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OPENSEQ.org
PGLYRP1-HSP70
Genes: A B A+B
Length: 196 641 781
Sequences: 948 3084 76
Seq/Len: 4.84 4.81 0.1
MirrorTree (Pazo et al. 2001) 0.48
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 0.05 0.06 0.00
2 0.05 0.06 0.00
5 0.05 0.06 0.00
10 0.05 0.07 0.00
20 0.05 0.07 0.00
100 0.06 0.07 0.02
∞ 0.14 0.10 0.09
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
129_I 521_E 1.40 0.17 0.00
59_V 429_T 1.28 0.14 0.00
183_L 377_A 1.25 0.14 0.00
172_D 334_L 1.23 0.13 0.00
145_I 330_Q 1.22 0.13 0.00
129_I 114_F 1.17 0.12 0.00
139_V 514_E 1.15 0.11 0.00
41_A 377_A 1.14 0.11 0.00
62_T 492_D 1.11 0.10 0.00
152_L 521_E 1.10 0.10 0.00
126_S 220_K 1.10 0.10 0.00
94_G 170_L 1.08 0.10 0.00
144_A 103_V 1.08 0.10 0.00
44_S 486_L 1.07 0.10 0.00
171_R 471_V 1.07 0.10 0.00
152_L 163_V 1.07 0.10 0.00
121_L 355_N 1.06 0.10 0.00
129_I 305_L 1.06 0.10 0.00
90_W 308_D 1.05 0.10 0.00
127_I 305_L 1.05 0.09 0.00
129_I 327_D 1.05 0.09 0.00
35_P 139_V 1.05 0.09 0.00
97_F 502_T 1.05 0.09 0.00
171_R 168_N 1.05 0.09 0.00
96_N 239_N 1.05 0.09 0.00
161_L 63_P 1.04 0.09 0.00
128_G 330_Q 1.04 0.09 0.00
153_A 335_V 1.04 0.09 0.00
94_G 153_S 1.04 0.09 0.00
95_Y 236_R 1.03 0.09 0.00
102_D 313_T 1.02 0.09 0.00
121_L 511_S 1.01 0.09 0.00
100_G 368_A 1.01 0.09 0.00
37_N 320_A 1.01 0.09 0.00
122_W 363_I 1.01 0.09 0.00
169_G 593_E 1.01 0.09 0.00
97_F 593_E 1.00 0.09 0.00
99_I 361_K 1.00 0.09 0.00
140_P 227_H 1.00 0.09 0.00
81_Q 368_A 1.00 0.09 0.00
145_I 320_A 0.99 0.08 0.00
92_D 485_I 0.99 0.08 0.00
184_Y 514_E 0.99 0.08 0.00
187_I 51_I 0.99 0.08 0.00
40_K 463_G 0.99 0.08 0.00
97_F 173_I 0.99 0.08 0.00
31_S 335_V 0.99 0.08 0.00
84_H 413_L 0.99 0.08 0.00
147_A 133_A 0.98 0.08 0.00
104_L 582_D 0.98 0.08 0.00
153_A 123_V 0.98 0.08 0.00
64_G 520_Q 0.98 0.08 0.00
63_A 520_Q 0.97 0.08 0.00
41_A 429_T 0.97 0.08 0.00
130_S 527_A 0.97 0.08 0.00
135_Y 546_A 0.97 0.08 0.00
83_Y 133_A 0.97 0.08 0.00
105_V 173_I 0.97 0.08 0.00
58_V 521_E 0.96 0.08 0.00
62_T 359_L 0.96 0.08 0.00
35_P 562_I 0.95 0.08 0.00
33_I 173_I 0.95 0.08 0.00
118_S 427_I 0.94 0.08 0.00
94_G 471_V 0.94 0.08 0.00
84_H 308_D 0.94 0.08 0.00
153_A 281_S 0.94 0.08 0.00
133_G 169_V 0.94 0.08 0.00
133_G 275_S 0.94 0.08 0.00
183_L 260_V 0.94 0.08 0.00
102_D 17_C 0.93 0.07 0.00
105_V 568_K 0.93 0.07 0.00
151_L 344_P 0.93 0.07 0.00
35_P 138_P 0.93 0.07 0.00
67_C 123_V 0.93 0.07 0.00
126_S 245_F 0.93 0.07 0.00
122_W 160_D 0.93 0.07 0.00
169_G 300_A 0.92 0.07 0.00
82_H 300_A 0.92 0.07 0.00
59_V 377_A 0.92 0.07 0.00
100_G 231_E 0.92 0.07 0.00
129_I 544_S 0.92 0.07 0.00
136_M 546_A 0.92 0.07 0.00
132_M 595_K 0.91 0.07 0.00
102_D 41_Y 0.91 0.07 0.00
33_I 452_D 0.91 0.07 0.00
105_V 355_N 0.91 0.07 0.00
62_T 149_Y 0.90 0.07 0.00
80_V 595_K 0.90 0.07 0.00
56_Y 305_L 0.90 0.07 0.00
58_V 535_R 0.90 0.07 0.00
176_T 543_E 0.90 0.07 0.00
173_V 576_E 0.90 0.07 0.00
90_W 481_D 0.90 0.07 0.00
75_Q 494_S 0.90 0.07 0.00
167_L 545_Y 0.89 0.07 0.00
80_V 358_D 0.89 0.07 0.00
176_T 308_D 0.89 0.07 0.00
183_L 63_P 0.89 0.07 0.00
74_Q 612_Q 0.89 0.07 0.00
78_R 588_E 0.89 0.07 0.00
35_P 597_K 0.89 0.07 0.00
126_S 331_I 0.89 0.07 0.00
187_I 19_G 0.89 0.07 0.00
97_F 117_E 0.88 0.07 0.00
58_V 79_G 0.88 0.07 0.00
190_W 444_E 0.88 0.07 0.00
169_G 320_A 0.88 0.07 0.00
133_G 485_I 0.88 0.07 0.00
169_G 251_K 0.88 0.07 0.00
151_L 63_P 0.88 0.07 0.00
35_P 330_Q 0.88 0.07 0.00
187_I 41_Y 0.87 0.07 0.00
121_L 209_I 0.87 0.07 0.00
102_D 7_I 0.87 0.07 0.00
167_L 70_A 0.87 0.07 0.00
187_I 280_A 0.87 0.07 0.00
134_N 313_T 0.87 0.07 0.00
146_R 521_E 0.87 0.07 0.00
41_A 246_K 0.86 0.07 0.00
147_A 186_D 0.86 0.07 0.00
94_G 241_F 0.86 0.07 0.00
66_S 198_F 0.86 0.07 0.00
95_Y 118_E 0.86 0.07 0.00
169_G 573_K 0.85 0.07 0.00
115_G 312_S 0.85 0.07 0.00
88_L 432_S 0.85 0.07 0.00
71_A 512_K 0.85 0.07 0.00
102_D 321_L 0.85 0.07 0.00
97_F 509_R 0.85 0.07 0.00
99_I 434_N 0.85 0.07 0.00
131_F 160_D 0.85 0.07 0.00
105_V 111_T 0.85 0.07 0.00
105_V 564_E 0.85 0.07 0.00
53_P 88_K 0.85 0.07 0.00
77_A 304_E 0.85 0.07 0.00
178_S 181_I 0.85 0.07 0.00
174_Q 114_F 0.84 0.06 0.00
156_V 330_Q 0.84 0.06 0.00
132_M 207_V 0.84 0.06 0.00
60_S 309_L 0.84 0.06 0.00
94_G 99_D 0.84 0.06 0.00
178_S 267_C 0.84 0.06 0.00
158_Q 215_G 0.84 0.06 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
10467 0.1 PGLYRP1-HSP70 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10466 0.1 PGLYRP1-HSP70 Δgene:(0, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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