PNCA - ECOLI - GREMLIN Contacts

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PNCA - Pyrazinamidase/nicotinamidase

UniProt:	P21369	Sequences: MPPRALLLVDLQNDFCAGGALAVPEGDSTVDVANRLIDWCQSRGEAVIASQDWHPANHGSFASQHGVEPYTPGQLDGLPQTFWPDHCVQNSEGAQLHPLLHQKAIAAVFHKGENPLVDSYSAFFDNGRRQKTSLDDWLRDHEIDELIVMGLATDYCVKFTVLDALQLGYKVNVITDGCRGVNIQPQDSAHAFMEMSAAGATLYTLADWEETQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11135
Length:	213 (176)
Sequences:	9521 (6582)
Seq/√Len:	496.1

ECOLI - PNCA RUTB YECD YCAC
BACSU - YWOC YAAI PNCA YDDQ 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
135_D	139_R	3.213	1.00
51_Q	110_H	2.878	1.00
135_D	169_Y	2.761	1.00
145_E	170_K	2.747	1.00
121_S	163_D	2.747	1.00
40_C	45_E	2.516	1.00
4_R	145_E	2.440	1.00
33_A	149_M	2.419	1.00
135_D	167_L	2.264	1.00
11_L	33_A	2.235	1.00
148_V	161_V	2.201	1.00
36_L	174_I	2.193	1.00
145_E	172_N	2.160	1.00
195_M	200_A	2.023	1.00
13_N	92_E	1.992	1.00
14_D	93_G	1.960	1.00
133_S	137_W	1.922	1.00
164_A	171_V	1.850	1.00
5_A	143_I	1.845	1.00
3_P	144_D	1.840	1.00
122_A	160_T	1.833	1.00
158_K	162_L	1.819	1.00
204_T	207_D	1.818	1.00
39_W	43_R	1.807	1.00
109_F	137_W	1.795	1.00
175_T	202_L	1.792	1.00
175_T	204_T	1.784	1.00
183_I	189_A	1.782	1.00
32_V	177_G	1.776	1.00
32_V	205_L	1.754	1.00
32_V	35_R	1.739	1.00
153_T	188_S	1.726	1.00
13_N	98_P	1.639	1.00
4_R	147_I	1.585	1.00
16_C	97_H	1.567	1.00
48_I	137_W	1.565	1.00
180_G	188_S	1.530	1.00
41_Q	106_A	1.489	1.00
176_D	205_L	1.481	1.00
147_I	174_I	1.478	1.00
158_K	194_E	1.475	1.00
50_S	122_A	1.469	1.00
107_A	137_W	1.458	1.00
40_C	147_I	1.452	1.00
8_L	149_M	1.446	1.00
8_L	37_I	1.438	1.00
153_T	192_F	1.420	1.00
34_N	38_D	1.412	1.00
146_L	164_A	1.384	1.00
153_T	178_C	1.380	1.00
154_D	180_G	1.373	1.00
157_V	173_V	1.368	1.00
46_A	141_H	1.357	1.00
35_R	206_A	1.353	1.00
92_E	95_Q	1.348	1.00
25_E	28_S	1.336	1.00
7_L	148_V	1.327	1.00
53_W	94_A	1.310	1.00
189_A	193_M	1.299	1.00
148_V	160_T	1.294	1.00
63_S	85_D	1.272	1.00
186_Q	189_A	1.270	1.00
8_L	11_L	1.244	1.00
175_T	192_F	1.241	1.00
158_K	191_A	1.231	1.00
89_Q	110_H	1.227	1.00
136_D	140_D	1.215	1.00
38_D	42_S	1.215	1.00
139_R	169_Y	1.201	1.00
137_W	141_H	1.197	1.00
177_G	205_L	1.189	1.00
6_L	40_C	1.185	1.00
29_T	33_A	1.179	1.00
31_D	99_L	1.175	1.00
34_N	99_L	1.166	1.00
9_V	156_C	1.160	1.00
8_L	33_A	1.142	1.00
51_Q	96_L	1.124	1.00
37_I	41_Q	1.114	1.00
182_N	186_Q	1.109	1.00
173_V	178_C	1.101	1.00
133_S	136_D	1.095	1.00
51_Q	108_V	1.082	1.00
147_I	172_N	1.077	1.00
163_D	167_L	1.056	1.00
13_N	95_Q	1.055	1.00
36_L	177_G	1.050	1.00
172_N	201_T	1.041	1.00
178_C	188_S	1.024	1.00
32_V	176_D	1.020	1.00
161_V	173_V	1.016	1.00
4_R	45_E	1.015	1.00
170_K	201_T	1.009	1.00
146_L	171_V	0.984	1.00
95_Q	101_H	0.977	1.00
153_T	180_G	0.975	1.00
161_V	195_M	0.968	1.00
37_I	49_A	0.957	1.00
85_D	88_V	0.950	1.00
96_L	108_V	0.943	1.00
144_D	170_K	0.942	1.00
39_W	42_S	0.939	1.00
55_P	89_Q	0.930	1.00
182_N	187_D	0.930	1.00
53_W	110_H	0.928	1.00
10_D	111_K	0.924	1.00
5_A	48_I	0.923	1.00
34_N	102_Q	0.915	1.00
186_Q	190_H	0.913	1.00
123_F	164_A	0.907	1.00
119_S	168_G	0.903	1.00
46_A	143_I	0.902	1.00
172_N	203_Y	0.895	1.00
174_I	203_Y	0.889	1.00
192_F	202_L	0.870	1.00
186_Q	193_M	0.869	1.00
7_L	134_L	0.867	1.00
35_R	39_W	0.867	1.00
174_I	177_G	0.867	1.00
188_S	192_F	0.856	1.00
9_V	148_V	0.852	1.00
159_F	162_L	0.850	1.00
57_N	60_S	0.847	1.00
137_W	140_D	0.845	1.00
53_W	89_Q	0.841	1.00
35_R	38_D	0.831	1.00
13_N	17_A	0.826	1.00
49_A	96_L	0.819	1.00
28_S	31_D	0.818	1.00
11_L	151_L	0.815	1.00
17_A	27_D	0.811	1.00
31_D	35_R	0.811	1.00
122_A	134_L	0.810	1.00
203_Y	207_D	0.808	1.00
163_D	166_Q	0.801	1.00
5_A	138_L	0.799	1.00
103_K	106_A	0.793	1.00
3_P	145_E	0.792	1.00
191_A	195_M	0.792	1.00
37_I	47_V	0.791	1.00
149_M	177_G	0.790	1.00
102_Q	106_A	0.788	1.00
36_L	149_M	0.787	1.00
193_M	196_S	0.786	1.00
154_D	187_D	0.784	1.00
92_E	98_P	0.773	1.00
151_L	179_R	0.772	1.00
29_T	179_R	0.771	1.00
30_V	34_N	0.761	1.00
148_V	157_V	0.755	1.00
31_D	34_N	0.751	1.00
49_A	102_Q	0.748	1.00
33_A	177_G	0.746	1.00
48_I	141_H	0.746	1.00
13_N	97_H	0.741	1.00
49_A	105_I	0.735	1.00
62_A	65_H	0.729	1.00
8_L	49_A	0.725	1.00
46_A	137_W	0.719	1.00
91_S	94_A	0.717	1.00
90_N	95_Q	0.715	1.00
138_L	169_Y	0.713	1.00
154_D	194_E	0.713	1.00
190_H	194_E	0.707	1.00
136_D	139_R	0.702	1.00
98_P	101_H	0.698	1.00
35_R	205_L	0.698	1.00
165_L	200_A	0.692	1.00
187_D	190_H	0.692	1.00
16_C	30_V	0.690	1.00
30_V	97_H	0.689	1.00
193_M	197_A	0.688	1.00
36_L	205_L	0.684	1.00
65_H	82_F	0.678	1.00
14_D	87_C	0.676	1.00
173_V	192_F	0.668	1.00
29_T	151_L	0.665	1.00
38_D	101_H	0.663	1.00
15_F	156_C	0.663	1.00
14_D	19_G	0.662	1.00
27_D	99_L	0.660	1.00
34_N	101_H	0.658	1.00
154_D	181_V	0.656	1.00
3_P	142_E	0.655	1.00
119_S	131_K	0.653	1.00
51_Q	95_Q	0.652	1.00
187_D	193_M	0.650	1.00
190_H	193_M	0.650	1.00
48_I	107_A	0.649	1.00
161_V	200_A	0.645	1.00
49_A	108_V	0.645	1.00
18_G	22_A	0.644	1.00
36_L	40_C	0.644	1.00
38_D	103_K	0.641	1.00
178_C	192_F	0.640	1.00
11_L	29_T	0.639	1.00
55_P	60_S	0.639	1.00
6_L	149_M	0.635	1.00
131_K	136_D	0.635	1.00
148_V	171_V	0.624	1.00
24_P	28_S	0.623	1.00
55_P	58_H	0.620	1.00
37_I	106_A	0.620	1.00
37_I	40_C	0.619	1.00
159_F	199_G	0.617	1.00
56_A	85_D	0.615	1.00
41_Q	105_I	0.615	1.00
26_G	151_L	0.614	1.00
130_Q	167_L	0.610	0.99
16_C	26_G	0.602	0.99
40_C	44_G	0.602	0.99
102_Q	108_V	0.602	0.99
175_T	196_S	0.598	0.99
107_A	141_H	0.598	0.99
88_V	91_S	0.596	0.99
19_G	22_A	0.594	0.99
6_L	36_L	0.593	0.99
162_L	198_A	0.592	0.99
152_A	155_Y	0.590	0.99
87_C	93_G	0.590	0.99
49_A	106_A	0.588	0.99
155_Y	181_V	0.586	0.99
48_I	109_F	0.583	0.99
57_N	64_Q	0.580	0.99
41_Q	103_K	0.580	0.99
15_F	152_A	0.579	0.99
192_F	196_S	0.579	0.99
30_V	100_L	0.576	0.99
175_T	188_S	0.574	0.99
11_L	100_L	0.566	0.99
49_A	100_L	0.563	0.99
171_V	174_I	0.561	0.99
83_W	86_H	0.560	0.99
11_L	97_H	0.560	0.99
120_Y	166_Q	0.556	0.99
6_L	37_I	0.556	0.99
59_G	64_Q	0.546	0.99
173_V	195_M	0.544	0.99
6_L	47_V	0.543	0.99
183_I	186_Q	0.543	0.99
46_A	107_A	0.542	0.99
97_H	100_L	0.534	0.99
13_N	93_G	0.534	0.99
148_V	164_A	0.533	0.99
102_Q	105_I	0.531	0.99
41_Q	47_V	0.529	0.99
120_Y	160_T	0.528	0.99
109_F	133_S	0.527	0.98
9_V	157_V	0.527	0.98
54_H	60_S	0.527	0.98
121_S	166_Q	0.526	0.98
194_E	197_A	0.522	0.98
41_Q	49_A	0.520	0.98
152_A	180_G	0.520	0.98
161_V	171_V	0.516	0.98
5_A	46_A	0.513	0.98
157_V	178_C	0.511	0.98
20_A	23_V	0.510	0.98
12_Q	51_Q	0.504	0.98
149_M	174_I	0.504	0.98
22_A	27_D	0.504	0.98
61_F	64_Q	0.502	0.98
46_A	106_A	0.500	0.98
12_Q	50_S	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
3v8eA	2	0.9484	100	0.242	Contact Map
3hb7A	3	0.8404	100	0.242	Contact Map
1im5A	1	0.8404	100	0.243	Contact Map
2wt9A	2	0.9577	100	0.243	Contact Map
1nbaA	4	0.8873	100	0.247	Contact Map
3irvA	2	0.8873	100	0.247	Contact Map
3ot4A	4	0.8732	100	0.249	Contact Map
3hu5A	3	0.8826	100	0.25	Contact Map
3r2jA	2	0.8967	100	0.25	Contact Map
4l07A	4	0.8732	100	0.251	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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