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OPENSEQ.org
cIp_6_4_cyt1_2_human
Genes: A B A+B
Length: 213 325 489
Sequences: 542 747 51
Seq/Len: 2.54 2.3 0.1
MirrorTree (Pazo et al. 2001) 0.44
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.00
100 0.00 0.02 0.02
∞ 0.00 0.02 0.09
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
103_M 213_S 1.81 0.32 0.00
110_F 281_E 1.73 0.29 0.00
127_T 239_G 1.36 0.16 0.00
112_A 174_Y 1.35 0.16 0.00
81_P 109_S 1.35 0.16 0.00
199_R 224_G 1.31 0.15 0.00
98_A 110_I 1.30 0.15 0.00
104_D 109_S 1.30 0.15 0.00
72_N 81_A 1.29 0.14 0.00
173_I 180_P 1.28 0.14 0.00
97_A 211_V 1.27 0.14 0.00
145_R 135_L 1.26 0.14 0.00
142_P 268_K 1.24 0.13 0.00
110_F 111_R 1.23 0.13 0.00
65_A 119_Q 1.22 0.13 0.00
103_M 309_H 1.22 0.13 0.00
47_P 294_M 1.21 0.12 0.00
99_P 148_L 1.21 0.12 0.00
170_C 271_C 1.21 0.12 0.00
119_V 240_Q 1.18 0.12 0.00
68_D 191_G 1.18 0.12 0.00
94_M 286_K 1.18 0.12 0.00
146_Y 109_S 1.17 0.12 0.00
195_L 303_V 1.16 0.11 0.00
72_N 70_G 1.15 0.11 0.00
148_V 266_I 1.15 0.11 0.00
104_D 281_E 1.13 0.11 0.00
195_L 156_D 1.12 0.11 0.00
178_I 212_F 1.12 0.11 0.00
109_V 272_T 1.12 0.11 0.00
68_D 239_G 1.12 0.11 0.00
145_R 191_G 1.11 0.10 0.00
80_W 307_K 1.11 0.10 0.00
47_P 312_S 1.10 0.10 0.00
81_P 224_G 1.10 0.10 0.00
136_K 164_M 1.10 0.10 0.00
112_A 315_K 1.10 0.10 0.00
196_Q 146_K 1.09 0.10 0.00
80_W 108_T 1.09 0.10 0.00
202_K 109_S 1.09 0.10 0.00
49_A 307_K 1.09 0.10 0.00
142_P 240_Q 1.09 0.10 0.00
95_H 238_P 1.08 0.10 0.00
81_P 132_Y 1.07 0.10 0.00
80_W 222_P 1.06 0.10 0.00
47_P 102_L 1.06 0.10 0.00
109_V 109_S 1.06 0.10 0.00
104_D 132_Y 1.05 0.10 0.00
195_L 313_V 1.05 0.09 0.00
64_V 301_P 1.04 0.09 0.00
63_V 252_V 1.03 0.09 0.00
49_A 126_S 1.03 0.09 0.00
127_T 286_K 1.02 0.09 0.00
104_D 291_K 1.02 0.09 0.00
65_A 85_S 1.02 0.09 0.00
187_A 203_A 1.02 0.09 0.00
112_A 131_A 1.02 0.09 0.00
199_R 291_K 1.01 0.09 0.00
142_P 211_V 1.01 0.09 0.00
127_T 118_K 1.01 0.09 0.00
127_T 166_M 1.01 0.09 0.00
170_C 161_D 1.00 0.09 0.00
80_W 184_A 1.00 0.09 0.00
74_A 199_Y 1.00 0.09 0.00
195_L 87_L 1.00 0.09 0.00
99_P 221_P 1.00 0.09 0.00
74_A 202_R 1.00 0.09 0.00
47_P 156_D 1.00 0.09 0.00
191_L 99_R 1.00 0.09 0.00
81_P 307_K 1.00 0.09 0.00
65_A 252_V 0.99 0.09 0.00
49_A 306_I 0.99 0.09 0.00
81_P 281_E 0.99 0.08 0.00
126_L 249_Y 0.99 0.08 0.00
32_Q 37_L 0.99 0.08 0.00
204_E 143_D 0.99 0.08 0.00
95_H 249_Y 0.99 0.08 0.00
70_L 72_A 0.99 0.08 0.00
70_L 166_M 0.99 0.08 0.00
81_P 291_K 0.99 0.08 0.00
63_V 171_L 0.99 0.08 0.00
104_D 307_K 0.98 0.08 0.00
30_V 46_A 0.98 0.08 0.00
39_P 46_A 0.98 0.08 0.00
126_L 271_C 0.98 0.08 0.00
137_V 203_A 0.97 0.08 0.00
30_V 47_L 0.97 0.08 0.00
109_V 282_H 0.97 0.08 0.00
44_P 48_S 0.97 0.08 0.00
196_Q 142_E 0.96 0.08 0.00
64_V 286_K 0.96 0.08 0.00
83_T 199_Y 0.96 0.08 0.00
108_V 87_L 0.96 0.08 0.00
148_V 261_A 0.95 0.08 0.00
127_T 137_G 0.95 0.08 0.00
72_N 71_G 0.95 0.08 0.00
61_E 300_V 0.94 0.08 0.00
36_T 52_G 0.94 0.08 0.00
194_I 193_L 0.94 0.08 0.00
50_R 307_K 0.94 0.08 0.00
81_P 272_T 0.93 0.07 0.00
39_P 49_S 0.93 0.07 0.00
81_P 159_N 0.93 0.07 0.00
206_R 84_A 0.93 0.07 0.00
173_I 186_R 0.93 0.07 0.00
49_A 235_P 0.93 0.07 0.00
126_L 161_D 0.92 0.07 0.00
112_A 130_V 0.92 0.07 0.00
52_V 155_Q 0.92 0.07 0.00
68_D 291_K 0.92 0.07 0.00
52_V 205_H 0.92 0.07 0.00
72_N 107_H 0.92 0.07 0.00
36_T 42_P 0.92 0.07 0.00
194_I 314_L 0.92 0.07 0.00
103_M 126_S 0.92 0.07 0.00
112_A 183_E 0.92 0.07 0.00
195_L 240_Q 0.92 0.07 0.00
75_R 110_I 0.92 0.07 0.00
37_D 322_R 0.92 0.07 0.00
64_V 140_Y 0.91 0.07 0.00
80_W 230_G 0.91 0.07 0.00
36_T 41_T 0.91 0.07 0.00
66_K 256_D 0.91 0.07 0.00
142_P 239_G 0.91 0.07 0.00
103_M 85_S 0.90 0.07 0.00
104_D 272_T 0.90 0.07 0.00
80_W 185_A 0.90 0.07 0.00
80_W 236_Y 0.90 0.07 0.00
29_G 35_G 0.90 0.07 0.00
99_P 176_P 0.90 0.07 0.00
109_V 243_A 0.90 0.07 0.00
191_L 163_E 0.90 0.07 0.00
119_V 314_L 0.90 0.07 0.00
27_A 47_L 0.90 0.07 0.00
94_M 99_R 0.90 0.07 0.00
99_P 90_H 0.90 0.07 0.00
112_A 291_K 0.90 0.07 0.00
66_K 119_Q 0.90 0.07 0.00
204_E 220_E 0.89 0.07 0.00
49_A 298_L 0.89 0.07 0.00
25_V 46_A 0.89 0.07 0.00
67_L 132_Y 0.89 0.07 0.00
67_L 249_Y 0.89 0.07 0.00
203_R 103_S 0.89 0.07 0.00
213_R 52_G 0.89 0.07 0.00
106_F 251_D 0.88 0.07 0.00
61_E 103_S 0.88 0.07 0.00
112_A 176_P 0.88 0.07 0.00
67_L 105_L 0.88 0.07 0.00
54_P 93_S 0.88 0.07 0.00
80_W 178_P 0.88 0.07 0.00
80_W 194_P 0.87 0.07 0.00
61_E 316_S 0.87 0.07 0.00
199_R 255_F 0.87 0.07 0.00
142_P 315_K 0.87 0.07 0.00
97_A 240_Q 0.87 0.07 0.00
72_N 136_V 0.87 0.07 0.00
83_T 203_A 0.87 0.07 0.00
54_P 307_K 0.87 0.07 0.00
69_D 271_C 0.86 0.07 0.00
27_A 296_M 0.86 0.07 0.00
36_T 60_M 0.86 0.07 0.00
36_T 296_M 0.86 0.07 0.00
110_F 171_L 0.86 0.07 0.00
146_Y 145_A 0.86 0.07 0.00
104_D 224_G 0.86 0.07 0.00
133_A 204_R 0.86 0.07 0.00
62_Y 225_V 0.86 0.07 0.00
95_H 190_N 0.86 0.07 0.00
62_Y 105_L 0.86 0.07 0.00
58_S 303_V 0.85 0.07 0.00
27_A 38_P 0.85 0.07 0.00
191_L 284_H 0.85 0.07 0.00
79_L 110_I 0.85 0.07 0.00
199_R 130_V 0.85 0.07 0.00
178_I 70_G 0.85 0.07 0.00
74_A 133_R 0.85 0.07 0.00
74_A 210_Y 0.85 0.07 0.00
24_A 38_P 0.85 0.07 0.00
142_P 241_A 0.85 0.07 0.00
199_R 228_R 0.85 0.07 0.00
21_V 322_R 0.85 0.07 0.00
34_V 36_Q 0.85 0.07 0.00
119_V 87_L 0.85 0.07 0.00
104_D 159_N 0.85 0.07 0.00
31_H 37_L 0.85 0.06 0.00
139_D 214_L 0.84 0.06 0.00
37_D 34_P 0.84 0.06 0.00
110_F 136_V 0.84 0.06 0.00
72_N 267_A 0.84 0.06 0.00
103_M 88_E 0.84 0.06 0.00
103_M 298_L 0.84 0.06 0.00
68_D 224_G 0.84 0.06 0.00
195_L 99_R 0.84 0.06 0.00
51_A 159_N 0.84 0.06 0.00
29_G 37_L 0.84 0.06 0.00
32_Q 36_Q 0.84 0.06 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
5911 0.07 cIp_6_40_cyt1_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5908 0.1 cIp_6_4_cyt1_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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