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OPENSEQ.org
DNJB1HSPA4 (A, 1-100) (B, 1-540)
Genes: A B A+B
Length: 100 540 570
Sequences: 1584 4702 168
Seq/Len: 15.84 8.71 0.29
MirrorTree (Pazo et al. 2001) 0.53
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.06 0.20
2 0.02 0.06 0.22
5 0.02 0.07 0.23
10 0.02 0.07 0.25
20 0.02 0.07 0.26
100 0.04 0.08 0.37
∞ 0.11 0.14 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
53_D 371_A 1.89 0.66 0.01
38_E 429_S 1.30 0.29 0.00
54_V 198_V 1.29 0.28 0.00
53_D 161_Q 1.28 0.28 0.00
29_L 4_V 1.27 0.27 0.00
25_R 487_H 1.22 0.25 0.00
26_R 452_L 1.21 0.24 0.00
66_R 127_E 1.21 0.24 0.00
11_L 40_S 1.20 0.24 0.00
49_A 228_D 1.17 0.22 0.00
25_R 219_K 1.17 0.22 0.00
26_R 371_A 1.17 0.22 0.00
53_D 351_K 1.16 0.22 0.00
29_L 201_V 1.15 0.21 0.00
71_G 267_S 1.11 0.20 0.00
48_I 466_K 1.11 0.20 0.00
24_Y 245_C 1.08 0.18 0.00
11_L 373_T 1.07 0.18 0.00
44_K 380_C 1.06 0.17 0.00
49_A 430_K 1.02 0.16 0.00
36_N 472_D 1.02 0.16 0.00
35_K 89_Y 1.01 0.16 0.00
38_E 466_K 1.01 0.16 0.00
29_L 261_R 1.00 0.15 0.00
19_E 465_Q 1.00 0.15 0.00
72_L 201_V 1.00 0.15 0.00
66_R 331_K 1.00 0.15 0.00
48_I 67_F 1.00 0.15 0.00
38_E 42_G 0.99 0.15 0.00
44_K 314_L 0.98 0.15 0.00
52_Y 16_A 0.98 0.15 0.00
66_R 339_E 0.98 0.15 0.00
62_E 166_N 0.98 0.15 0.00
29_L 268_Q 0.97 0.14 0.00
19_E 418_E 0.97 0.14 0.00
30_R 260_I 0.96 0.14 0.00
49_A 357_F 0.95 0.14 0.00
29_L 357_F 0.94 0.14 0.00
44_K 493_S 0.94 0.13 0.00
11_L 382_I 0.94 0.13 0.00
37_K 220_L 0.94 0.13 0.00
72_L 127_E 0.94 0.13 0.00
8_T 102_K 0.93 0.13 0.00
22_R 139_D 0.93 0.13 0.00
62_E 183_I 0.93 0.13 0.00
49_A 490_F 0.92 0.13 0.00
30_R 418_E 0.92 0.13 0.00
44_K 481_K 0.92 0.13 0.00
66_R 198_V 0.92 0.13 0.00
35_K 243_H 0.91 0.12 0.00
7_Q 305_K 0.91 0.12 0.00
63_I 201_V 0.90 0.12 0.00
13_R 245_C 0.90 0.12 0.00
62_E 46_R 0.90 0.12 0.00
29_L 199_V 0.90 0.12 0.00
25_R 216_N 0.90 0.12 0.00
71_G 465_Q 0.89 0.12 0.00
62_E 422_K 0.89 0.12 0.00
56_S 197_N 0.89 0.12 0.00
72_L 267_S 0.89 0.12 0.00
3_K 195_P 0.88 0.12 0.00
30_R 334_D 0.88 0.12 0.00
72_L 418_E 0.88 0.12 0.00
8_T 422_K 0.88 0.12 0.00
16_S 247_E 0.88 0.12 0.00
70_E 224_A 0.87 0.11 0.00
16_S 302_N 0.87 0.11 0.00
49_A 491_S 0.86 0.11 0.00
49_A 210_V 0.86 0.11 0.00
56_S 116_Q 0.86 0.11 0.00
29_L 125_L 0.86 0.11 0.00
19_E 360_K 0.86 0.11 0.00
77_P 316_R 0.85 0.11 0.00
63_I 243_H 0.85 0.11 0.00
11_L 23_I 0.85 0.11 0.00
74_G 241_V 0.85 0.11 0.00
31_Y 215_F 0.85 0.11 0.00
11_L 168_L 0.84 0.11 0.00
25_R 39_I 0.84 0.11 0.00
37_K 286_L 0.84 0.11 0.00
26_R 344_A 0.84 0.11 0.00
25_R 217_R 0.84 0.11 0.00
29_L 14_Y 0.84 0.10 0.00
26_R 38_C 0.84 0.10 0.00
13_R 381_A 0.83 0.10 0.00
56_S 125_L 0.83 0.10 0.00
74_G 67_F 0.83 0.10 0.00
39_P 151_A 0.83 0.10 0.00
62_E 454_Y 0.83 0.10 0.00
66_R 166_N 0.83 0.10 0.00
10_G 266_L 0.82 0.10 0.00
61_R 216_N 0.82 0.10 0.00
30_R 347_I 0.81 0.10 0.00
54_V 187_D 0.81 0.10 0.00
49_A 314_L 0.81 0.10 0.00
40_G 314_L 0.81 0.10 0.00
58_P 332_K 0.80 0.10 0.00
49_A 251_K 0.80 0.10 0.00
35_K 229_T 0.80 0.10 0.00
72_L 115_E 0.80 0.10 0.00
74_G 195_P 0.80 0.10 0.00
56_S 38_C 0.79 0.09 0.00
25_R 301_M 0.79 0.09 0.00
48_I 365_T 0.78 0.09 0.00
67_Y 331_K 0.78 0.09 0.00
50_E 361_E 0.78 0.09 0.00
16_S 357_F 0.78 0.09 0.00
3_K 57_I 0.78 0.09 0.00
35_K 392_F 0.78 0.09 0.00
48_I 334_D 0.78 0.09 0.00
67_Y 166_N 0.78 0.09 0.00
54_V 330_L 0.77 0.09 0.00
27_Q 198_V 0.77 0.09 0.00
66_R 361_E 0.77 0.09 0.00
7_Q 247_E 0.77 0.09 0.00
40_G 416_D 0.77 0.09 0.00
48_I 228_D 0.77 0.09 0.00
74_G 254_L 0.77 0.09 0.00
25_R 263_L 0.77 0.09 0.00
58_P 452_L 0.77 0.09 0.00
8_T 466_K 0.76 0.09 0.00
25_R 230_T 0.76 0.09 0.00
30_R 226_A 0.76 0.09 0.00
62_E 245_C 0.76 0.09 0.00
49_A 252_Y 0.76 0.09 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)
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