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OPENSEQ.org
cIp_3_40_cIV_B_40
Genes: A B A+B
Length: 674 298 927
Sequences: 1916 2549 646
Seq/Len: 2.84 8.55 0.7
MirrorTree (Pazo et al. 2001) 0.31
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 0.01 0.00 0.01
10 0.01 0.01 0.01
20 0.01 0.01 0.02
100 0.03 0.02 0.08
∞ 0.09 0.06 0.66
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
599_G 241_Y 1.29 0.49 0.00
507_V 195_V 1.18 0.40 0.00
567_A 54_S 1.16 0.39 0.00
188_I 201_V 1.16 0.39 0.00
429_L 199_V 1.10 0.34 0.00
518_I 54_S 1.10 0.34 0.00
233_I 145_A 1.09 0.34 0.00
431_S 241_Y 0.99 0.27 0.00
84_I 142_V 0.99 0.27 0.00
602_R 76_I 0.99 0.26 0.00
573_E 199_V 0.96 0.24 0.00
289_I 35_D 0.96 0.24 0.00
171_V 32_V 0.95 0.24 0.00
232_S 269_E 0.95 0.24 0.00
377_L 141_L 0.95 0.24 0.00
604_L 143_I 0.94 0.23 0.00
574_G 205_A 0.92 0.22 0.00
151_V 274_G 0.91 0.22 0.00
296_R 196_G 0.91 0.21 0.00
402_K 76_I 0.91 0.21 0.00
553_L 90_N 0.89 0.20 0.00
591_T 264_S 0.87 0.19 0.00
445_V 254_A 0.87 0.19 0.00
584_L 106_I 0.87 0.19 0.00
239_L 98_A 0.86 0.19 0.00
445_V 28_L 0.86 0.19 0.00
593_P 191_V 0.86 0.19 0.00
252_V 269_E 0.86 0.19 0.00
286_R 228_I 0.86 0.18 0.00
260_H 191_V 0.85 0.18 0.00
7_I 236_D 0.84 0.18 0.00
262_G 199_V 0.83 0.17 0.00
525_I 139_P 0.83 0.17 0.00
84_I 34_G 0.83 0.17 0.00
255_I 88_R 0.82 0.17 0.00
371_D 263_V 0.82 0.17 0.00
16_V 263_V 0.82 0.17 0.00
336_V 172_A 0.82 0.17 0.00
365_R 143_I 0.82 0.17 0.00
335_L 199_V 0.82 0.17 0.00
378_I 241_Y 0.81 0.16 0.00
151_V 73_A 0.81 0.16 0.00
402_K 193_V 0.81 0.16 0.00
483_G 201_V 0.81 0.16 0.00
305_E 240_V 0.80 0.16 0.00
378_I 145_A 0.80 0.16 0.00
562_Q 271_W 0.80 0.15 0.00
33_V 63_L 0.79 0.15 0.00
634_S 117_I 0.79 0.15 0.00
375_I 228_I 0.79 0.15 0.00
188_I 195_V 0.79 0.15 0.00
72_D 161_V 0.79 0.15 0.00
520_Q 266_E 0.78 0.15 0.00
160_S 106_I 0.78 0.15 0.00
429_L 269_E 0.77 0.15 0.00
33_V 236_D 0.77 0.15 0.00
125_A 146_I 0.77 0.14 0.00
70_V 232_W 0.77 0.14 0.00
315_K 241_Y 0.77 0.14 0.00
314_K 109_I 0.76 0.14 0.00
54_E 40_G 0.76 0.14 0.00
313_G 143_I 0.76 0.14 0.00
446_I 193_V 0.76 0.14 0.00
194_Q 241_Y 0.76 0.14 0.00
273_R 208_V 0.75 0.14 0.00
524_V 86_I 0.75 0.14 0.00
69_Q 187_T 0.75 0.14 0.00
281_R 195_V 0.74 0.13 0.00
602_R 196_G 0.74 0.13 0.00
435_S 264_S 0.74 0.13 0.00
500_A 87_V 0.74 0.13 0.00
33_V 138_D 0.74 0.13 0.00
339_L 143_I 0.74 0.13 0.00
92_K 273_A 0.74 0.13 0.00
359_A 106_I 0.73 0.13 0.00
343_V 248_L 0.73 0.13 0.00
338_G 143_I 0.73 0.13 0.00
393_I 266_E 0.73 0.13 0.00
406_V 93_A 0.73 0.13 0.00
290_R 115_V 0.73 0.13 0.00
421_T 141_L 0.73 0.13 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
4011 0.7 cIp_3_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4010 0.78 cIp_3_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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