FMT - ECOLI - GREMLIN Contacts

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FMT - Methionyl-tRNA formyltransferase

UniProt:	P23882	Sequences: MSESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPAGRGKKLMPSPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCINVHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTGDMLYKLSCPITAEDTSGTLYDKLAELGPQGLITTLKQLADGTAKPEVQDETLVTYAEKLSKEEARIDWSLSAAQLERCIRAFNPWPMSWLEIEGQPVKVWKASVIDTATNAAPGTILEANKQGIQVATGDGILNLLSLQPAGKKAMSAQDLLNSRREWFVPGNRLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11268
Length:	315 (301)
Sequences:	5535 (4016)
Seq/√Len:	231.5

ECOLI - FMT ARNA PUR3
BACSU - FMT PUR3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_E	156_S	3.891	1.00
97_K	144_V	3.561	1.00
97_K	101_E	3.392	1.00
198_D	201_L	3.236	1.00
296_S	299_D	3.060	1.00
219_L	223_Q	2.894	1.00
155_L	182_T	2.699	1.00
24_L	59_K	2.619	1.00
215_I	224_L	2.575	1.00
138_T	151_M	2.556	1.00
163_D	171_K	2.519	1.00
143_D	148_T	2.430	1.00
163_D	167_T	2.384	1.00
21_D	55_L	2.321	1.00
6_R	29_N	2.240	1.00
145_G	148_T	2.218	1.00
252_S	285_L	2.213	1.00
252_S	283_N	2.202	1.00
225_E	251_A	2.194	1.00
117_R	132_D	2.160	1.00
228_I	251_A	2.146	1.00
139_I	183_T	2.142	1.00
186_Q	191_T	2.142	1.00
250_K	286_S	2.127	1.00
286_S	294_A	2.106	1.00
219_L	227_C	2.067	1.00
32_G	81_L	2.029	1.00
21_D	25_S	2.024	1.00
55_L	59_K	2.021	1.00
250_K	285_L	2.008	1.00
118_W	130_A	1.999	1.00
118_W	132_D	1.993	1.00
274_Q	281_I	1.984	1.00
76_Q	80_E	1.970	1.00
85_V	184_L	1.933	1.00
220_S	223_Q	1.908	1.00
274_Q	283_N	1.908	1.00
125_Q	165_S	1.871	1.00
129_W	230_A	1.851	1.00
166_G	233_P	1.846	1.00
284_L	287_L	1.813	1.00
134_E	158_P	1.804	1.00
298_Q	302_N	1.788	1.00
261_A	264_T	1.779	1.00
157_C	175_L	1.765	1.00
244_Q	290_A	1.757	1.00
62_P	77_L	1.752	1.00
141_Q	194_P	1.751	1.00
199_E	202_V	1.751	1.00
150_D	196_V	1.744	1.00
299_D	302_N	1.691	1.00
19_H	110_V	1.669	1.00
157_C	171_K	1.656	1.00
249_W	294_A	1.653	1.00
8_I	83_A	1.640	1.00
217_W	239_L	1.608	1.00
55_L	58_E	1.590	1.00
160_T	163_D	1.585	1.00
155_L	178_Q	1.570	1.00
126_R	212_E	1.554	1.00
272_G	283_N	1.537	1.00
251_A	282_L	1.536	1.00
77_L	80_E	1.516	1.00
6_R	31_V	1.516	1.00
24_L	55_L	1.510	1.00
49_P	57_E	1.493	1.00
54_V	57_E	1.485	1.00
131_G	226_R	1.479	1.00
215_I	248_V	1.477	1.00
216_D	219_L	1.473	1.00
222_A	226_R	1.465	1.00
224_L	282_L	1.453	1.00
155_L	175_L	1.453	1.00
22_A	178_Q	1.446	1.00
138_T	154_K	1.438	1.00
83_A	102_M	1.438	1.00
22_A	181_I	1.426	1.00
83_A	86_M	1.425	1.00
114_L	136_G	1.422	1.00
266_L	281_I	1.419	1.00
154_K	195_E	1.406	1.00
38_D	53_K	1.404	1.00
164_T	232_N	1.403	1.00
53_K	65_Q	1.396	1.00
53_K	57_E	1.394	1.00
17_A	55_L	1.392	1.00
286_S	296_S	1.388	1.00
273_I	297_A	1.351	1.00
150_D	194_P	1.346	1.00
214_R	240_E	1.334	1.00
225_E	253_V	1.331	1.00
54_V	58_E	1.329	1.00
152_L	194_P	1.326	1.00
7_I	85_V	1.321	1.00
151_M	154_K	1.301	1.00
160_T	171_K	1.288	1.00
214_R	238_W	1.285	1.00
129_W	227_C	1.284	1.00
273_I	284_L	1.282	1.00
72_Q	76_Q	1.281	1.00
260_A	264_T	1.279	1.00
21_D	58_E	1.274	1.00
225_E	229_R	1.273	1.00
8_I	32_G	1.269	1.00
221_A	253_V	1.266	1.00
129_W	231_F	1.265	1.00
19_H	180_L	1.264	1.00
289_P	295_M	1.257	1.00
153_Y	183_T	1.254	1.00
275_V	284_L	1.254	1.00
70_R	96_P	1.244	1.00
239_L	248_V	1.243	1.00
182_T	186_Q	1.243	1.00
141_Q	152_L	1.237	1.00
153_Y	186_Q	1.231	1.00
28_H	185_K	1.219	1.00
26_S	181_I	1.219	1.00
86_M	107_C	1.208	1.00
254_I	274_Q	1.200	1.00
220_S	279_D	1.192	1.00
110_V	180_L	1.192	1.00
64_F	81_L	1.179	1.00
143_D	150_D	1.179	1.00
221_A	277_T	1.172	1.00
114_L	154_K	1.169	1.00
153_Y	179_G	1.165	1.00
12_T	50_S	1.162	1.00
24_L	30_V	1.158	1.00
94_I	146_L	1.148	1.00
135_T	159_I	1.135	1.00
41_A	44_G	1.132	1.00
186_Q	192_A	1.132	1.00
126_R	129_W	1.128	1.00
254_I	283_N	1.124	1.00
126_R	130_A	1.118	1.00
76_Q	79_A	1.111	1.00
246_V	287_L	1.106	1.00
221_A	279_D	1.096	1.00
198_D	202_V	1.090	1.00
162_E	225_E	1.088	1.00
32_G	64_F	1.087	1.00
41_A	48_M	1.086	1.00
153_Y	182_T	1.084	1.00
128_L	168_L	1.083	1.00
117_R	203_T	1.083	1.00
248_V	284_L	1.078	1.00
160_T	167_T	1.077	1.00
84_D	104_R	1.076	1.00
240_E	243_G	1.073	1.00
19_H	89_V	1.065	1.00
34_F	74_N	1.058	1.00
239_L	246_V	1.048	1.00
288_Q	294_A	1.048	1.00
49_P	54_V	1.037	1.00
9_F	19_H	1.035	1.00
121_A	207_K	1.016	1.00
139_I	153_Y	1.015	1.00
159_I	163_D	1.013	1.00
35_T	50_S	1.002	1.00
108_I	152_L	0.996	1.00
300_L	304_R	0.988	1.00
122_A	126_R	0.983	1.00
79_A	98_A	0.982	1.00
31_V	81_L	0.970	1.00
79_A	102_M	0.966	1.00
155_L	179_G	0.961	1.00
28_H	188_A	0.960	1.00
33_V	61_L	0.959	1.00
75_Q	98_A	0.959	1.00
124_I	169_Y	0.955	1.00
217_W	275_V	0.950	1.00
100_L	142_M	0.948	1.00
164_T	167_T	0.942	1.00
185_K	188_A	0.939	1.00
289_P	300_L	0.939	1.00
39_R	67_V	0.931	1.00
161_A	222_A	0.927	1.00
269_N	272_G	0.923	1.00
240_E	245_P	0.922	1.00
209_S	212_E	0.919	1.00
152_L	187_L	0.917	1.00
264_T	276_A	0.915	1.00
103_P	107_C	0.910	1.00
110_V	139_I	0.901	0.99
254_I	281_I	0.899	0.99
64_F	77_L	0.899	0.99
152_L	192_A	0.897	0.99
211_E	214_R	0.895	0.99
226_R	229_R	0.891	0.99
23_L	184_L	0.886	0.99
162_E	250_K	0.879	0.99
107_C	142_M	0.878	0.99
292_K	295_M	0.874	0.99
36_Q	39_R	0.872	0.99
228_I	237_S	0.872	0.99
223_Q	226_R	0.871	0.99
260_A	276_A	0.869	0.99
21_D	59_K	0.869	0.99
232_N	249_W	0.868	0.99
167_T	171_K	0.868	0.99
10_A	34_F	0.865	0.99
133_A	158_P	0.864	0.99
162_E	252_S	0.862	0.99
225_E	282_L	0.861	0.99
69_L	74_N	0.858	0.99
224_L	277_T	0.857	0.99
75_Q	99_V	0.857	0.99
110_V	137_V	0.857	0.99
227_C	231_F	0.855	0.99
74_N	77_L	0.853	0.99
117_R	201_L	0.853	0.99
18_R	173_A	0.848	0.99
10_A	86_M	0.847	0.99
122_A	205_A	0.845	0.99
246_V	289_P	0.843	0.99
5_L	188_A	0.841	0.99
287_L	300_L	0.837	0.99
187_L	192_A	0.830	0.99
218_S	278_G	0.825	0.99
174_E	178_Q	0.825	0.99
44_G	48_M	0.823	0.99
248_V	251_A	0.822	0.99
222_A	225_E	0.821	0.99
26_S	185_K	0.811	0.99
276_A	281_I	0.810	0.99
18_R	21_D	0.809	0.99
161_A	225_E	0.809	0.99
297_A	301_L	0.807	0.99
108_I	139_I	0.806	0.99
126_R	205_A	0.805	0.99
22_A	25_S	0.803	0.99
22_A	26_S	0.803	0.99
163_D	168_L	0.803	0.99
238_W	245_P	0.802	0.99
245_P	290_A	0.790	0.99
13_P	90_A	0.790	0.99
112_G	124_I	0.786	0.99
6_R	82_Q	0.786	0.99
15_F	112_G	0.783	0.99
179_G	183_T	0.780	0.99
262_P	276_A	0.779	0.99
268_A	273_I	0.768	0.98
127_S	159_I	0.767	0.98
38_D	65_Q	0.764	0.98
32_G	77_L	0.762	0.98
25_S	59_K	0.762	0.98
213_A	238_W	0.756	0.98
223_Q	227_C	0.755	0.98
269_N	274_Q	0.753	0.98
175_L	179_G	0.750	0.98
25_S	55_L	0.749	0.98
72_Q	75_Q	0.749	0.98
289_P	292_K	0.748	0.98
34_F	64_F	0.748	0.98
247_K	288_Q	0.748	0.98
69_L	75_Q	0.746	0.98
186_Q	189_D	0.745	0.98
50_S	65_Q	0.738	0.98
85_V	106_G	0.737	0.98
71_P	74_N	0.735	0.98
41_A	46_K	0.734	0.98
244_Q	289_P	0.728	0.98
89_V	139_I	0.728	0.98
126_R	206_E	0.723	0.98
68_S	71_P	0.723	0.98
185_K	189_D	0.722	0.98
86_M	103_P	0.718	0.97
69_L	93_L	0.716	0.97
267_E	274_Q	0.712	0.97
128_L	230_A	0.709	0.97
271_Q	298_Q	0.707	0.97
64_F	74_N	0.706	0.97
24_L	61_L	0.705	0.97
72_Q	98_A	0.704	0.97
135_T	168_L	0.702	0.97
112_G	172_L	0.702	0.97
7_I	28_H	0.701	0.97
73_E	76_Q	0.700	0.97
249_W	288_Q	0.699	0.97
85_V	108_I	0.698	0.97
222_A	279_D	0.697	0.97
258_T	276_A	0.697	0.97
213_A	234_W	0.696	0.97
101_E	144_V	0.694	0.97
258_T	281_I	0.693	0.97
295_M	299_D	0.693	0.97
125_Q	234_W	0.687	0.97
241_I	246_V	0.686	0.97
170_D	174_E	0.684	0.97
108_I	180_L	0.684	0.97
88_V	142_M	0.681	0.97
110_V	176_G	0.680	0.96
139_I	179_G	0.680	0.96
157_C	163_D	0.680	0.96
213_A	236_M	0.677	0.96
78_V	99_V	0.676	0.96
22_A	177_P	0.674	0.96
23_L	30_V	0.671	0.96
8_I	34_F	0.669	0.96
166_G	170_D	0.666	0.96
16_A	19_H	0.665	0.96
83_A	103_P	0.660	0.96
48_M	54_V	0.660	0.96
265_I	275_V	0.659	0.96
130_A	206_E	0.655	0.96
138_T	152_L	0.652	0.96
8_I	78_V	0.650	0.95
255_D	280_G	0.650	0.95
128_L	159_I	0.649	0.95
9_F	20_L	0.649	0.95
8_I	86_M	0.649	0.95
133_A	161_A	0.647	0.95
19_H	22_A	0.647	0.95
19_H	177_P	0.647	0.95
40_P	45_K	0.646	0.95
178_Q	182_T	0.646	0.95
125_Q	230_A	0.645	0.95
100_L	107_C	0.640	0.95
13_P	16_A	0.639	0.95
75_Q	79_A	0.639	0.95
236_M	249_W	0.638	0.95
221_A	280_G	0.636	0.95
164_T	250_K	0.634	0.95
213_A	231_F	0.632	0.95
82_Q	104_R	0.632	0.95
151_M	195_E	0.630	0.95
77_L	81_L	0.630	0.95
141_Q	150_D	0.627	0.94
124_I	165_S	0.626	0.94
66_P	91_Y	0.626	0.94
145_G	199_E	0.626	0.94
222_A	253_V	0.626	0.94
68_S	93_L	0.624	0.94
15_F	124_I	0.623	0.94
137_V	175_L	0.618	0.94
105_L	188_A	0.618	0.94
175_L	178_Q	0.614	0.94
79_A	82_Q	0.614	0.94
20_L	33_V	0.613	0.94
273_I	287_L	0.613	0.94
112_G	127_S	0.612	0.94
68_S	74_N	0.612	0.94
108_I	194_P	0.610	0.94
262_P	277_T	0.609	0.94
277_T	281_I	0.609	0.94
165_S	169_Y	0.607	0.94
106_G	141_Q	0.605	0.93
114_L	156_S	0.605	0.93
89_V	176_G	0.603	0.93
112_G	125_Q	0.600	0.93
287_L	297_A	0.596	0.93
15_F	176_G	0.593	0.93
27_G	185_K	0.590	0.93
289_P	304_R	0.590	0.93
78_V	86_M	0.590	0.93
260_A	281_I	0.588	0.92
5_L	28_H	0.586	0.92
273_I	283_N	0.585	0.92
126_R	207_K	0.583	0.92
266_L	276_A	0.582	0.92
232_N	236_M	0.582	0.92
217_W	224_L	0.581	0.92
36_Q	93_L	0.581	0.92
24_L	27_G	0.580	0.92
98_A	101_E	0.577	0.92
117_R	202_V	0.577	0.92
165_S	208_L	0.575	0.92
127_S	132_D	0.571	0.91
171_K	175_L	0.570	0.91
133_A	222_A	0.569	0.91
93_L	96_P	0.569	0.91
18_R	174_E	0.569	0.91
228_I	248_V	0.568	0.91
33_V	56_A	0.568	0.91
8_I	81_L	0.567	0.91
283_N	297_A	0.567	0.91
69_L	99_V	0.566	0.91
210_K	213_A	0.566	0.91
126_R	230_A	0.566	0.91
232_N	294_A	0.564	0.91
196_V	199_E	0.562	0.91
220_S	278_G	0.562	0.91
127_S	135_T	0.562	0.91
177_P	181_I	0.561	0.91
35_T	65_Q	0.557	0.90
167_T	225_E	0.556	0.90
112_G	169_Y	0.556	0.90
35_T	52_V	0.554	0.90
208_L	234_W	0.552	0.90
49_P	53_K	0.550	0.90
19_H	173_A	0.549	0.90
95_L	107_C	0.548	0.90
67_V	71_P	0.547	0.89
43_R	47_L	0.546	0.89
293_K	299_D	0.546	0.89
225_E	228_I	0.544	0.89
86_M	102_M	0.543	0.89
15_F	89_V	0.542	0.89
44_G	47_L	0.542	0.89
124_I	172_L	0.541	0.89
5_L	29_N	0.537	0.89
138_T	143_D	0.536	0.88
108_I	183_T	0.536	0.88
92_G	140_M	0.535	0.88
68_S	75_Q	0.535	0.88
157_C	172_L	0.535	0.88
268_A	301_L	0.533	0.88
112_G	154_K	0.532	0.88
144_V	148_T	0.531	0.88
16_A	112_G	0.531	0.88
208_L	212_E	0.530	0.88
113_S	123_P	0.529	0.88
34_F	69_L	0.529	0.88
34_F	78_V	0.529	0.88
215_I	227_C	0.529	0.88
15_F	110_V	0.528	0.88
30_V	61_L	0.528	0.88
125_Q	208_L	0.527	0.88
118_W	205_A	0.527	0.88
109_N	140_M	0.526	0.88
139_I	180_L	0.526	0.88
161_A	253_V	0.525	0.87
157_C	160_T	0.524	0.87
167_T	250_K	0.523	0.87
182_T	185_K	0.522	0.87
40_P	47_L	0.522	0.87
166_G	232_N	0.521	0.87
16_A	89_V	0.521	0.87
34_F	91_Y	0.520	0.87
112_G	165_S	0.518	0.87
85_V	187_L	0.517	0.87
237_S	251_A	0.516	0.87
257_A	279_D	0.515	0.86
139_I	176_G	0.515	0.86
272_G	297_A	0.514	0.86
34_F	77_L	0.512	0.86
253_V	282_L	0.512	0.86
256_T	260_A	0.511	0.86
33_V	52_V	0.510	0.86
251_A	285_L	0.510	0.86
165_S	230_A	0.509	0.86
213_A	232_N	0.505	0.85
241_I	305_R	0.505	0.85
131_G	222_A	0.504	0.85
295_M	301_L	0.503	0.85
85_V	141_Q	0.503	0.85
8_I	31_V	0.503	0.85
232_N	250_K	0.501	0.85
5_L	84_D	0.501	0.85
292_K	303_S	0.500	0.85
143_D	146_L	0.500	0.85
125_Q	169_Y	0.500	0.85

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
3q0iA	1	0.9524	100	0.088	Contact Map
1fmtA	1	0.9714	100	0.09	Contact Map
3tqqA	1	0.9556	100	0.093	Contact Map
4iqfA	1	0.9905	100	0.1	Contact Map
2blnA	1	0.9429	100	0.135	Contact Map
4wkgA	5	0.9524	100	0.15	Contact Map
2bw0A	1	0.9238	100	0.151	Contact Map
4lxqA	2	0.8571	100	0.278	Contact Map
4xczA	2	0.9302	100	0.312	Contact Map
1zghA	1	0.7048	100	0.354	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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