PAAY - ECOLI - GREMLIN Contacts

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PAAY - Phenylacetic acid degradation protein PaaY

UniProt:	P77181	Sequences: MPIYQIDGLTPVVPEESFVHPTAVLIGDVILGKGVYVGPNASLRGDFGRIVVKDGANIQDNCVMHGFPEQDTVVGEDGHIGHSAILHGCIIRRNALVGMNAVVMDGAVIGENSIVGASAFVKAKAEMPANYLIVGSPAKAIRELSEQELAWKKQGTHEYQVLVTRCKQTLHQVEPLREIEPGRKRLVFDENLRPKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13747
Length:	196 (157)
Sequences:	5651 (3301)
Seq/√Len:	263.4

ECOLI - PAAY CAIE YRDA LPXA THGA WBBJ WCAF
BACSU - YTOA DAPH EPSM MAA
SULSO - Q980E1

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_G	55_G	3.769	1.00
55_G	77_D	3.708	1.00
64_M	72_T	2.999	1.00
33_K	54_D	2.694	1.00
54_D	76_E	2.627	1.00
94_N	112_N	2.545	1.00
127_M	133_I	2.543	1.00
92_R	111_E	2.543	1.00
14_P	33_K	2.444	1.00
77_D	94_N	2.295	1.00
108_V	126_E	2.291	1.00
75_G	93_R	2.278	1.00
116_G	134_V	2.232	1.00
70_Q	106_G	2.172	1.00
30_I	51_V	2.123	1.00
93_R	111_E	2.078	1.00
112_N	130_N	2.019	1.00
32_G	54_D	1.910	1.00
111_E	129_A	1.830	1.00
76_E	93_R	1.803	1.00
145_S	148_E	1.778	1.00
39_P	166_C	1.719	1.00
12_V	30_I	1.703	1.00
35_V	76_E	1.658	1.00
16_E	34_G	1.612	1.00
122_K	125_A	1.583	1.00
130_N	149_L	1.581	1.00
74_V	78_G	1.580	1.00
28_D	49_R	1.563	1.00
55_G	160_Q	1.516	1.00
92_R	108_V	1.514	1.00
20_H	39_P	1.511	1.00
103_V	107_A	1.509	1.00
110_G	129_A	1.505	1.00
63_V	83_S	1.477	1.00
86_L	89_C	1.475	1.00
110_G	126_E	1.470	1.00
22_T	40_N	1.469	1.00
37_V	43_L	1.462	1.00
113_S	131_Y	1.416	1.00
128_P	140_A	1.410	1.00
90_I	108_V	1.395	1.00
40_N	61_N	1.377	1.00
51_V	73_V	1.374	1.00
61_N	83_S	1.364	1.00
30_I	49_R	1.358	1.00
131_Y	143_E	1.343	1.00
128_P	131_Y	1.333	1.00
131_Y	140_A	1.328	1.00
119_A	138_A	1.326	1.00
73_V	90_I	1.316	1.00
115_V	121_V	1.298	1.00
83_S	100_N	1.293	1.00
105_D	123_A	1.285	1.00
25_L	29_V	1.267	1.00
85_I	100_N	1.251	1.00
13_V	17_S	1.246	1.00
134_V	141_I	1.244	1.00
31_L	37_V	1.201	1.00
133_I	140_A	1.200	1.00
95_A	129_A	1.182	1.00
58_I	64_M	1.181	1.00
113_S	129_A	1.181	1.00
16_E	33_K	1.173	1.00
35_V	56_A	1.167	1.00
112_N	149_L	1.150	1.00
115_V	127_M	1.112	1.00
102_V	118_S	1.107	1.00
56_A	78_G	1.098	1.00
31_L	35_V	1.086	1.00
41_A	62_C	1.081	1.00
91_I	95_A	1.079	1.00
133_I	138_A	1.071	1.00
48_G	71_D	1.071	1.00
19_V	23_A	1.052	1.00
110_G	128_P	1.045	1.00
14_P	17_S	1.043	1.00
146_E	150_A	1.035	1.00
120_F	136_S	1.026	1.00
29_V	43_L	1.002	1.00
32_G	76_E	0.999	1.00
150_A	154_Q	0.997	1.00
53_K	76_E	0.996	1.00
32_G	51_V	0.996	1.00
24_V	40_N	0.989	1.00
106_G	124_K	0.979	1.00
154_Q	158_E	0.979	1.00
58_I	62_C	0.970	1.00
85_I	99_M	0.955	1.00
58_I	80_I	0.951	1.00
79_H	155_G	0.945	1.00
75_G	90_I	0.944	1.00
22_T	39_P	0.937	1.00
48_G	69_E	0.935	1.00
165_R	169_T	0.934	1.00
15_E	33_K	0.928	1.00
152_K	155_G	0.920	1.00
43_L	52_V	0.917	1.00
72_T	86_L	0.914	1.00
95_A	113_S	0.913	1.00
25_L	31_L	0.904	1.00
112_N	142_R	0.897	1.00
62_C	84_A	0.888	1.00
35_V	54_D	0.885	1.00
135_G	138_A	0.879	1.00
128_P	133_I	0.873	1.00
140_A	143_E	0.871	1.00
150_A	153_K	0.868	1.00
121_V	138_A	0.867	1.00
146_E	149_L	0.861	1.00
75_G	92_R	0.853	1.00
56_A	76_E	0.846	0.99
162_L	165_R	0.846	0.99
34_G	164_T	0.830	0.99
142_R	148_E	0.824	0.99
130_N	143_E	0.819	0.99
157_H	161_V	0.814	0.99
97_V	103_V	0.802	0.99
91_I	97_V	0.795	0.99
154_Q	157_H	0.781	0.99
112_N	153_K	0.772	0.99
115_V	133_I	0.771	0.99
29_V	45_G	0.770	0.99
43_L	50_I	0.768	0.99
101_A	115_V	0.764	0.99
102_V	120_F	0.760	0.99
165_R	168_Q	0.754	0.99
49_R	71_D	0.749	0.99
122_K	138_A	0.749	0.99
95_A	111_E	0.744	0.99
119_A	136_S	0.742	0.99
12_V	28_D	0.737	0.99
85_I	102_V	0.733	0.99
130_N	146_E	0.733	0.99
92_R	95_A	0.725	0.98
52_V	56_A	0.722	0.98
109_I	113_S	0.715	0.98
59_Q	81_G	0.711	0.98
49_R	73_V	0.707	0.98
24_V	42_S	0.702	0.98
80_I	86_L	0.699	0.98
127_M	140_A	0.698	0.98
97_V	115_V	0.696	0.98
88_G	105_D	0.694	0.98
113_S	133_I	0.693	0.98
92_R	113_S	0.689	0.98
56_A	93_R	0.683	0.98
158_E	162_L	0.680	0.98
17_S	163_V	0.680	0.98
102_V	117_A	0.677	0.98
48_G	70_Q	0.676	0.98
122_K	136_S	0.676	0.98
56_A	74_V	0.673	0.97
107_A	121_V	0.668	0.97
18_F	39_P	0.665	0.97
112_N	144_L	0.664	0.97
120_F	134_V	0.663	0.97
13_V	25_L	0.662	0.97
86_L	91_I	0.662	0.97
74_V	80_I	0.654	0.97
37_V	41_A	0.651	0.97
94_N	111_E	0.646	0.97
92_R	129_A	0.646	0.97
132_L	144_L	0.641	0.97
14_P	32_G	0.639	0.97
59_Q	82_H	0.639	0.97
43_L	64_M	0.634	0.96
77_D	160_Q	0.634	0.96
13_V	31_L	0.633	0.96
77_D	153_K	0.628	0.96
81_G	98_G	0.627	0.96
144_L	148_E	0.626	0.96
55_G	76_E	0.624	0.96
17_S	31_L	0.624	0.96
34_G	54_D	0.622	0.96
92_R	110_G	0.613	0.96
66_G	69_E	0.611	0.96
114_I	144_L	0.609	0.95
94_N	153_K	0.604	0.95
74_V	86_L	0.603	0.95
148_E	151_W	0.600	0.95
40_N	83_S	0.599	0.95
113_S	127_M	0.598	0.95
42_S	61_N	0.596	0.95
17_S	35_V	0.593	0.95
66_G	70_Q	0.593	0.95
60_D	82_H	0.588	0.95
61_N	85_I	0.587	0.95
66_G	72_T	0.587	0.95
13_V	16_E	0.584	0.94
65_H	87_H	0.584	0.94
23_A	41_A	0.582	0.94
104_M	120_F	0.575	0.94
28_D	51_V	0.575	0.94
78_G	111_E	0.574	0.94
151_W	155_G	0.573	0.94
122_K	134_V	0.572	0.94
64_M	74_V	0.570	0.94
152_K	156_T	0.570	0.94
157_H	160_Q	0.568	0.94
56_A	75_G	0.565	0.93
120_F	137_P	0.565	0.93
101_A	119_A	0.564	0.93
84_A	101_A	0.563	0.93
164_T	169_T	0.562	0.93
164_T	168_Q	0.561	0.93
98_G	101_A	0.559	0.93
70_Q	88_G	0.559	0.93
14_P	31_L	0.556	0.93
128_P	143_E	0.554	0.93
24_V	39_P	0.552	0.93
115_V	138_A	0.551	0.92
161_V	164_T	0.551	0.92
18_F	163_V	0.547	0.92
48_G	66_G	0.545	0.92
96_L	114_I	0.542	0.92
103_V	115_V	0.538	0.92
81_G	99_M	0.533	0.91
97_V	101_A	0.530	0.91
122_K	137_P	0.529	0.91
57_N	79_H	0.520	0.90
34_G	160_Q	0.514	0.90
125_A	133_I	0.512	0.89
47_F	158_E	0.511	0.89
156_T	159_Y	0.509	0.89
158_E	161_V	0.508	0.89
47_F	66_G	0.506	0.89
53_K	93_R	0.506	0.89
42_S	60_D	0.506	0.89
47_F	105_D	0.505	0.89
91_I	103_V	0.505	0.89
127_M	131_Y	0.504	0.89
32_G	35_V	0.504	0.89
100_N	117_A	0.502	0.89
82_H	99_M	0.501	0.88
13_V	19_V	0.500	0.88

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1v3wA	3	0.8827	100	0.376	Contact Map
4n27A	3	0.8776	100	0.395	Contact Map
1xhdA	3	0.8673	100	0.4	Contact Map
3r3rA	3	0.8724	100	0.402	Contact Map
3ixcA	3	0.8316	100	0.405	Contact Map
3r1wA	3	0.8827	100	0.411	Contact Map
4r36A	3	0.9847	100	0.412	Contact Map
3hsqA	3	0.9847	100	0.413	Contact Map
1j2zA	3	0.9745	100	0.414	Contact Map
3r0sA	3	0.949	100	0.425	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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