1.47 0.47 0.00
136_T 44_Q 1.47 0.46 0.00
170_T 340_G 1.45 0.46 0.00
207_E 231_G 1.44 0.45 0.00
206_D 185_L 1.39 0.41 0.00
171_L 37_L 1.39 0.41 0.00
165_P 68_H 1.39 0.41 0.00
197_T 49_L 1.34 0.38 0.00
231_L 188_I 1.30 0.35 0.00
198_A 43_L 1.29 0.34 0.00
93_L 238_S 1.29 0.34 0.00
136_T 317_F 1.21 0.29 0.00
214_P 350_I 1.21 0.29 0.00
171_L 32_N 1.19 0.28 0.00
204_I 364_I 1.19 0.28 0.00
101_V 232_L 1.18 0.27 0.00
198_A 40_C 1.18 0.27 0.00
131_H 343_V 1.17 0.27 0.00
136_T 54_H 1.15 0.26 0.00
59_N 364_I 1.15 0.26 0.00
94_P 374_N 1.14 0.25 0.00
122_Y 103_Y 1.14 0.25 0.00
122_Y 296_L 1.11 0.24 0.00
114_E 54_H 1.11 0.24 0.00
213_I 15_N 1.09 0.23 0.00
214_P 231_G 1.09 0.23 0.00
171_L 36_L 1.08 0.22 0.00
98_M 4_M 1.08 0.22 0.00
64_E 156_I 1.08 0.22 0.00
117_T 195_L 1.06 0.21 0.00
155_K 246_S 1.06 0.21 0.00
84_D 37_L 1.06 0.21 0.00
150_E 114_N 1.06 0.21 0.00
121_M 280_I 1.05 0.21 0.00
106_Q 189_I 1.05 0.21 0.00
162_E 65_S 1.04 0.20 0.00
187_Q 149_L 1.04 0.20 0.00
208_L 205_S 1.04 0.20 0.00
156_L 37_L 1.04 0.20 0.00
156_L 35_S 1.03 0.20 0.00
129_K 303_M 1.03 0.20 0.00
129_K 96_L 1.03 0.20 0.00
153_Q 8_N 1.02 0.19 0.00
161_G 205_S 1.02 0.19 0.00
166_D 239_L 1.02 0.19 0.00
94_P 98_I 1.00 0.18 0.00
141_M 44_Q 0.99 0.18 0.00
193_Y 82_L 0.99 0.18 0.00
98_M 164_I 0.99 0.18 0.00
233_S 127_A 0.98 0.18 0.00
76_A 171_D 0.98 0.18 0.00
216_P 82_L 0.98 0.18 0.00
59_N 326_W 0.98 0.18 0.00
147_S 218_I 0.98 0.18 0.00
190_D 171_D 0.98 0.17 0.00
164_T 102_L 0.98 0.17 0.00
161_G 79_I 0.97 0.17 0.00
204_I 340_G 0.97 0.17 0.00
51_T 5_R 0.97 0.17 0.00
171_L 35_S 0.97 0.17 0.00
99_N 148_N 0.97 0.17 0.00
161_G 156_I 0.96 0.17 0.00
94_P 168_Y 0.96 0.17 0.00
69_N 120_L 0.96 0.17 0.00
146_D 361_T 0.95 0.17 0.00
165_P 121_L 0.95 0.17 0.00
203_E 178_F 0.95 0.16 0.00
191_N 315_M 0.95 0.16 0.00
197_T 171_D 0.95 0.16 0.00
45_P 156_I 0.95 0.16 0.00
145_S 352_Q 0.94 0.16 0.00
208_L 35_S 0.94 0.16 0.00
212_K 23_T 0.94 0.16 0.00
193_Y 47_T 0.94 0.16 0.00
215_K 21_L 0.94 0.16 0.00
169_F 370_S 0.94 0.16 0.00
122_Y 57_P 0.93 0.16 0.00
208_L 322_Q 0.93 0.16 0.00
82_V 355_S 0.93 0.15 0.00
91_G 171_D 0.92 0.15 0.00
94_P 311_K 0.92 0.15 0.00
122_Y 350_I 0.92 0.15 0.00
67_V 82_L 0.92 0.15 0.00
68_K 47_T 0.92 0.15 0.00
73_G 85_N 0.91 0.15 0.00
228_A 78_I 0.91 0.15 0.00
96_S 163_W 0.91 0.15 0.00
127_V 359_F 0.90 0.14 0.00
94_P 149_L 0.90 0.14 0.00
188_I 231_G 0.90 0.14 0.00
208_L 233_L 0.90 0.14 0.00
81_P 353_V 0.90 0.14 0.00
104_V 189_I 0.90 0.14 0.00
220_S 169_S 0.90 0.14 0.00
72_E 292_L 0.90 0.14 0.00
101_V 322_Q 0.89 0.14 0.00
130_Y 364_I 0.89 0.14 0.00
94_P 337_W 0.89 0.14 0.00
148_I 205_S 0.89 0.14 0.00
146_D 340_G 0.88 0.14 0.00
114_E 265_P 0.88 0.14 0.00
69_N 112_T 0.88 0.14 0.00
142_L 358_Y 0.88 0.14 0.00
170_T 68_H 0.88 0.14 0.00
190_D 322_Q 0.88 0.14 0.00
237_P 371_L 0.88 0.14 0.00
75_K 47_T 0.88 0.14 0.00
162_E 320_L 0.87 0.14 0.00
61_K 49_L 0.87 0.14 0.00
213_I 122_A 0.87 0.14 0.00
106_Q 277_A 0.87 0.14 0.00
59_N 150_L 0.87 0.14 0.00
220_S 58_D 0.87 0.13 0.00
61_K 155_Y 0.87 0.13 0.00
187_Q 31_W 0.87 0.13 0.00
76_A 345_Y 0.87 0.13 0.00
215_K 96_L 0.86 0.13 0.00
165_P 189_I 0.86 0.13 0.00
148_I 239_L 0.86 0.13 0.00
66_I 221_H 0.86 0.13 0.00
201_I 348_T 0.86 0.13 0.00
120_T 256_Y 0.86 0.13 0.00
161_G 4_M 0.86 0.13 0.00
106_Q 49_L 0.86 0.13 0.00
219_R 249_L 0.86 0.13 0.00
210_A 353_V 0.86 0.13 0.00
147_S 169_S 0.85 0.13 0.00
236_E 371_L 0.85 0.13 0.00
197_T 84_A 0.85 0.13 0.00
150_E 363_L 0.85 0.13 0.00
82_V 150_L 0.85 0.13 0.00
204_I 252_D 0.85 0.13 0.00
214_P 118_I 0.85 0.13 0.00
172_I 169_S 0.85 0.13 0.00
161_G 299_L 0.85 0.13 0.00
64_E 36_L 0.85 0.13 0.00
53_F 310_S 0.85 0.13 0.00
169_F 285_P 0.85 0.13 0.00
186_V 14_I 0.84 0.13 0.00
67_V 329_A 0.84 0.13 0.00
85_L 85_N 0.84 0.13 0.00
61_K 99_G 0.84 0.12 0.00
188_I 173_P 0.84 0.12 0.00
94_P 263_N 0.84 0.12 0.00
96_S 173_P 0.84 0.12 0.00
74_H 79_I 0.84 0.12 0.00
68_K 372_I 0.84 0.12 0.00
236_E 190_A 0.84 0.12 0.00
54_D 191_A 0.84 0.12 0.00
94_P 297_S 0.84 0.12 0.00
223_F 258_L 0.84 0.12 0.00
210_A 194_T 0.84 0.12 0.00
199_K 365_L 0.84 0.12 0.00
204_I 10_L 0.84 0.12 0.00
130_Y 243_T 0.84 0.12 0.00
77_A 164_I 0.84 0.12 0.00
75_K 39_A 0.84 0.12 0.00
221_G 337_W 0.84 0.12 0.00
200_D 171_D 0.83 0.12 0.00
67_V 47_T 0.83 0.12 0.00
142_L 225_T 0.83 0.12 0.00
94_P 303_M 0.83 0.12 0.00
165_P 153_I 0.83 0.12 0.00
100_K 237_L 0.83 0.12 0.00
221_G 237_L 0.83 0.12 0.00
229_G 121_L 0.83 0.12 0.00
186_V 189_I 0.83 0.12 0.00
240_G 125_A 0.83 0.12 0.00
61_K 78_I 0.83 0.12 0.00
103_E 79_I 0.82 0.12 0.00
85_L 18_L 0.82 0.12 0.00
66_I 205_S 0.82 0.12 0.00
82_V 326_W 0.82 0.12 0.00
159_K 43_L 0.82 0.12 0.00
214_P 286_N 0.82 0.12 0.00
84_D 32_N 0.82 0.12 0.00
228_A 211_I 0.82 0.12 0.00
201_I 44_Q 0.82 0.12 0.00
92_W 88_S 0.82 0.12 0.00
117_T 229_A 0.82 0.12 0.00
225_C 303_M 0.82 0.12 0.00
153_Q 153_I 0.82 0.12 0.00
137_T 54_H 0.81 0.12 0.00
168_L 190_A 0.81 0.12 0.00
45_P 89_M 0.81 0.12 0.00
90_N 21_L 0.81 0.12 0.00
239_K 321_S 0.81 0.12 0.00
60_Y 148_N 0.81 0.12 0.00
66_I 334_I 0.81 0.12 0.00
154_K 351_G 0.81 0.12 0.00
66_I 16_H 0.81 0.12 0.00
200_D 148_N 0.81 0.12 0.00
201_I 162_Q 0.81 0.11 0.00
215_K 309_M 0.81 0.11 0.00
138_T 237_L 0.81 0.11 0.00
80_L 12_K 0.81 0.11 0.00
64_E 281_L 0.81 0.11 0.00
85_L 350_I 0.80 0.11 0.00
171_L 93_C 0.80 0.11 0.00
228_A 318_R 0.80 0.11 0.00
127_V 336_T 0.80 0.11 0.00
107_V 109_Y 0.80 0.11 0.00
117_T 369_I 0.80 0.11 0.00
146_D 170_V 0.80 0.11 0.00
98_M 148_N 0.80 0.11 0.00
210_A 185_L 0.80 0.11 0.00
155_K 188_I 0.80 0.11 0.00
215_K 59_A 0.80 0.11 0.00
179_A 173_P 0.80 0.11 0.00
61_K 10_L 0.80 0.11 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
5865 0.25 cIp_2_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5864 0.39 cIp_2_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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