PNCA - BACSU - GREMLIN Contacts

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PNCA - Uncharacterized isochorismatase family protein PncA

UniProt:	O32091	Sequences: MKKALICIDYTNDFVASDGKLTCGEPGRMIEEAIVNLTKEFITNGDYVVLAVDSHDEGDQYHPETRLFPPHNIKGTEGKDLYGKLLPLYQKHEHEPNVYYMEKTRYSAFAGTDLELKLRERQIGELHLAGVCTDICVLHTAVDAYNKGFRIVVHKQAVASFNQEGHAWALSHFANSIGAQVAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	183 (163)
Sequences:	9660 (6826)
Seq/√Len:	534.7

ECOLI - RUTB PNCA YECD YCAC
BACSU - PNCA YAAI YDDQ YWOC YRDC
HALSA - Q9HMH5 Q9HQL7
SULSO - Q97VZ5 Q97YW7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_E	119_R	3.475	1.00
115_E	149_F	2.812	1.00
107_S	143_D	2.795	1.00
125_E	150_R	2.783	1.00
41_F	46_D	2.666	1.00
3_K	125_E	2.553	1.00
34_I	129_A	2.415	1.00
125_E	152_V	2.371	1.00
115_E	147_K	2.357	1.00
10_Y	34_I	2.324	1.00
37_L	154_H	2.315	1.00
128_L	141_A	2.255	1.00
163_Q	167_A	2.110	1.00
113_D	117_K	2.067	1.00
138_L	142_V	2.030	1.00
13_D	78_G	2.023	1.00
4_A	123_I	1.951	1.00
12_N	77_E	1.937	1.00
33_A	157_A	1.893	1.00
40_E	44_N	1.865	1.00
52_V	102_E	1.865	1.00
33_A	36_N	1.817	1.00
144_A	151_I	1.816	1.00
49_V	117_K	1.773	1.00
108_A	140_T	1.762	1.00
3_K	127_H	1.696	1.00
12_N	83_G	1.683	1.00
7_C	38_T	1.584	1.00
127_H	154_H	1.582	1.00
51_A	108_A	1.570	1.00
41_F	127_H	1.557	1.00
15_V	82_Y	1.549	1.00
35_V	39_K	1.537	1.00
47_Y	121_R	1.536	1.00
42_I	98_V	1.508	1.00
54_S	79_K	1.460	1.00
77_E	80_D	1.436	1.00
7_C	129_A	1.432	1.00
101_M	117_K	1.429	1.00
137_V	153_V	1.422	1.00
126_L	144_A	1.420	1.00
133_T	158_V	1.420	1.00
99_Y	117_K	1.399	1.00
138_L	172_H	1.391	1.00
128_L	140_T	1.385	1.00
164_E	167_A	1.372	1.00
134_D	160_S	1.361	1.00
133_T	166_H	1.359	1.00
117_K	121_R	1.357	1.00
6_I	128_L	1.355	1.00
64_E	70_P	1.335	1.00
153_V	158_V	1.329	1.00
26_P	29_M	1.304	1.00
160_S	166_H	1.303	1.00
39_K	43_T	1.267	1.00
35_V	84_K	1.265	1.00
38_T	42_I	1.265	1.00
7_C	34_I	1.254	1.00
143_D	147_K	1.251	1.00
133_T	170_L	1.228	1.00
33_A	156_Q	1.225	1.00
167_A	171_S	1.225	1.00
52_V	81_L	1.223	1.00
119_R	149_F	1.217	1.00
7_C	10_Y	1.213	1.00
116_L	120_E	1.211	1.00
74_K	102_E	1.206	1.00
32_E	84_K	1.204	1.00
5_L	41_F	1.183	1.00
95_E	98_V	1.164	1.00
127_H	152_V	1.162	1.00
30_I	34_I	1.149	1.00
3_K	46_D	1.136	1.00
54_S	74_K	1.124	1.00
37_L	157_A	1.121	1.00
8_I	136_C	1.120	1.00
12_N	80_D	1.109	1.00
139_H	142_V	1.102	1.00
141_A	153_V	1.091	1.00
54_S	102_E	1.087	1.00
56_D	74_K	1.059	1.00
113_D	116_L	1.045	1.00
155_K	170_L	1.022	1.00
30_I	159_A	1.020	1.00
38_T	50_L	1.013	1.00
133_T	160_S	1.012	1.00
126_L	151_I	0.982	1.00
138_L	169_A	0.975	1.00
154_H	157_A	0.967	1.00
124_G	150_R	0.959	1.00
4_A	49_V	0.950	1.00
117_K	120_E	0.946	1.00
171_S	175_N	0.945	1.00
10_Y	131_V	0.934	1.00
40_E	43_T	0.933	1.00
80_D	86_L	0.930	1.00
36_N	40_E	0.928	1.00
36_N	39_K	0.926	1.00
50_L	81_L	0.924	1.00
129_A	157_A	0.920	1.00
17_S	28_R	0.914	1.00
47_Y	123_I	0.905	1.00
6_I	114_L	0.905	1.00
162_N	165_G	0.902	1.00
164_E	171_S	0.897	1.00
35_V	87_P	0.894	1.00
141_A	173_F	0.892	1.00
165_G	168_W	0.878	1.00
171_S	174_A	0.869	1.00
158_V	166_H	0.864	1.00
70_P	73_I	0.859	1.00
110_A	147_K	0.853	1.00
105_R	148_G	0.845	1.00
109_F	144_A	0.842	1.00
143_D	146_N	0.840	1.00
8_I	128_L	0.835	1.00
118_L	149_F	0.834	1.00
108_A	114_L	0.829	1.00
38_T	48_V	0.829	1.00
76_T	79_K	0.821	1.00
166_H	170_L	0.819	1.00
37_L	129_A	0.802	1.00
18_D	22_T	0.800	1.00
31_E	35_V	0.796	1.00
50_L	87_P	0.795	1.00
49_V	121_R	0.788	1.00
87_P	98_V	0.781	1.00
4_A	118_L	0.776	1.00
29_M	32_E	0.774	1.00
168_W	171_S	0.771	1.00
7_C	50_L	0.765	1.00
169_A	173_F	0.763	1.00
32_E	35_V	0.763	1.00
34_I	157_A	0.762	1.00
19_G	22_T	0.759	1.00
47_Y	117_K	0.751	1.00
50_L	98_V	0.743	1.00
128_L	137_V	0.742	1.00
32_E	36_N	0.741	1.00
105_R	111_G	0.737	1.00
82_Y	85_L	0.734	1.00
131_V	159_A	0.730	1.00
41_F	45_G	0.726	1.00
77_E	83_G	0.719	1.00
13_D	19_G	0.713	1.00
164_E	168_W	0.712	1.00
10_Y	82_Y	0.710	1.00
35_V	86_L	0.706	1.00
132_C	135_I	0.701	1.00
110_A	146_N	0.693	1.00
116_L	119_R	0.690	1.00
14_F	136_C	0.690	1.00
52_V	100_Y	0.689	1.00
10_Y	30_I	0.689	1.00
49_V	99_Y	0.688	1.00
73_I	76_T	0.682	1.00
31_E	82_Y	0.677	1.00
30_I	131_V	0.674	1.00
12_N	82_Y	0.672	1.00
42_I	97_N	0.672	1.00
42_I	95_E	0.672	1.00
27_G	131_V	0.671	1.00
128_L	151_I	0.671	1.00
165_G	171_S	0.670	1.00
5_L	37_L	0.668	1.00
15_V	31_E	0.668	1.00
56_D	59_D	0.660	1.00
168_W	172_H	0.659	1.00
5_L	129_A	0.657	1.00
52_V	96_P	0.653	1.00
83_G	86_L	0.648	1.00
165_G	175_N	0.645	1.00
39_K	86_L	0.644	1.00
134_D	161_F	0.643	1.00
155_K	174_A	0.636	1.00
15_V	27_G	0.635	1.00
75_G	80_D	0.633	1.00
127_H	156_Q	0.632	1.00
39_K	95_E	0.631	1.00
151_I	154_H	0.624	1.00
31_E	85_L	0.619	1.00
58_G	101_M	0.617	1.00
129_A	154_H	0.617	1.00
50_L	85_L	0.610	1.00
134_D	172_H	0.609	1.00
37_L	127_H	0.608	1.00
172_H	175_N	0.606	1.00
38_T	98_V	0.603	1.00
9_D	103_K	0.602	1.00
132_C	160_S	0.598	1.00
86_L	95_E	0.598	1.00
141_A	151_I	0.596	1.00
134_D	165_G	0.596	1.00
99_Y	121_R	0.592	1.00
41_F	47_Y	0.592	1.00
137_V	158_V	0.591	1.00
52_V	80_D	0.588	0.99
23_C	26_P	0.587	0.99
38_T	41_F	0.587	0.99
132_C	161_F	0.587	0.99
68_F	71_H	0.584	0.99
111_G	116_L	0.583	0.99
10_Y	85_L	0.581	0.99
5_L	38_T	0.578	0.99
101_M	113_D	0.577	0.99
106_Y	140_T	0.573	0.99
106_Y	146_N	0.571	0.99
110_A	143_D	0.571	0.99
42_I	48_V	0.571	0.99
87_P	100_Y	0.570	0.99
107_S	146_N	0.570	0.99
21_L	24_G	0.570	0.99
65_T	69_P	0.569	0.99
14_F	132_C	0.568	0.99
37_L	41_F	0.568	0.99
65_T	68_F	0.566	0.99
135_I	161_F	0.564	0.99
13_D	72_N	0.558	0.99
49_V	101_M	0.555	0.99
52_V	79_K	0.552	0.99
8_I	137_V	0.549	0.99
5_L	48_V	0.546	0.99
153_V	173_F	0.544	0.99
26_P	159_A	0.542	0.99
105_R	110_A	0.540	0.99
106_Y	135_I	0.536	0.99
63_P	66_R	0.535	0.99
106_Y	145_Y	0.533	0.99
10_Y	31_E	0.528	0.99
49_V	114_L	0.527	0.99
3_K	152_V	0.527	0.99
155_K	166_H	0.526	0.99
155_K	158_V	0.524	0.99
66_R	69_P	0.520	0.99
56_D	104_T	0.519	0.99
22_T	28_R	0.516	0.99
28_R	84_K	0.515	0.99
145_Y	151_I	0.514	0.99
42_I	50_L	0.510	0.99
53_D	72_N	0.509	0.99
17_S	22_T	0.508	0.99
47_Y	99_Y	0.508	0.99
170_L	174_A	0.501	0.98
19_G	23_C	0.500	0.98

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
3o94A	4	0.9945	100	0.118	Contact Map
3v8eA	2	0.9563	100	0.155	Contact Map
1nbaA	4	0.9508	100	0.171	Contact Map
3hb7A	3	0.929	100	0.173	Contact Map
1im5A	1	0.9344	100	0.176	Contact Map
3irvA	2	0.9508	100	0.177	Contact Map
3eefA	4	0.9126	100	0.182	Contact Map
3hu5A	3	0.9508	100	0.182	Contact Map
4l07A	4	0.9454	100	0.184	Contact Map
3ot4A	4	0.9454	100	0.189	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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