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OPENSEQ.org
NifH-NifDalpha Interaction_Lower E value
Genes: A B A+B
Length: 290 492 761
Sequences: 610 2123 579
Seq/Len: 2.1 4.32 0.76
MirrorTree (Pazo et al. 2001) 0.80
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 0.52 0.32
2 0.02 0.53 0.52
5 0.03 0.53 0.69
10 0.04 0.53 0.73
20 0.07 0.55 0.74
100 0.11 0.56 0.81
∞ 0.18 0.56 0.85
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
104_I 160_G 1.42 0.63 0.00
48_L 249_C 1.27 0.50 0.00
260_I 319_S 1.25 0.49 0.00
32_K 284_R 1.22 0.46 0.00
250_D 339_V 1.17 0.41 0.00
205_G 116_S 1.16 0.40 0.00
84_V 317_D 1.14 0.39 0.00
158_A 127_G 1.12 0.38 0.00
55_Q 156_I 1.11 0.37 0.00
263_D 40_T 1.11 0.36 0.00
51_H 307_E 1.10 0.36 0.00
263_D 39_V 1.07 0.34 0.00
195_E 244_E 1.07 0.34 0.00
20_T 289_K 1.05 0.32 0.00
74_E 39_V 1.04 0.32 0.00
23_L 437_P 1.04 0.31 0.00
163_N 85_P 1.04 0.31 0.00
119_D 238_S 1.01 0.29 0.00
261_T 249_C 1.01 0.29 0.00
140_I 84_G 1.01 0.29 0.00
34_V 37_P 1.00 0.29 0.00
33_K 467_L 1.00 0.28 0.00
155_E 91_Y 0.99 0.28 0.00
164_N 88_C 0.98 0.27 0.00
114_G 310_R 0.98 0.27 0.00
172_Y 339_V 0.98 0.27 0.00
112_E 223_V 0.97 0.27 0.00
166_S 132_A 0.97 0.26 0.00
152_C 206_V 0.96 0.26 0.00
74_E 390_T 0.96 0.26 0.00
102_G 88_C 0.96 0.26 0.00
231_Y 38_A 0.96 0.25 0.00
51_H 431_F 0.95 0.25 0.00
172_Y 122_D 0.95 0.25 0.00
107_I 83_H 0.95 0.25 0.00
202_N 289_K 0.95 0.25 0.00
258_N 322_K 0.95 0.25 0.00
262_M 13_I 0.94 0.24 0.00
118_D 307_E 0.94 0.24 0.00
270_M 423_S 0.94 0.24 0.00
239_D 329_A 0.94 0.24 0.00
260_I 261_E 0.93 0.24 0.00
183_L 247_L 0.93 0.24 0.00
81_Y 306_I 0.93 0.23 0.00
235_A 344_P 0.92 0.23 0.00
104_I 159_I 0.92 0.23 0.00
4_R 428_K 0.92 0.23 0.00
83_G 14_Q 0.91 0.23 0.00
75_D 148_I 0.91 0.22 0.00
84_V 372_M 0.91 0.22 0.00
166_S 473_K 0.91 0.22 0.00
5_Q 27_D 0.90 0.22 0.00
28_A 334_E 0.90 0.22 0.00
270_M 24_A 0.90 0.22 0.00
84_V 304_K 0.90 0.22 0.00
54_A 249_C 0.90 0.22 0.00
217_V 272_L 0.90 0.22 0.00
202_N 251_A 0.89 0.22 0.00
103_V 245_M 0.89 0.21 0.00
148_I 160_G 0.89 0.21 0.00
58_I 72_W 0.89 0.21 0.00
178_V 249_C 0.89 0.21 0.00
250_D 165_S 0.89 0.21 0.00
256_I 436_I 0.88 0.21 0.00
103_V 72_W 0.88 0.21 0.00
85_K 152_S 0.88 0.21 0.00
84_V 311_A 0.87 0.20 0.00
250_D 36_D 0.87 0.20 0.00
230_E 104_T 0.87 0.20 0.00
26_A 173_E 0.87 0.20 0.00
220_R 170_K 0.87 0.20 0.00
34_V 178_I 0.87 0.20 0.00
172_Y 181_V 0.87 0.20 0.00
234_K 217_A 0.87 0.20 0.00
145_A 275_C 0.87 0.20 0.00
37_V 291_G 0.86 0.20 0.00
137_A 364_I 0.86 0.20 0.00
53_K 456_F 0.86 0.20 0.00
152_C 292_I 0.86 0.20 0.00
117_E 122_D 0.86 0.19 0.00
57_T 400_L 0.85 0.19 0.00
101_R 88_C 0.85 0.19 0.00
6_C 114_F 0.85 0.19 0.00
29_E 312_I 0.85 0.19 0.00
34_V 480_E 0.85 0.19 0.00
212_V 303_T 0.85 0.19 0.00
230_E 136_D 0.85 0.19 0.00
172_Y 474_K 0.85 0.19 0.00
244_L 194_G 0.85 0.19 0.00
212_V 368_E 0.84 0.19 0.00
264_E 294_W 0.84 0.19 0.00
181_G 431_F 0.84 0.19 0.00
59_M 224_A 0.84 0.19 0.00
195_E 396_D 0.84 0.19 0.00
115_A 81_I 0.84 0.19 0.00
74_E 329_A 0.84 0.18 0.00
28_A 89_G 0.84 0.18 0.00
49_I 300_F 0.83 0.18 0.00
145_A 160_G 0.83 0.18 0.00
6_C 14_Q 0.83 0.18 0.00
152_C 35_N 0.83 0.18 0.00
260_I 314_A 0.83 0.18 0.00
243_A 179_V 0.83 0.18 0.00
206_T 312_I 0.83 0.18 0.00
5_Q 247_L 0.83 0.18 0.00
34_V 306_I 0.83 0.18 0.00
76_V 487_K 0.83 0.18 0.00
196_L 436_I 0.83 0.18 0.00
26_A 324_C 0.83 0.18 0.00
83_G 37_P 0.82 0.18 0.00
58_I 177_T 0.82 0.18 0.00
75_D 219_T 0.82 0.17 0.00
175_S 25_R 0.82 0.17 0.00
183_L 161_D 0.82 0.17 0.00
58_I 140_T 0.81 0.17 0.00
159_M 353_L 0.81 0.17 0.00
206_T 131_L 0.81 0.17 0.00
83_G 204_D 0.81 0.17 0.00
274_I 314_A 0.81 0.17 0.00
173_A 73_G 0.81 0.17 0.00
59_M 25_R 0.81 0.17 0.00
49_I 322_K 0.81 0.17 0.00
164_N 160_G 0.81 0.17 0.00
125_Y 155_P 0.81 0.17 0.00
43_A 317_D 0.80 0.17 0.00
103_V 224_A 0.80 0.17 0.00
75_D 287_E 0.80 0.17 0.00
267_E 395_G 0.80 0.17 0.00
250_D 272_L 0.80 0.17 0.00
5_Q 450_Y 0.80 0.17 0.00
256_I 351_V 0.80 0.17 0.00
220_R 129_K 0.80 0.16 0.00
79_A 34_V 0.80 0.16 0.00
24_V 437_P 0.79 0.16 0.00
178_V 422_G 0.79 0.16 0.00
234_K 473_K 0.79 0.16 0.00
225_R 35_N 0.79 0.16 0.00
222_E 88_C 0.79 0.16 0.00
239_D 417_K 0.79 0.16 0.00
23_L 480_E 0.79 0.16 0.00
232_D 267_K 0.79 0.16 0.00
158_A 166_V 0.79 0.16 0.00
243_A 135_I 0.79 0.16 0.00
51_H 169_V 0.79 0.16 0.00
102_G 160_G 0.79 0.16 0.00
110_L 237_S 0.79 0.16 0.00
112_E 239_R 0.79 0.16 0.00
183_L 271_N 0.78 0.16 0.00
117_E 263_E 0.78 0.16 0.00
71_L 307_E 0.78 0.16 0.00
34_V 257_G 0.78 0.16 0.00
20_T 156_I 0.78 0.16 0.00
274_I 202_V 0.78 0.16 0.00
83_G 22_E 0.78 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.55 > 0.4) of paralogs.
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