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OPENSEQ.org
KJ_coli
Genes: A B A+B
Length: 638 376 1004
Sequences: 4126 3335 1238
Seq/Len: 6.47 8.87 1.23
MirrorTree (Pazo et al. 2001) 0.71
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 0.02 0.00 1.00
2 0.02 0.00 1.15
5 0.02 0.00 1.19
10 0.02 0.00 1.20
20 0.02 0.00 1.22
100 0.04 0.01 1.37
∞ 0.09 0.03 1.90
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
208_D 26_K 1.41 0.76 0.02
187_N 23_K 1.38 0.74 0.02
422_H 51_K 1.14 0.53 0.01
425_V 145_D 0.98 0.37 0.01
257_L 125_L 0.98 0.37 0.01
515_M 225_R 0.95 0.34 0.01
107_G 39_G 0.95 0.34 0.01
630_E 150_S 0.93 0.33 0.01
390_L 29_A 0.92 0.32 0.01
190_I 28_L 0.92 0.32 0.01
164_E 9_I 0.90 0.30 0.01
480_A 29_A 0.89 0.29 0.01
515_M 291_L 0.88 0.28 0.01
285_Y 322_L 0.86 0.27 0.00
382_L 29_A 0.86 0.27 0.00
222_N 212_L 0.85 0.26 0.00
225_T 30_M 0.85 0.26 0.00
540_D 221_D 0.85 0.26 0.00
379_G 55_E 0.84 0.26 0.00
390_L 41_K 0.82 0.24 0.00
356_F 30_M 0.82 0.24 0.00
598_L 227_R 0.81 0.23 0.00
565_I 45_A 0.80 0.23 0.00
281_V 17_E 0.80 0.23 0.00
605_Q 239_A 0.80 0.23 0.00
392_L 29_A 0.80 0.23 0.00
149_A 39_G 0.80 0.22 0.00
237_I 311_K 0.79 0.22 0.00
460_D 89_D 0.79 0.22 0.00
413_A 105_G 0.79 0.22 0.00
498_K 135_E 0.79 0.21 0.00
587_K 25_Y 0.79 0.21 0.00
533_V 64_A 0.78 0.21 0.00
156_D 4_Q 0.78 0.21 0.00
523_A 241_A 0.78 0.21 0.00
241_V 171_Q 0.78 0.21 0.00
607_A 15_T 0.77 0.21 0.00
435_A 73_A 0.77 0.21 0.00
463_N 37_N 0.77 0.20 0.00
237_I 303_F 0.77 0.20 0.00
430_E 140_T 0.77 0.20 0.00
417_T 29_A 0.77 0.20 0.00
263_K 303_F 0.77 0.20 0.00
113_P 73_A 0.77 0.20 0.00
518_D 156_T 0.77 0.20 0.00
439_H 129_V 0.76 0.20 0.00
23_T 125_L 0.76 0.20 0.00
337_V 317_A 0.75 0.19 0.00
497_Q 291_L 0.75 0.19 0.00
543_L 136_I 0.75 0.19 0.00
337_V 262_N 0.75 0.19 0.00
48_T 181_Q 0.75 0.19 0.00
208_D 363_F 0.75 0.19 0.00
17_A 63_R 0.74 0.19 0.00
309_V 282_V 0.74 0.19 0.00
578_G 216_I 0.74 0.18 0.00
558_P 334_N 0.74 0.18 0.00
357_F 195_D 0.74 0.18 0.00
189_T 334_N 0.73 0.18 0.00
567_S 299_T 0.73 0.18 0.00
389_V 81_G 0.73 0.18 0.00
390_L 328_E 0.73 0.18 0.00
466_P 6_Y 0.73 0.18 0.00
435_A 328_E 0.73 0.18 0.00
15_C 265_C 0.73 0.18 0.00
43_T 40_D 0.73 0.18 0.00
107_G 19_R 0.73 0.18 0.00
245_K 27_R 0.73 0.18 0.00
189_T 95_G 0.72 0.18 0.00
546_T 95_G 0.72 0.18 0.00
235_R 163_T 0.72 0.18 0.00
515_M 227_R 0.72 0.17 0.00
320_L 176_F 0.72 0.17 0.00
135_V 246_V 0.72 0.17 0.00
386_V 294_P 0.72 0.17 0.00
437_T 36_R 0.71 0.17 0.00
204_I 340_L 0.71 0.17 0.00
52_Q 234_A 0.71 0.17 0.00
239_Y 228_L 0.71 0.17 0.00
456_Q 216_I 0.71 0.17 0.00
584_I 121_M 0.71 0.17 0.00
398_S 273_M 0.71 0.17 0.00
67_F 124_T 0.71 0.17 0.00
630_E 91_S 0.71 0.17 0.00
421_K 201_H 0.71 0.17 0.00
534_Q 327_V 0.71 0.17 0.00
506_G 291_L 0.71 0.17 0.00
562_K 338_K 0.71 0.17 0.00
113_P 310_V 0.70 0.17 0.00
321_K 9_I 0.70 0.17 0.00
287_T 41_K 0.70 0.17 0.00
236_L 19_R 0.70 0.17 0.00
2_G 25_Y 0.70 0.16 0.00
105_V 56_V 0.69 0.16 0.00
300_V 285_L 0.69 0.16 0.00
189_T 328_E 0.69 0.16 0.00
190_I 198_N 0.69 0.16 0.00
386_V 125_L 0.69 0.16 0.00
190_I 153_K 0.69 0.16 0.00
186_G 263_L 0.69 0.16 0.00
534_Q 50_I 0.69 0.16 0.00
513_Q 19_R 0.69 0.16 0.00
149_A 343_E 0.69 0.16 0.00
389_V 210_K 0.69 0.16 0.00
484_L 9_I 0.69 0.16 0.00
119_V 246_V 0.68 0.16 0.00
5_I 93_I 0.68 0.15 0.00
182_D 60_S 0.68 0.15 0.00
328_G 37_N 0.68 0.15 0.00
379_G 237_H 0.68 0.15 0.00
19_M 220_V 0.68 0.15 0.00
78_Q 14_K 0.68 0.15 0.00
373_I 339_Q 0.68 0.15 0.00
594_V 195_D 0.68 0.15 0.00
137_E 237_H 0.68 0.15 0.00
335_D 240_P 0.67 0.15 0.00
294_K 150_S 0.67 0.15 0.00
411_L 213_S 0.67 0.15 0.00
502_K 125_L 0.67 0.15 0.00
282_N 40_D 0.67 0.15 0.00
613_G 299_T 0.67 0.15 0.00
481_D 26_K 0.67 0.15 0.00
333_D 269_I 0.67 0.15 0.00
379_G 113_R 0.67 0.15 0.00
263_K 220_V 0.67 0.15 0.00
271_I 331_V 0.67 0.15 0.00
225_T 36_R 0.67 0.15 0.00
147_N 329_T 0.66 0.14 0.00
219_L 95_G 0.66 0.14 0.00
518_D 367_V 0.66 0.14 0.00
203_S 235_G 0.66 0.14 0.00
147_N 228_L 0.66 0.14 0.00
30_A 298_Q 0.66 0.14 0.00
215_T 51_K 0.66 0.14 0.00
485_H 41_K 0.66 0.14 0.00
136_T 279_E 0.66 0.14 0.00
59_V 118_R 0.66 0.14 0.00
336_D 221_D 0.66 0.14 0.00
321_K 343_E 0.66 0.14 0.00
425_V 259_E 0.66 0.14 0.00
291_T 286_D 0.66 0.14 0.00
487_S 201_H 0.65 0.14 0.00
178_A 228_L 0.65 0.14 0.00
377_V 257_E 0.65 0.14 0.00
282_N 180_Q 0.65 0.14 0.00
78_Q 212_L 0.65 0.14 0.00
334_I 280_I 0.65 0.14 0.00
452_K 125_L 0.65 0.14 0.00
164_E 184_P 0.65 0.14 0.00
314_N 142_E 0.65 0.14 0.00
190_I 52_E 0.65 0.14 0.00
169_I 102_F 0.65 0.14 0.00
427_S 72_A 0.65 0.14 0.00
289_D 231_E 0.65 0.14 0.00
216_F 224_D 0.64 0.14 0.00
542_L 39_G 0.64 0.14 0.00
191_A 30_M 0.64 0.14 0.00
254_N 336_R 0.64 0.14 0.00
219_L 328_E 0.64 0.14 0.00
551_E 146_V 0.64 0.14 0.00
439_H 310_V 0.64 0.14 0.00
578_G 196_P 0.64 0.14 0.00
220_A 72_A 0.64 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
8448 0.67 dnak and dnaj interaction Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.07 Done - Shared
0250 1.23 KJ_coli Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.02 Done
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