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OPENSEQ.org
cIp_4_40_cytb_40_human
Genes: A B A+B
Length: 463 379 772
Sequences: 2956 4492 669
Seq/Len: 6.38 11.85 0.87
MirrorTree (Pazo et al. 2001) 0.47
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 0.01
2 0.00 0.00 0.02
5 0.00 0.00 0.03
10 0.00 0.00 0.06
20 0.00 0.00 0.08
100 0.01 0.00 0.18
∞ 0.05 0.00 0.79
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
348_L 355_A 1.27 0.54 0.00
416_S 156_Y 1.21 0.48 0.00
127_K 78_W 1.17 0.45 0.00
106_V 365_I 1.14 0.42 0.00
344_I 44_L 1.13 0.42 0.00
317_D 121_L 1.13 0.42 0.00
347_C 303_A 1.11 0.40 0.00
212_E 190_I 1.09 0.39 0.00
396_T 119_I 1.06 0.36 0.00
444_L 307_I 1.06 0.36 0.00
244_I 319_R 1.05 0.35 0.00
155_V 152_S 1.04 0.34 0.00
173_L 43_I 1.03 0.34 0.00
105_M 231_L 1.03 0.34 0.00
291_V 38_L 1.02 0.33 0.00
342_R 361_T 1.01 0.32 0.00
444_L 76_Y 1.00 0.31 0.00
279_T 119_I 1.00 0.31 0.00
386_T 6_R 1.00 0.31 0.00
82_L 333_L 1.00 0.31 0.00
438_M 93_I 1.00 0.31 0.00
439_S 93_I 0.99 0.30 0.00
332_C 239_S 0.97 0.29 0.00
313_Q 67_I 0.97 0.29 0.00
256_D 370_I 0.96 0.28 0.00
291_V 41_C 0.96 0.28 0.00
318_V 230_A 0.96 0.28 0.00
348_L 300_L 0.96 0.28 0.00
278_V 240_L 0.96 0.28 0.00
157_K 219_I 0.95 0.28 0.00
348_L 242_T 0.95 0.27 0.00
99_M 259_L 0.95 0.27 0.00
155_V 339_I 0.94 0.27 0.00
422_C 152_S 0.94 0.27 0.00
341_L 331_A 0.93 0.26 0.00
260_E 19_L 0.93 0.26 0.00
82_L 60_A 0.92 0.25 0.00
438_M 242_T 0.91 0.25 0.00
318_V 115_N 0.90 0.24 0.00
162_R 83_L 0.89 0.23 0.00
418_R 50_L 0.89 0.23 0.00
211_F 263_L 0.89 0.23 0.00
349_N 58_P 0.89 0.23 0.00
274_D 90_M 0.88 0.23 0.00
320_V 196_L 0.88 0.23 0.00
377_S 299_I 0.87 0.22 0.00
349_N 195_T 0.87 0.22 0.00
177_I 198_L 0.87 0.22 0.00
248_S 194_A 0.86 0.22 0.00
400_I 233_L 0.86 0.21 0.00
220_A 275_F 0.86 0.21 0.00
320_V 130_M 0.86 0.21 0.00
281_E 108_F 0.86 0.21 0.00
445_A 53_A 0.85 0.21 0.00
218_S 321_L 0.85 0.21 0.00
249_K 303_A 0.85 0.21 0.00
225_A 246_F 0.85 0.21 0.00
456_I 48_T 0.85 0.21 0.00
163_P 165_I 0.84 0.20 0.00
155_V 174_P 0.84 0.20 0.00
232_V 157_I 0.84 0.20 0.00
194_L 96_F 0.84 0.20 0.00
334_V 241_M 0.84 0.20 0.00
414_D 331_A 0.84 0.20 0.00
332_C 304_M 0.84 0.20 0.00
438_M 121_L 0.84 0.20 0.00
377_S 9_N 0.83 0.20 0.00
344_I 324_S 0.83 0.20 0.00
82_L 261_N 0.83 0.20 0.00
136_F 257_Y 0.83 0.20 0.00
306_Q 48_T 0.83 0.20 0.00
115_L 232_G 0.83 0.20 0.00
289_S 180_F 0.82 0.19 0.00
342_R 261_N 0.82 0.19 0.00
155_V 293_L 0.82 0.19 0.00
168_Q 334_L 0.82 0.19 0.00
347_C 329_L 0.82 0.19 0.00
250_N 50_L 0.81 0.19 0.00
451_I 275_F 0.81 0.19 0.00
429_F 126_A 0.81 0.18 0.00
139_L 154_I 0.81 0.18 0.00
177_I 24_T 0.81 0.18 0.00
188_T 185_I 0.80 0.18 0.00
393_P 239_S 0.80 0.18 0.00
220_A 141_F 0.80 0.18 0.00
244_I 308_L 0.80 0.18 0.00
101_L 234_L 0.80 0.18 0.00
151_Y 194_A 0.80 0.18 0.00
280_A 48_T 0.80 0.18 0.00
422_C 145_T 0.80 0.18 0.00
435_L 152_S 0.79 0.18 0.00
106_V 113_T 0.79 0.18 0.00
441_G 80_I 0.79 0.18 0.00
152_S 347_P 0.79 0.18 0.00
252_S 109_L 0.79 0.18 0.00
414_D 192_A 0.79 0.17 0.00
98_V 239_S 0.79 0.17 0.00
261_L 182_F 0.79 0.17 0.00
451_I 192_A 0.78 0.17 0.00
324_G 135_P 0.78 0.17 0.00
444_L 83_L 0.78 0.17 0.00
142_V 54_M 0.78 0.17 0.00
161_I 153_A 0.78 0.17 0.00
269_R 177_T 0.78 0.17 0.00
102_S 243_L 0.78 0.17 0.00
200_F 16_N 0.78 0.17 0.00
238_L 159_T 0.78 0.17 0.00
229_P 337_T 0.77 0.17 0.00
453_T 45_Q 0.77 0.17 0.00
161_I 216_S 0.77 0.17 0.00
106_V 370_I 0.77 0.17 0.00
334_V 356_S 0.77 0.17 0.00
318_V 262_P 0.77 0.17 0.00
82_L 235_L 0.77 0.17 0.00
390_Q 190_I 0.77 0.17 0.00
445_A 48_T 0.77 0.17 0.00
440_K 299_I 0.76 0.16 0.00
177_I 6_R 0.76 0.16 0.00
143_S 196_L 0.76 0.16 0.00
255_L 43_I 0.76 0.16 0.00
441_G 76_Y 0.76 0.16 0.00
150_A 48_T 0.76 0.16 0.00
453_T 346_Y 0.76 0.16 0.00
315_E 154_I 0.76 0.16 0.00
197_M 125_M 0.76 0.16 0.00
448_V 196_L 0.76 0.16 0.00
173_L 15_I 0.76 0.16 0.00
106_V 305_I 0.76 0.16 0.00
335_E 97_L 0.75 0.16 0.00
274_D 161_L 0.75 0.16 0.00
110_D 165_I 0.75 0.15 0.00
246_Q 334_L 0.75 0.15 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
5881 0.87 cIp_4_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5879 0.95 cIp_4_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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