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OPENSEQ.org
cIp_5_2_cIV_1_10
Genes: A B A+B
Length: 264 513 723
Sequences: 308 4400 81
Seq/Len: 1.17 8.58 0.11
MirrorTree (Pazo et al. 2001) 0.05
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.03 0.01
100 0.00 0.04 0.03
∞ 0.00 0.08 0.10
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
86_V 419_I 2.14 0.51 0.03
176_V 466_M 2.11 0.49 0.02
207_Y 419_I 1.45 0.20 0.00
103_H 216_N 1.41 0.19 0.00
174_F 69_M 1.38 0.18 0.00
220_V 253_M 1.36 0.17 0.00
173_M 481_K 1.34 0.17 0.00
73_V 460_I 1.32 0.16 0.00
154_E 270_Y 1.32 0.16 0.00
174_F 463_T 1.27 0.15 0.00
143_V 48_L 1.27 0.15 0.00
58_L 470_F 1.26 0.14 0.00
170_I 198_S 1.25 0.14 0.00
115_T 264_K 1.25 0.14 0.00
164_N 392_G 1.23 0.14 0.00
246_R 23_G 1.22 0.13 0.00
78_V 258_V 1.14 0.12 0.00
161_K 314_I 1.13 0.12 0.00
93_V 110_L 1.12 0.11 0.00
180_N 120_A 1.12 0.11 0.00
174_F 7_L 1.12 0.11 0.00
86_V 343_G 1.10 0.11 0.00
121_T 198_S 1.10 0.11 0.00
204_L 279_S 1.09 0.11 0.00
220_V 174_P 1.08 0.10 0.00
160_F 339_L 1.08 0.10 0.00
220_V 73_I 1.07 0.10 0.00
84_L 389_I 1.07 0.10 0.00
187_I 231_Y 1.06 0.10 0.00
235_L 37_I 1.06 0.10 0.00
176_V 511_M 1.05 0.10 0.00
173_M 18_L 1.04 0.10 0.00
127_E 306_T 1.04 0.10 0.00
67_E 21_L 1.04 0.10 0.00
156_A 168_I 1.04 0.10 0.00
171_W 472_I 1.04 0.10 0.00
173_M 465_V 1.03 0.10 0.00
217_K 414_F 1.02 0.09 0.00
176_V 36_L 1.02 0.09 0.00
73_V 511_M 1.02 0.09 0.00
147_T 93_A 1.02 0.09 0.00
108_F 505_F 1.01 0.09 0.00
114_L 478_S 1.01 0.09 0.00
187_I 453_L 1.00 0.09 0.00
171_W 231_Y 0.99 0.09 0.00
112_V 114_A 0.99 0.09 0.00
204_L 423_L 0.99 0.09 0.00
220_V 191_T 0.99 0.09 0.00
135_L 472_I 0.99 0.09 0.00
107_Q 28_V 0.98 0.09 0.00
65_V 340_W 0.98 0.09 0.00
145_T 298_D 0.97 0.09 0.00
145_T 279_S 0.97 0.08 0.00
127_E 409_Y 0.96 0.08 0.00
65_V 458_S 0.96 0.08 0.00
115_T 464_A 0.96 0.08 0.00
229_E 49_G 0.95 0.08 0.00
111_L 303_A 0.95 0.08 0.00
161_K 203_A 0.95 0.08 0.00
205_S 137_S 0.95 0.08 0.00
159_V 501_P 0.95 0.08 0.00
230_F 100_M 0.94 0.08 0.00
114_L 403_Y 0.94 0.08 0.00
127_E 307_S 0.94 0.08 0.00
162_A 511_M 0.94 0.08 0.00
207_Y 459_F 0.94 0.08 0.00
174_F 258_V 0.94 0.08 0.00
194_E 473_W 0.94 0.08 0.00
60_A 456_V 0.94 0.08 0.00
110_S 267_P 0.93 0.08 0.00
179_A 393_F 0.93 0.08 0.00
85_E 286_I 0.93 0.08 0.00
221_A 489_S 0.93 0.08 0.00
135_L 336_A 0.92 0.08 0.00
147_T 359_A 0.92 0.08 0.00
116_A 467_L 0.92 0.08 0.00
60_A 338_V 0.92 0.08 0.00
162_A 460_I 0.92 0.08 0.00
148_D 453_L 0.92 0.08 0.00
93_V 511_M 0.91 0.08 0.00
160_F 7_L 0.91 0.08 0.00
86_V 340_W 0.91 0.08 0.00
152_P 46_N 0.91 0.08 0.00
179_A 97_M 0.91 0.07 0.00
180_N 489_S 0.90 0.07 0.00
164_N 23_G 0.90 0.07 0.00
114_L 456_V 0.90 0.07 0.00
159_V 469_I 0.90 0.07 0.00
65_V 474_E 0.90 0.07 0.00
127_E 441_S 0.90 0.07 0.00
148_D 169_I 0.89 0.07 0.00
78_V 75_I 0.89 0.07 0.00
215_E 324_L 0.89 0.07 0.00
108_F 339_L 0.89 0.07 0.00
160_F 477_A 0.89 0.07 0.00
108_F 350_V 0.89 0.07 0.00
173_M 447_Y 0.89 0.07 0.00
173_M 392_G 0.88 0.07 0.00
230_F 359_A 0.88 0.07 0.00
198_F 463_T 0.88 0.07 0.00
148_D 223_A 0.88 0.07 0.00
229_E 162_I 0.88 0.07 0.00
97_L 453_L 0.88 0.07 0.00
69_L 64_V 0.88 0.07 0.00
153_I 62_A 0.87 0.07 0.00
85_E 253_M 0.87 0.07 0.00
220_V 279_S 0.87 0.07 0.00
90_P 395_H 0.87 0.07 0.00
224_V 489_S 0.87 0.07 0.00
96_V 392_G 0.87 0.07 0.00
73_V 159_L 0.87 0.07 0.00
247_Q 23_G 0.87 0.07 0.00
252_L 424_T 0.87 0.07 0.00
78_V 159_L 0.86 0.07 0.00
198_F 162_I 0.86 0.07 0.00
171_W 267_P 0.86 0.07 0.00
86_V 28_V 0.86 0.07 0.00
132_L 234_L 0.86 0.07 0.00
205_S 216_N 0.86 0.07 0.00
204_L 406_D 0.86 0.07 0.00
93_V 127_T 0.86 0.07 0.00
81_F 264_K 0.85 0.07 0.00
229_E 198_S 0.85 0.07 0.00
187_I 391_G 0.85 0.07 0.00
170_I 188_V 0.85 0.07 0.00
68_I 359_A 0.85 0.07 0.00
171_W 303_A 0.85 0.07 0.00
78_V 343_G 0.85 0.07 0.00
224_V 468_M 0.85 0.07 0.00
241_A 489_S 0.85 0.07 0.00
205_S 489_S 0.84 0.07 0.00
62_G 24_A 0.84 0.07 0.00
116_A 264_K 0.84 0.07 0.00
214_D 229_I 0.84 0.07 0.00
196_H 390_M 0.84 0.07 0.00
179_A 477_A 0.84 0.07 0.00
119_V 196_I 0.84 0.07 0.00
176_V 58_V 0.84 0.07 0.00
90_P 118_V 0.84 0.07 0.00
139_S 48_L 0.83 0.07 0.00
160_F 311_I 0.83 0.07 0.00
177_F 489_S 0.83 0.07 0.00
114_L 282_F 0.83 0.07 0.00
81_F 388_A 0.83 0.07 0.00
86_V 107_P 0.83 0.07 0.00
215_E 66_I 0.83 0.07 0.00
181_H 483_L 0.82 0.06 0.00
116_A 117_M 0.82 0.06 0.00
230_F 445_D 0.82 0.06 0.00
171_W 333_K 0.82 0.06 0.00
225_E 395_H 0.82 0.06 0.00
116_A 464_A 0.82 0.06 0.00
242_F 264_K 0.82 0.06 0.00
82_N 37_I 0.82 0.06 0.00
68_I 391_G 0.82 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
4349 0.11 cIp_5_2_cIV_1_20 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4348 0.1 cIp_5_2_cIV_1_40 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4347 0.11 cIp_5_4_cIV_1_10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4340 0.11 cIp_5_2_cIV_1_10 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4339 0.11 cIp_5_2_cIV_1_4 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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