RIMK - ECOLI - GREMLIN Contacts

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RIMK - Ribosomal protein S6--L-glutamate ligase

UniProt:	P0C0U4	Sequences: MKIAILSRDGTLYSCKRLREAAIQRGHLVEILDPLSCYMNINPAASSIHYKGRKLPHFDAVIPRIGTAITFYGTAALRQFEMLGSYPLNESVAIARARDKLRSMQLLARQGIDLPVTGIAHSPDDTSDLIDMVGGAPLVVKLVEGTQGIGVVLAETRQAAESVIDAFRGLNAHILVQEYIKEAQGCDIRCLVVGDEVVAAIERRAKEGDFRSNLHRGGAASVASITPQEREIAIKAARTMALDVAGVDILRANRGPLVMEVNASPGLEGIEKTTGIDIAGKMIRWIERHATTEYCLKTGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10852
Length:	300 (269)
Sequences:	28137 (16732)
Seq/√Len:	1020.2

ECOLI - RIMK PURT PUR2 DDLB ACCC DDLA GSHB PURK CARB
BACSU - PUR2 PURT ACCC2 ACCC1 PURK DDL BACD CARB CARY PYC
HALSA - Q9HSS5 Q9HQ67 Q9HRM3 Q9HPP8 CARB
SULSO - Q7LXR0 LYSX Q97VY6 Q7LXR2 PURT PURK Q97W91 CARB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
116_V	178_E	4.048	1.00
231_E	235_K	3.366	1.00
156_T	159_A	3.205	1.00
131_D	157_R	2.973	1.00
127_S	161_E	2.923	1.00
136_A	157_R	2.712	1.00
51_K	55_L	2.604	1.00
122_S	125_D	2.511	1.00
78_R	95_A	2.455	1.00
107_L	236_A	2.353	1.00
107_L	258_V	2.342	1.00
118_G	132_M	2.304	1.00
234_I	238_R	2.248	1.00
101_L	119_I	2.160	1.00
181_K	253_N	2.079	1.00
157_R	161_E	2.056	1.00
104_M	177_Q	2.025	1.00
153_L	179_Y	2.009	1.00
78_R	82_M	1.995	1.00
284_R	289_H	1.989	1.00
105_Q	109_R	1.948	1.00
101_L	105_Q	1.923	1.00
155_E	159_A	1.897	1.00
127_S	157_R	1.858	1.00
102_R	105_Q	1.844	1.00
54_K	83_L	1.838	1.00
161_E	165_D	1.807	1.00
108_A	116_V	1.806	1.00
129_L	133_V	1.778	1.00
252_A	255_G	1.739	1.00
103_S	107_L	1.731	1.00
79_Q	83_L	1.718	1.00
105_Q	108_A	1.693	1.00
52_G	56_P	1.671	1.00
232_I	256_P	1.666	1.00
129_L	132_M	1.660	1.00
96_R	102_R	1.659	1.00
109_R	239_T	1.653	1.00
99_D	143_V	1.643	1.00
280_G	284_R	1.628	1.00
95_A	102_R	1.618	1.00
22_A	29_V	1.610	1.00
61_V	85_S	1.599	1.00
237_A	245_A	1.585	1.00
73_G	98_R	1.585	1.00
277_D	280_G	1.578	1.00
113_D	232_I	1.571	1.00
96_R	106_L	1.561	1.00
228_Q	232_I	1.544	1.00
110_Q	239_T	1.542	1.00
235_K	238_R	1.542	1.00
251_R	256_P	1.528	1.00
46_S	49_H	1.519	1.00
162_S	166_A	1.498	1.00
123_P	165_D	1.498	1.00
139_V	153_L	1.483	1.00
232_I	235_K	1.482	1.00
123_P	161_E	1.477	1.00
127_S	131_D	1.470	1.00
130_I	136_A	1.469	1.00
90_E	93_A	1.465	1.00
235_K	239_T	1.464	1.00
155_E	181_K	1.459	1.00
118_G	129_L	1.445	1.00
152_V	166_A	1.444	1.00
228_Q	231_E	1.408	1.00
123_P	127_S	1.396	1.00
192_V	197_V	1.394	1.00
178_E	257_L	1.392	1.00
112_I	258_V	1.391	1.00
128_D	132_M	1.385	1.00
164_I	168_R	1.382	1.00
186_C	202_E	1.382	1.00
92_V	96_R	1.377	1.00
79_Q	82_M	1.351	1.00
121_H	173_H	1.349	1.00
252_A	257_L	1.345	1.00
106_L	239_T	1.343	1.00
283_I	287_E	1.341	1.00
24_Q	280_G	1.337	1.00
143_V	173_H	1.337	1.00
138_L	176_V	1.332	1.00
47_S	50_Y	1.330	1.00
101_L	143_V	1.329	1.00
108_A	114_L	1.329	1.00
236_A	240_M	1.310	1.00
46_S	50_Y	1.308	1.00
106_L	109_R	1.302	1.00
139_V	179_Y	1.293	1.00
236_A	239_T	1.283	1.00
51_K	54_K	1.271	1.00
25_R	284_R	1.270	1.00
81_E	91_S	1.269	1.00
139_V	151_V	1.267	1.00
168_R	172_A	1.265	1.00
247_V	261_V	1.260	1.00
27_H	283_I	1.246	1.00
25_R	280_G	1.242	1.00
136_A	156_T	1.241	1.00
106_L	110_Q	1.234	1.00
104_M	114_L	1.231	1.00
116_V	132_M	1.221	1.00
250_L	259_M	1.209	1.00
208_G	212_S	1.208	1.00
78_R	91_S	1.198	1.00
281_K	284_R	1.184	1.00
81_E	87_P	1.181	1.00
21_A	280_G	1.175	1.00
188_I	251_R	1.169	1.00
180_I	259_M	1.166	1.00
119_I	173_H	1.164	1.00
121_H	125_D	1.163	1.00
230_R	234_I	1.162	1.00
185_G	193_V	1.160	1.00
81_E	90_E	1.159	1.00
18_L	62_I	1.157	1.00
180_I	257_L	1.145	1.00
105_Q	117_T	1.144	1.00
97_A	240_M	1.138	1.00
53_R	58_F	1.132	1.00
116_V	133_V	1.129	1.00
166_A	169_G	1.125	1.00
80_F	87_P	1.116	1.00
182_E	253_N	1.111	1.00
133_V	138_L	1.109	1.00
61_V	80_F	1.104	1.00
128_D	131_D	1.102	1.00
16_K	20_E	1.099	1.00
92_V	95_A	1.091	1.00
125_D	128_D	1.088	1.00
276_I	281_K	1.081	1.00
138_L	154_A	1.079	1.00
113_D	257_L	1.079	1.00
120_A	129_L	1.077	1.00
167_F	174_I	1.075	1.00
154_A	163_V	1.073	1.00
17_R	20_E	1.058	1.00
165_D	169_G	1.053	1.00
152_V	163_V	1.052	1.00
123_P	164_I	1.045	1.00
124_D	127_S	1.045	1.00
101_L	173_H	1.043	1.00
136_A	160_A	1.042	1.00
237_A	240_M	1.025	1.00
24_Q	279_A	1.025	1.00
130_I	138_L	1.015	1.00
80_F	85_S	1.015	1.00
16_K	45_A	1.013	1.00
21_A	24_Q	1.012	1.00
78_R	92_V	1.012	1.00
229_E	256_P	1.012	1.00
186_C	251_R	1.008	1.00
223_A	273_T	1.007	1.00
97_A	261_V	1.004	1.00
196_E	238_R	1.004	1.00
115_P	180_I	0.998	1.00
178_E	252_A	0.996	1.00
19_R	29_V	0.995	1.00
99_D	144_E	0.991	1.00
227_P	231_E	0.989	1.00
27_H	287_E	0.988	1.00
53_R	56_P	0.978	1.00
166_A	170_L	0.978	1.00
204_R	220_A	0.971	1.00
162_S	165_D	0.967	1.00
271_E	274_T	0.965	1.00
195_D	238_R	0.964	1.00
191_L	244_V	0.961	1.00
152_V	167_F	0.960	1.00
143_V	175_L	0.960	1.00
126_T	160_A	0.960	1.00
130_I	157_R	0.951	1.00
181_K	252_A	0.950	1.00
190_C	233_A	0.950	1.00
232_I	236_A	0.940	1.00
188_I	229_E	0.938	1.00
108_A	117_T	0.936	1.00
117_T	177_Q	0.934	1.00
94_I	263_A	0.928	1.00
244_V	264_S	0.928	1.00
231_E	234_I	0.918	1.00
86_Y	287_E	0.914	1.00
52_G	55_L	0.902	1.00
228_Q	255_G	0.896	1.00
168_R	174_I	0.894	1.00
20_E	24_Q	0.894	1.00
219_A	222_V	0.893	1.00
182_E	185_G	0.892	1.00
233_A	249_I	0.889	1.00
159_A	162_S	0.888	1.00
229_E	232_I	0.879	1.00
228_Q	235_K	0.874	1.00
22_A	27_H	0.870	1.00
124_D	128_D	0.870	1.00
33_D	38_Y	0.870	1.00
199_A	230_R	0.867	1.00
123_P	168_R	0.865	1.00
73_G	76_A	0.861	1.00
23_I	45_A	0.859	1.00
30_E	58_F	0.854	1.00
77_L	87_P	0.840	1.00
185_G	191_L	0.833	1.00
254_R	257_L	0.829	1.00
251_R	255_G	0.825	1.00
75_A	78_R	0.819	1.00
202_E	205_A	0.818	1.00
140_V	176_V	0.816	1.00
158_Q	161_E	0.815	1.00
123_P	126_T	0.814	1.00
83_L	86_Y	0.813	1.00
211_R	215_H	0.811	1.00
31_I	42_N	0.808	1.00
67_T	74_T	0.808	1.00
191_L	281_K	0.807	1.00
54_K	58_F	0.806	1.00
140_V	154_A	0.804	1.00
130_I	160_A	0.800	1.00
99_D	173_H	0.800	1.00
53_R	85_S	0.797	1.00
283_I	286_I	0.796	1.00
76_A	80_F	0.795	1.00
135_G	178_E	0.793	1.00
115_P	257_L	0.784	1.00
225_I	251_R	0.782	1.00
62_I	282_M	0.781	1.00
126_T	164_I	0.780	1.00
215_H	218_G	0.780	1.00
23_I	26_G	0.780	1.00
120_A	126_T	0.779	1.00
101_L	175_L	0.778	1.00
203_R	206_K	0.777	1.00
232_I	249_I	0.776	1.00
284_R	287_E	0.776	1.00
251_R	254_R	0.775	1.00
229_E	249_I	0.769	1.00
19_R	45_A	0.769	1.00
189_R	192_V	0.766	1.00
21_A	25_R	0.765	1.00
19_R	23_I	0.758	1.00
140_V	163_V	0.758	1.00
140_V	174_I	0.754	1.00
28_L	48_I	0.750	1.00
72_Y	76_A	0.747	1.00
218_G	221_S	0.746	1.00
158_Q	162_S	0.734	1.00
180_I	252_A	0.734	1.00
187_D	193_V	0.733	1.00
131_D	161_E	0.733	1.00
213_N	216_R	0.731	1.00
135_G	138_L	0.729	1.00
125_D	129_L	0.727	1.00
249_I	256_P	0.725	1.00
271_E	275_G	0.722	1.00
107_L	261_V	0.722	1.00
23_I	29_V	0.722	1.00
230_R	233_A	0.720	1.00
17_R	278_I	0.719	1.00
99_D	102_R	0.718	1.00
247_V	258_V	0.717	1.00
204_R	222_V	0.715	1.00
193_V	196_E	0.715	1.00
265_P	278_I	0.715	1.00
93_A	241_A	0.713	1.00
188_I	200_A	0.712	1.00
92_V	102_R	0.708	1.00
227_P	230_R	0.706	1.00
130_I	133_V	0.705	1.00
233_A	247_V	0.699	1.00
60_A	88_L	0.695	1.00
35_L	38_Y	0.692	1.00
102_R	106_L	0.691	1.00
45_A	49_H	0.690	1.00
278_I	282_M	0.690	1.00
78_R	81_E	0.687	1.00
197_V	234_I	0.687	1.00
167_F	171_N	0.686	1.00
97_A	263_A	0.684	1.00
133_V	178_E	0.684	1.00
163_V	167_F	0.682	1.00
72_Y	77_L	0.680	1.00
185_G	189_R	0.678	1.00
22_A	283_I	0.673	1.00
77_L	81_E	0.671	1.00
72_Y	75_A	0.667	1.00
220_A	223_A	0.664	1.00
112_I	232_I	0.663	1.00
54_K	57_H	0.659	1.00
61_V	64_R	0.656	1.00
60_A	289_H	0.648	1.00
188_I	191_L	0.647	1.00
189_R	193_V	0.646	1.00
164_I	174_I	0.645	1.00
90_E	241_A	0.644	1.00
19_R	31_I	0.643	1.00
106_L	236_A	0.643	1.00
224_S	255_G	0.641	1.00
41_I	45_A	0.641	1.00
21_A	277_D	0.639	1.00
242_L	245_A	0.638	1.00
64_R	67_T	0.638	1.00
74_T	95_A	0.637	1.00
144_E	171_N	0.637	1.00
179_Y	250_L	0.634	1.00
73_G	77_L	0.634	1.00
244_V	265_P	0.632	1.00
127_S	130_I	0.628	1.00
199_A	223_A	0.622	1.00
38_Y	41_I	0.619	1.00
108_A	118_G	0.617	1.00
199_A	203_R	0.617	1.00
106_L	240_M	0.617	1.00
101_L	117_T	0.616	1.00
216_R	219_A	0.616	1.00
105_Q	119_I	0.615	1.00
60_A	63_P	0.613	1.00
80_F	83_L	0.612	1.00
91_S	95_A	0.611	1.00
36_S	42_N	0.611	1.00
192_V	234_I	0.609	1.00
39_M	44_A	0.608	1.00
237_A	242_L	0.608	1.00
132_M	135_G	0.606	1.00
93_A	242_L	0.604	1.00
167_F	170_L	0.602	1.00
110_Q	236_A	0.600	1.00
87_P	91_S	0.598	1.00
137_P	179_Y	0.598	1.00
33_D	43_P	0.595	1.00
267_L	270_I	0.594	1.00
155_E	179_Y	0.585	1.00
279_A	283_I	0.585	1.00
194_G	288_R	0.584	1.00
144_E	173_H	0.584	1.00
28_L	47_S	0.583	1.00
140_V	164_I	0.583	1.00
225_I	228_Q	0.582	1.00
130_I	135_G	0.579	1.00
109_R	240_M	0.578	1.00
196_E	234_I	0.576	1.00
112_I	235_K	0.575	1.00
204_R	207_E	0.574	1.00
89_N	242_L	0.573	1.00
76_A	79_Q	0.572	1.00
202_E	222_V	0.569	1.00
154_A	159_A	0.568	1.00
210_F	213_N	0.567	1.00
182_E	187_D	0.565	1.00
233_A	237_A	0.565	1.00
236_A	258_V	0.565	1.00
186_C	189_R	0.564	1.00
114_L	117_T	0.564	1.00
152_V	162_S	0.560	1.00
93_A	97_A	0.558	1.00
154_A	160_A	0.555	1.00
104_M	117_T	0.554	1.00
181_K	250_L	0.552	1.00
53_R	61_V	0.552	1.00
202_E	226_T	0.552	1.00
193_V	281_K	0.550	1.00
115_P	178_E	0.550	1.00
228_Q	256_P	0.549	1.00
115_P	259_M	0.549	1.00
190_C	249_I	0.548	1.00
218_G	273_T	0.548	1.00
198_V	201_I	0.547	1.00
113_D	255_G	0.546	1.00
77_L	80_F	0.544	1.00
191_L	285_W	0.543	1.00
160_A	164_I	0.543	1.00
193_V	198_V	0.540	1.00
214_L	217_G	0.539	1.00
237_A	247_V	0.539	1.00
159_A	163_V	0.538	1.00
284_R	288_R	0.537	1.00
152_V	170_L	0.537	1.00
113_D	228_Q	0.534	1.00
188_I	230_R	0.532	1.00
25_R	283_I	0.532	1.00
127_S	165_D	0.532	1.00
215_H	219_A	0.531	1.00
193_V	285_W	0.530	1.00
16_K	19_R	0.528	1.00
107_L	110_Q	0.526	1.00
110_Q	240_M	0.525	1.00
92_V	241_A	0.524	1.00
75_A	95_A	0.523	1.00
187_D	192_V	0.523	1.00
190_C	237_A	0.519	1.00
137_P	153_L	0.517	1.00
233_A	236_A	0.517	1.00
136_A	155_E	0.517	1.00
276_I	284_R	0.516	1.00
212_S	215_H	0.514	1.00
63_P	88_L	0.514	1.00
163_V	166_A	0.512	1.00
104_M	175_L	0.510	1.00
75_A	79_Q	0.509	1.00
129_L	176_V	0.508	1.00
17_R	269_G	0.507	1.00
168_R	171_N	0.507	1.00
207_E	212_S	0.506	1.00
192_V	247_V	0.503	1.00
107_L	114_L	0.502	1.00
89_N	93_A	0.500	1.00

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
4iwxA	3	0.9667	100	0.284	Contact Map
3vpbA	3	0.9233	100	0.313	Contact Map
3vpdA	3	0.9233	100	0.319	Contact Map
1a9xA	3	0.9767	100	0.322	Contact Map
3se7A	4	0.9433	100	0.34	Contact Map
3u9tA	3	0.9533	100	0.342	Contact Map
4qshA	4	0.8	100	0.343	Contact Map
3n6rA	1	0.7767	100	0.344	Contact Map
2qf7A	4	0.8567	100	0.347	Contact Map
3hblA	4	0.98	100	0.348	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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