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OPENSEQ.org
pbp1a_lpoa_HHblits
Genes: A B A+B
Length: 858 425 1135
Sequences: 979 1816 354
Seq/Len: 1.14 4.27 0.31
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.03 0.00
2 0.00 0.03 0.00
5 0.00 0.03 0.01
10 0.00 0.04 0.01
20 0.00 0.04 0.02
100 0.00 0.06 0.05
∞ 0.01 0.13 0.28
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
747_V 130_V 1.42 0.37 0.00
391_R 231_E 1.41 0.37 0.00
303_V 6_I 1.40 0.36 0.00
456_F 195_L 1.39 0.35 0.00
198_Q 215_K 1.30 0.30 0.00
503_D 110_T 1.19 0.24 0.00
709_G 30_A 1.18 0.24 0.00
586_A 400_T 1.18 0.23 0.00
481_T 130_V 1.18 0.23 0.00
603_I 200_S 1.15 0.22 0.00
584_G 27_F 1.15 0.22 0.00
494_L 130_V 1.12 0.21 0.00
579_M 215_K 1.12 0.21 0.00
172_L 30_A 1.11 0.21 0.00
573_S 122_V 1.11 0.20 0.00
361_A 383_Q 1.10 0.20 0.00
434_N 170_A 1.10 0.20 0.00
243_I 358_V 1.09 0.20 0.00
603_I 415_Q 1.08 0.19 0.00
669_L 424_V 1.08 0.19 0.00
196_V 207_N 1.07 0.19 0.00
552_Y 131_V 1.06 0.18 0.00
58_I 224_Q 1.06 0.18 0.00
570_A 180_A 1.06 0.18 0.00
207_I 121_Q 1.05 0.18 0.00
438_V 209_F 1.05 0.18 0.00
311_V 403_P 1.05 0.18 0.00
812_I 9_L 1.04 0.17 0.00
172_L 20_G 1.03 0.17 0.00
721_I 130_V 1.03 0.17 0.00
581_V 149_L 1.02 0.17 0.00
434_N 103_A 1.02 0.17 0.00
58_I 129_I 1.01 0.16 0.00
212_K 13_N 1.01 0.16 0.00
284_Y 321_Q 1.00 0.16 0.00
789_M 397_G 1.00 0.16 0.00
203_E 291_P 1.00 0.16 0.00
538_V 313_L 1.00 0.16 0.00
168_L 20_G 1.00 0.16 0.00
177_L 195_L 0.99 0.16 0.00
207_I 194_V 0.99 0.15 0.00
416_I 236_V 0.98 0.15 0.00
549_A 181_A 0.97 0.15 0.00
327_P 117_Q 0.97 0.15 0.00
58_I 120_S 0.97 0.15 0.00
573_S 226_F 0.97 0.15 0.00
299_I 191_A 0.97 0.15 0.00
207_I 12_L 0.97 0.15 0.00
551_E 23_I 0.96 0.15 0.00
394_R 208_A 0.95 0.14 0.00
832_E 105_L 0.95 0.14 0.00
586_A 22_T 0.94 0.14 0.00
237_M 153_A 0.94 0.14 0.00
256_I 266_L 0.94 0.14 0.00
181_A 32_N 0.94 0.14 0.00
611_I 170_A 0.94 0.14 0.00
93_T 135_L 0.94 0.14 0.00
239_D 130_V 0.93 0.14 0.00
494_L 224_Q 0.93 0.14 0.00
538_V 211_Q 0.92 0.13 0.00
690_L 338_S 0.92 0.13 0.00
432_E 105_L 0.92 0.13 0.00
62_D 314_Y 0.92 0.13 0.00
58_I 372_V 0.92 0.13 0.00
467_A 354_A 0.91 0.13 0.00
542_R 118_I 0.91 0.13 0.00
188_A 371_G 0.91 0.13 0.00
816_T 110_T 0.90 0.13 0.00
200_T 196_I 0.90 0.13 0.00
552_Y 27_F 0.90 0.13 0.00
387_V 242_I 0.90 0.13 0.00
273_S 3_T 0.90 0.13 0.00
732_K 131_V 0.90 0.13 0.00
317_D 238_G 0.90 0.12 0.00
500_S 303_M 0.89 0.12 0.00
709_G 208_A 0.89 0.12 0.00
788_Y 194_V 0.89 0.12 0.00
430_V 130_V 0.89 0.12 0.00
528_G 301_I 0.88 0.12 0.00
295_I 422_V 0.88 0.12 0.00
427_L 172_S 0.88 0.12 0.00
91_I 101_P 0.88 0.12 0.00
695_L 205_V 0.88 0.12 0.00
754_H 241_G 0.88 0.12 0.00
437_L 178_R 0.88 0.12 0.00
203_E 315_A 0.88 0.12 0.00
682_V 239_G 0.88 0.12 0.00
416_I 415_Q 0.88 0.12 0.00
558_F 7_A 0.88 0.12 0.00
152_V 281_R 0.87 0.12 0.00
250_Q 285_V 0.87 0.12 0.00
573_S 233_R 0.87 0.12 0.00
436_A 186_D 0.87 0.12 0.00
605_N 20_G 0.87 0.12 0.00
165_D 26_G 0.86 0.12 0.00
464_A 208_A 0.86 0.12 0.00
163_T 402_N 0.86 0.11 0.00
284_Y 389_G 0.86 0.11 0.00
313_N 12_L 0.85 0.11 0.00
570_A 152_L 0.85 0.11 0.00
467_A 29_A 0.85 0.11 0.00
603_I 223_Q 0.85 0.11 0.00
568_S 419_G 0.85 0.11 0.00
739_Y 387_V 0.85 0.11 0.00
82_I 312_T 0.85 0.11 0.00
408_D 20_G 0.85 0.11 0.00
328_A 341_P 0.84 0.11 0.00
727_T 30_A 0.84 0.11 0.00
135_R 304_R 0.84 0.11 0.00
695_L 99_A 0.84 0.11 0.00
104_V 170_A 0.84 0.11 0.00
165_D 28_E 0.84 0.11 0.00
437_L 15_Q 0.84 0.11 0.00
297_T 284_A 0.84 0.11 0.00
693_S 345_G 0.84 0.11 0.00
691_I 313_L 0.83 0.11 0.00
117_L 130_V 0.83 0.11 0.00
691_I 138_N 0.83 0.11 0.00
233_V 201_L 0.83 0.11 0.00
482_A 220_T 0.83 0.11 0.00
492_S 230_S 0.83 0.11 0.00
790_K 172_S 0.83 0.11 0.00
97_R 110_T 0.83 0.11 0.00
584_G 142_L 0.83 0.11 0.00
515_S 27_F 0.83 0.11 0.00
515_S 226_F 0.83 0.11 0.00
270_P 180_A 0.83 0.11 0.00
749_I 422_V 0.82 0.11 0.00
467_A 215_K 0.82 0.10 0.00
59_Y 422_V 0.82 0.10 0.00
536_V 13_N 0.82 0.10 0.00
192_F 32_N 0.82 0.10 0.00
538_V 236_V 0.82 0.10 0.00
588_M 175_D 0.82 0.10 0.00
361_A 126_G 0.82 0.10 0.00
177_L 30_A 0.82 0.10 0.00
753_D 115_L 0.82 0.10 0.00
258_A 169_F 0.82 0.10 0.00
539_R 155_N 0.82 0.10 0.00
790_K 20_G 0.82 0.10 0.00
204_M 198_R 0.82 0.10 0.00
295_I 8_L 0.82 0.10 0.00
250_Q 36_Q 0.81 0.10 0.00
709_G 159_N 0.81 0.10 0.00
43_D 180_A 0.81 0.10 0.00
695_L 237_N 0.81 0.10 0.00
58_I 144_K 0.81 0.10 0.00
584_G 236_V 0.81 0.10 0.00
392_P 20_G 0.81 0.10 0.00
328_A 154_L 0.81 0.10 0.00
744_V 285_V 0.81 0.10 0.00
58_I 5_K 0.81 0.10 0.00
471_V 294_I 0.81 0.10 0.00
818_Q 105_L 0.81 0.10 0.00
435_S 286_Y 0.81 0.10 0.00
744_V 370_M 0.81 0.10 0.00
788_Y 214_Q 0.81 0.10 0.00
196_V 102_S 0.81 0.10 0.00
356_P 125_D 0.81 0.10 0.00
812_I 316_S 0.81 0.10 0.00
758_L 424_V 0.81 0.10 0.00
603_I 106_K 0.80 0.10 0.00
196_V 164_V 0.80 0.10 0.00
542_R 149_L 0.80 0.10 0.00
695_L 138_N 0.80 0.10 0.00
106_P 284_A 0.80 0.10 0.00
60_S 195_L 0.80 0.10 0.00
451_V 284_A 0.80 0.10 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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