OTC1 - ECOLI - GREMLIN Contacts

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OTC1 - Ornithine carbamoyltransferase chain I

UniProt:	P04391	Sequences: MSGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10069
Length:	334 (296)
Sequences:	7168 (3655)
Seq/√Len:	212.5

ECOLI - OTC1 OTC2 YGEW PYRB
BACSU - OTC PYRB
HALSA - PYRB OTCC
SULSO - OTC PYRB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
258_S	304_E	4.115	1.00
158_T	183_D	3.837	1.00
41_A	44_T	3.381	1.00
158_T	185_R	3.297	1.00
271_F	301_V	3.125	1.00
160_V	226_A	3.100	1.00
220_A	263_L	2.992	1.00
31_K	147_E	2.830	1.00
145_M	228_F	2.793	1.00
26_L	329_V	2.733	1.00
98_G	122_S	2.718	1.00
227_D	266_N	2.626	1.00
99_R	315_D	2.609	1.00
148_H	312_I	2.594	1.00
218_D	221_K	2.565	1.00
270_K	312_I	2.558	1.00
28_A	146_Q	2.485	1.00
91_K	116_T	2.303	1.00
49_A	101_Y	2.303	1.00
11_K	133_F	2.295	1.00
25_Q	146_Q	2.261	1.00
67_A	72_A	2.191	1.00
272_L	312_I	2.185	1.00
28_A	143_L	2.118	1.00
48_I	67_A	2.112	1.00
103_G	328_M	2.105	1.00
21_N	146_Q	2.103	1.00
196_A	200_T	2.076	1.00
138_L	176_A	2.025	1.00
190_Q	217_E	1.995	1.00
187_V	222_G	1.941	1.00
193_W	217_E	1.940	1.00
149_L	268_E	1.939	1.00
223_V	229_I	1.904	1.00
142_L	176_A	1.900	1.00
278_F	299_M	1.879	1.00
69_D	325_K	1.843	1.00
148_H	315_D	1.836	1.00
261_M	269_V	1.828	1.00
177_A	184_L	1.816	1.00
99_R	318_E	1.802	1.00
17_P	21_N	1.798	1.00
258_S	262_Q	1.793	1.00
68_Y	73_R	1.761	1.00
105_Q	128_G	1.752	1.00
183_D	214_T	1.730	1.00
16_T	19_E	1.709	1.00
216_T	221_K	1.671	1.00
22_S	330_A	1.668	1.00
110_G	113_I	1.638	1.00
61_C	97_L	1.635	1.00
185_R	216_T	1.626	1.00
30_L	329_V	1.592	1.00
136_T	327_V	1.592	1.00
259_K	262_Q	1.579	1.00
264_T	269_V	1.567	1.00
48_I	103_G	1.566	1.00
149_L	157_M	1.542	1.00
23_L	330_A	1.518	1.00
192_C	250_L	1.506	1.00
190_Q	193_W	1.500	1.00
26_L	330_A	1.485	1.00
17_P	179_L	1.482	1.00
78_G	81_G	1.478	1.00
173_M	230_Y	1.474	1.00
53_E	113_I	1.464	1.00
183_D	212_N	1.463	1.00
220_A	260_M	1.462	1.00
133_F	175_E	1.458	1.00
160_V	187_V	1.455	1.00
7_K	19_E	1.453	1.00
269_V	310_A	1.452	1.00
9_F	139_L	1.447	1.00
17_P	155_N	1.417	1.00
246_E	250_L	1.415	1.00
228_F	270_K	1.405	1.00
27_A	143_L	1.388	1.00
42_K	329_V	1.380	1.00
225_G	266_N	1.366	1.00
230_Y	316_Q	1.356	1.00
95_R	307_E	1.342	1.00
136_T	324_I	1.341	1.00
24_L	146_Q	1.327	1.00
162_A	223_V	1.321	1.00
219_V	260_M	1.318	1.00
115_E	119_E	1.307	1.00
188_A	193_W	1.298	1.00
229_I	256_V	1.297	1.00
160_V	185_R	1.284	1.00
94_A	117_L	1.284	1.00
257_N	302_T	1.283	1.00
24_L	143_L	1.281	1.00
29_K	33_D	1.265	1.00
224_E	263_L	1.263	1.00
60_R	64_E	1.260	1.00
26_L	29_K	1.252	1.00
95_R	314_F	1.248	1.00
57_T	93_T	1.246	1.00
9_F	327_V	1.239	1.00
13_L	175_E	1.236	1.00
261_M	271_F	1.232	1.00
298_G	303_D	1.232	1.00
12_L	176_A	1.226	1.00
255_Q	302_T	1.226	1.00
231_T	256_V	1.224	1.00
48_I	105_Q	1.223	1.00
143_L	323_T	1.218	1.00
153_A	157_M	1.216	1.00
322_H	325_K	1.213	1.00
277_A	306_F	1.205	1.00
216_T	222_G	1.192	1.00
21_N	180_T	1.188	1.00
91_K	120_Y	1.183	1.00
57_T	87_K	1.180	1.00
157_M	228_F	1.168	1.00
185_R	214_T	1.157	1.00
34_K	69_D	1.150	1.00
68_Y	74_V	1.148	1.00
297_G	307_E	1.145	1.00
177_A	182_L	1.141	1.00
57_T	83_Q	1.138	1.00
8_H	118_A	1.127	1.00
139_L	327_V	1.120	1.00
104_I	123_V	1.118	1.00
245_A	249_A	1.118	1.00
223_V	260_M	1.113	1.00
66_A	328_M	1.102	1.00
261_M	310_A	1.096	1.00
149_L	227_D	1.094	1.00
21_N	25_Q	1.084	1.00
256_V	271_F	1.083	1.00
199_V	215_L	1.082	1.00
104_I	117_L	1.079	1.00
11_K	14_D	1.069	1.00
28_A	147_E	1.068	1.00
67_A	74_V	1.065	1.00
308_S	311_S	1.056	1.00
149_L	270_K	1.052	1.00
31_K	319_N	1.050	1.00
96_V	317_A	1.045	1.00
9_F	15_F	1.045	1.00
318_E	322_H	1.044	1.00
174_L	186_L	1.041	1.00
112_E	116_T	1.024	1.00
55_D	85_G	1.024	1.00
187_V	216_T	1.023	1.00
103_G	332_L	1.017	1.00
24_L	28_A	1.016	1.00
159_L	177_A	0.998	1.00
95_R	120_Y	0.990	1.00
138_L	173_M	0.990	1.00
138_L	169_M	0.988	1.00
20_L	180_T	0.977	1.00
142_L	180_T	0.967	1.00
250_L	253_E	0.965	1.00
69_D	321_M	0.960	1.00
24_L	323_T	0.958	1.00
159_L	173_M	0.956	1.00
64_E	76_Y	0.953	1.00
306_F	313_V	0.949	1.00
61_C	77_L	0.940	0.99
103_G	126_W	0.936	0.99
48_I	72_A	0.936	0.99
126_W	327_V	0.936	0.99
31_K	143_L	0.936	0.99
165_A	188_A	0.934	0.99
32_A	36_S	0.931	0.99
98_G	123_V	0.931	0.99
147_E	319_N	0.930	0.99
20_L	179_L	0.930	0.99
221_K	224_E	0.928	0.99
11_K	175_E	0.921	0.99
114_V	130_T	0.921	0.99
111_Q	115_E	0.921	0.99
83_Q	93_T	0.914	0.99
171_N	198_L	0.913	0.99
41_A	71_G	0.903	0.99
153_A	156_E	0.901	0.99
91_K	95_R	0.901	0.99
194_P	215_L	0.900	0.99
149_L	312_I	0.899	0.99
108_G	130_T	0.897	0.99
217_E	254_Y	0.896	0.99
91_K	307_E	0.893	0.99
297_G	306_F	0.889	0.99
47_N	73_R	0.889	0.99
8_H	98_G	0.886	0.99
246_E	249_A	0.886	0.99
145_M	157_M	0.882	0.99
106_Y	117_L	0.874	0.99
187_V	226_A	0.873	0.99
154_F	180_T	0.873	0.99
12_L	138_L	0.872	0.99
133_F	172_S	0.872	0.99
245_A	248_I	0.871	0.99
259_K	263_L	0.868	0.99
64_E	68_Y	0.865	0.99
25_Q	29_K	0.861	0.99
47_N	69_D	0.859	0.99
67_A	328_M	0.858	0.99
185_R	226_A	0.858	0.99
143_L	147_E	0.857	0.99
315_D	318_E	0.857	0.99
83_Q	86_H	0.854	0.99
8_H	121_A	0.851	0.99
132_E	195_E	0.848	0.99
64_E	74_V	0.842	0.99
258_S	308_S	0.839	0.99
158_T	225_G	0.839	0.99
220_A	224_E	0.838	0.99
139_L	323_T	0.836	0.99
33_D	40_E	0.835	0.99
33_D	36_S	0.831	0.99
63_F	136_T	0.827	0.99
165_A	170_G	0.823	0.99
297_G	303_D	0.820	0.99
303_D	307_E	0.817	0.99
29_K	32_A	0.816	0.99
53_E	84_I	0.814	0.99
46_K	102_D	0.813	0.98
261_M	305_V	0.812	0.98
162_A	229_I	0.812	0.98
185_R	225_G	0.812	0.98
187_V	219_V	0.808	0.98
83_Q	87_K	0.808	0.98
28_A	32_A	0.807	0.98
305_V	308_S	0.806	0.98
214_T	221_K	0.804	0.98
91_K	303_D	0.803	0.98
6_H	331_T	0.796	0.98
174_L	184_L	0.795	0.98
145_M	154_F	0.792	0.98
145_M	149_L	0.790	0.98
261_M	264_T	0.789	0.98
106_Y	113_I	0.784	0.98
47_N	65_V	0.773	0.98
144_T	312_I	0.773	0.98
22_S	26_L	0.767	0.98
162_A	260_M	0.767	0.98
20_L	176_A	0.764	0.98
10_L	118_A	0.759	0.98
116_T	120_Y	0.756	0.98
23_L	323_T	0.756	0.98
95_R	98_G	0.752	0.97
12_L	20_L	0.750	0.97
49_A	104_I	0.749	0.97
222_G	226_A	0.748	0.97
115_E	118_A	0.748	0.97
220_A	259_K	0.747	0.97
248_I	299_M	0.744	0.97
62_S	324_I	0.742	0.97
108_G	113_I	0.742	0.97
15_F	23_L	0.741	0.97
149_L	228_F	0.738	0.97
257_N	260_M	0.735	0.97
303_D	306_F	0.734	0.97
43_L	103_G	0.733	0.97
27_A	326_A	0.733	0.97
144_T	319_N	0.732	0.97
326_A	330_A	0.729	0.97
312_I	315_D	0.726	0.97
174_L	194_P	0.725	0.97
256_V	301_V	0.724	0.97
33_D	39_E	0.723	0.97
170_G	186_L	0.722	0.97
62_S	100_M	0.720	0.97
27_A	323_T	0.713	0.97
94_A	121_A	0.713	0.97
87_K	93_T	0.712	0.97
158_T	226_A	0.711	0.96
199_V	213_I	0.706	0.96
7_K	330_A	0.706	0.96
101_Y	123_V	0.706	0.96
150_P	154_F	0.706	0.96
173_M	177_A	0.705	0.96
110_G	131_N	0.701	0.96
145_M	177_A	0.700	0.96
261_M	301_V	0.699	0.96
26_L	30_L	0.699	0.96
150_P	156_E	0.698	0.96
116_T	119_E	0.696	0.96
162_A	219_V	0.694	0.96
145_M	270_K	0.692	0.96
66_A	324_I	0.691	0.96
229_I	269_V	0.689	0.96
23_L	326_A	0.684	0.96
223_V	263_L	0.680	0.95
258_S	302_T	0.680	0.95
50_L	67_A	0.679	0.95
112_E	115_E	0.676	0.95
235_V	243_K	0.675	0.95
18_A	21_N	0.674	0.95
9_F	331_T	0.673	0.95
50_L	74_V	0.670	0.95
82_S	87_K	0.670	0.95
90_I	113_I	0.669	0.95
260_M	263_L	0.668	0.95
252_R	255_Q	0.667	0.95
148_H	270_K	0.665	0.95
57_T	86_H	0.665	0.95
43_L	72_A	0.665	0.95
41_A	45_G	0.662	0.95
193_W	215_L	0.661	0.95
6_H	330_A	0.660	0.95
159_L	230_Y	0.657	0.95
50_L	76_Y	0.656	0.95
298_G	304_E	0.653	0.94
17_P	209_N	0.652	0.94
193_W	196_A	0.650	0.94
271_F	305_V	0.648	0.94
12_L	15_F	0.647	0.94
48_I	328_M	0.647	0.94
219_V	223_V	0.646	0.94
138_L	316_Q	0.644	0.94
142_L	146_Q	0.643	0.94
308_S	313_V	0.641	0.94
233_V	237_M	0.640	0.94
20_L	139_L	0.639	0.94
98_G	121_A	0.635	0.94
249_A	252_R	0.634	0.93
243_K	248_I	0.633	0.93
82_S	86_H	0.631	0.93
30_L	39_E	0.631	0.93
229_I	261_M	0.630	0.93
230_Y	233_V	0.630	0.93
262_Q	310_A	0.630	0.93
277_A	301_V	0.628	0.93
145_M	159_L	0.627	0.93
47_N	68_Y	0.626	0.93
57_T	82_S	0.624	0.93
63_F	324_I	0.624	0.93
30_L	33_D	0.619	0.93
65_V	75_T	0.617	0.93
62_S	136_T	0.617	0.93
103_G	331_T	0.615	0.92
162_A	231_T	0.613	0.92
89_S	307_E	0.612	0.92
23_L	327_V	0.605	0.92
230_Y	272_L	0.603	0.92
55_D	83_Q	0.601	0.92
160_V	222_G	0.600	0.91
126_W	331_T	0.597	0.91
194_P	199_V	0.596	0.91
69_D	102_D	0.596	0.91
129_L	168_N	0.595	0.91
233_V	278_F	0.595	0.91
93_T	97_L	0.594	0.91
18_A	22_S	0.594	0.91
251_L	302_T	0.592	0.91
55_D	81_G	0.589	0.91
176_A	180_T	0.589	0.91
175_E	198_L	0.588	0.91
328_M	332_L	0.587	0.91
126_W	328_M	0.587	0.91
54_K	238_G	0.587	0.91
12_L	133_F	0.584	0.90
160_V	216_T	0.584	0.90
142_L	154_F	0.584	0.90
55_D	87_K	0.584	0.90
241_K	246_E	0.583	0.90
112_E	130_T	0.583	0.90
258_S	310_A	0.581	0.90
188_A	194_P	0.581	0.90
306_F	311_S	0.581	0.90
138_L	142_L	0.580	0.90
30_L	42_K	0.579	0.90
146_Q	153_A	0.576	0.90
178_A	184_L	0.576	0.90
24_L	27_A	0.574	0.90
10_L	115_E	0.570	0.89
147_E	315_D	0.569	0.89
112_E	132_E	0.568	0.89
104_I	121_A	0.567	0.89
65_V	321_M	0.567	0.89
160_V	229_I	0.566	0.89
34_K	39_E	0.565	0.89
239_E	242_E	0.564	0.89
228_F	272_L	0.563	0.89
197_A	200_T	0.561	0.89
94_A	104_I	0.559	0.88
43_L	328_M	0.557	0.88
63_F	105_Q	0.557	0.88
14_D	179_L	0.556	0.88
133_F	198_L	0.556	0.88
9_F	20_L	0.556	0.88
169_M	230_Y	0.552	0.88
65_V	69_D	0.550	0.88
157_M	227_D	0.549	0.87
150_P	270_K	0.548	0.87
31_K	322_H	0.545	0.87
63_F	128_G	0.544	0.87
188_A	217_E	0.542	0.87
306_F	314_F	0.542	0.87
166_R	192_C	0.541	0.87
62_S	96_V	0.541	0.87
39_E	42_K	0.541	0.87
54_K	237_M	0.541	0.87
25_Q	28_A	0.540	0.87
242_E	247_R	0.540	0.87
96_V	99_R	0.540	0.87
8_H	122_S	0.540	0.87
247_R	251_L	0.539	0.87
19_E	22_S	0.538	0.86
178_A	211_G	0.537	0.86
178_A	209_N	0.535	0.86
105_Q	126_W	0.534	0.86
53_E	108_G	0.534	0.86
191_A	250_L	0.534	0.86
55_D	82_S	0.533	0.86
169_M	173_M	0.532	0.86
308_S	312_I	0.532	0.86
22_S	25_Q	0.532	0.86
149_L	153_A	0.531	0.86
54_K	109_Y	0.529	0.86
186_L	213_I	0.527	0.85
36_S	40_E	0.526	0.85
256_V	261_M	0.524	0.85
19_E	330_A	0.524	0.85
40_E	45_G	0.523	0.85
271_F	311_S	0.522	0.85
129_L	237_M	0.521	0.85
243_K	278_F	0.520	0.85
223_V	264_T	0.519	0.84
13_L	133_F	0.519	0.84
109_Y	113_I	0.518	0.84
187_V	223_V	0.517	0.84
60_R	76_Y	0.517	0.84
94_A	125_V	0.516	0.84
77_L	82_S	0.516	0.84
50_L	105_Q	0.513	0.84
216_T	219_V	0.513	0.84
191_A	249_A	0.510	0.83
88_E	92_D	0.509	0.83
90_I	106_Y	0.508	0.83
176_A	182_L	0.507	0.83
154_F	182_L	0.507	0.83
96_V	314_F	0.506	0.83
55_D	76_Y	0.505	0.83
11_K	115_E	0.504	0.83
178_A	213_I	0.504	0.83
146_Q	149_L	0.503	0.83
275_L	314_F	0.502	0.82
228_F	312_I	0.501	0.82
39_E	44_T	0.500	0.82

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
4h31A	3	0.991	100	0.053	Contact Map
1duvG	3	0.994	100	0.054	Contact Map
2w37A	5	0.985	100	0.058	Contact Map
1pvvA	6	0.9311	100	0.063	Contact Map
1dxhA	6	0.988	100	0.065	Contact Map
4nf2A	3	0.9162	100	0.067	Contact Map
2i6uA	3	0.9162	100	0.069	Contact Map
3gd5A	4	0.8533	100	0.069	Contact Map
4amuA	6	0.988	100	0.07	Contact Map
1vlvA	6	0.9012	100	0.075	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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