YRFG - ECOLI - GREMLIN Contacts

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YRFG - GMP/IMP nucleotidase YrfG

UniProt:	P64636	Sequences: MHINIAWQDVDTVLLDMDGTLLDLAFDNYFWQKLVPETWGAKNGVTPQEAMEYMRQQYHDVQHTLNWYCLDYWSEQLGLDICAMTTEMGPRAVLREDTIPFLEALKASGKQRILLTNAHPHNLAVKLEHTGLDAHLDLLLSTHTFGYPKEDQRLWHAVAEATGLKAERTLFIDDSEAILDAAAQFGIRYCLGVTNPDSGIAEKQYQRHPSLNDYRRLIPSLM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12928
Length:	222 (205)
Sequences:	29895 (24547)
Seq/√Len:	1714.5

ECOLI - YRFG GPH YNIC YIGB YIEH YFBT YJJG PGMB YQAB YIHX
BACSU - PPAX YHCW YSAA YFNB PGMB
HALSA - Q9HQE2 Q9HP74 Q9HSS2 Q9HMC4
SULSO - Q7LXL6 Q97ZU6 Q7LX46 Q97WT6 Q97X58 Q97YZ1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_D	168_R	4.067	1.00
128_E	133_D	2.995	1.00
147_Y	151_D	2.872	1.00
157_A	161_A	2.777	1.00
120_P	124_A	2.687	1.00
182_A	189_Y	2.536	1.00
103_E	135_H	2.476	1.00
12_T	164_L	2.461	1.00
99_I	103_E	2.408	1.00
113_I	138_L	2.397	1.00
111_Q	137_D	2.315	1.00
10_V	188_R	2.240	1.00
138_L	161_A	2.233	1.00
157_A	160_E	2.213	1.00
15_L	112_R	2.209	1.00
115_L	154_L	2.190	1.00
120_P	144_T	2.142	1.00
159_A	169_T	2.088	1.00
147_Y	153_R	2.084	1.00
183_A	208_H	2.036	1.00
179_L	189_Y	1.975	1.00
212_N	216_R	1.942	1.00
165_K	168_R	1.915	1.00
180_D	184_Q	1.910	1.00
13_V	110_K	1.889	1.00
106_K	135_H	1.805	1.00
116_T	123_L	1.787	1.00
159_A	187_I	1.775	1.00
104_A	108_S	1.774	1.00
188_R	208_H	1.762	1.00
171_F	182_A	1.745	1.00
170_L	190_C	1.691	1.00
106_K	137_D	1.663	1.00
14_L	158_V	1.651	1.00
98_T	214_Y	1.650	1.00
124_A	133_D	1.613	1.00
14_L	171_F	1.605	1.00
173_D	178_I	1.598	1.00
112_R	136_L	1.579	1.00
176_E	180_D	1.552	1.00
12_T	162_T	1.549	1.00
159_A	166_A	1.544	1.00
193_V	212_N	1.528	1.00
14_L	115_L	1.489	1.00
10_V	170_L	1.465	1.00
113_I	162_T	1.463	1.00
28_N	31_W	1.463	1.00
164_L	169_T	1.456	1.00
17_M	114_L	1.441	1.00
46_T	49_E	1.394	1.00
83_A	87_E	1.392	1.00
152_Q	156_H	1.384	1.00
101_F	214_Y	1.361	1.00
13_V	172_I	1.343	1.00
190_C	211_L	1.342	1.00
193_V	210_S	1.330	1.00
13_V	105_L	1.321	1.00
27_D	31_W	1.320	1.00
17_M	22_L	1.301	1.00
177_A	180_D	1.285	1.00
140_L	161_A	1.278	1.00
190_C	209_P	1.278	1.00
95_R	194_T	1.274	1.00
20_T	172_I	1.267	1.00
104_A	107_A	1.264	1.00
124_A	128_E	1.256	1.00
12_T	169_T	1.242	1.00
57_Q	61_V	1.239	1.00
213_D	216_R	1.219	1.00
17_M	123_L	1.214	1.00
73_W	76_Q	1.211	1.00
21_L	98_T	1.203	1.00
27_D	32_Q	1.203	1.00
30_F	33_K	1.181	1.00
14_L	169_T	1.177	1.00
140_L	158_V	1.173	1.00
12_T	111_Q	1.164	1.00
106_K	112_R	1.163	1.00
153_R	157_A	1.153	1.00
155_W	171_F	1.148	1.00
114_L	136_L	1.145	1.00
123_L	141_S	1.136	1.00
12_T	113_I	1.130	1.00
97_D	100_P	1.130	1.00
155_W	181_A	1.099	1.00
76_Q	80_D	1.098	1.00
28_N	32_Q	1.085	1.00
125_V	129_H	1.085	1.00
100_P	215_R	1.083	1.00
169_T	187_I	1.072	1.00
155_W	187_I	1.066	1.00
94_L	132_L	1.056	1.00
156_H	160_E	1.055	1.00
145_F	157_A	1.046	1.00
158_V	162_T	1.046	1.00
131_G	134_A	1.043	1.00
75_E	79_L	1.042	1.00
181_A	185_F	1.039	1.00
77_L	81_I	1.032	1.00
35_V	39_W	1.025	1.00
17_M	118_A	1.018	1.00
156_H	185_F	1.018	1.00
153_R	156_H	1.018	1.00
120_P	141_S	1.014	1.00
82_C	86_T	1.002	1.00
51_M	55_R	1.002	1.00
103_E	107_A	0.984	1.00
183_A	189_Y	0.982	1.00
99_I	135_H	0.980	1.00
125_V	128_E	0.977	1.00
115_L	158_V	0.973	1.00
56_Q	60_D	0.970	1.00
74_S	78_G	0.968	1.00
83_A	86_T	0.967	1.00
27_D	30_F	0.966	1.00
171_F	187_I	0.966	1.00
94_L	99_I	0.962	1.00
97_D	215_R	0.960	1.00
138_L	162_T	0.959	1.00
188_R	209_P	0.950	1.00
14_L	187_I	0.950	1.00
62_Q	66_N	0.948	1.00
58_Y	61_V	0.934	1.00
102_L	136_L	0.931	1.00
100_P	103_E	0.931	1.00
116_T	141_S	0.929	1.00
29_Y	33_K	0.928	1.00
31_W	34_L	0.926	1.00
55_R	61_V	0.924	1.00
30_F	34_L	0.922	1.00
97_D	213_D	0.914	1.00
140_L	157_A	0.910	1.00
69_C	72_Y	0.901	1.00
38_T	80_D	0.891	1.00
155_W	173_D	0.890	1.00
55_R	59_H	0.886	1.00
56_Q	61_V	0.881	1.00
18_D	24_L	0.877	1.00
179_L	207_R	0.877	1.00
18_D	116_T	0.876	1.00
120_P	143_H	0.875	1.00
189_Y	208_H	0.874	1.00
113_I	158_V	0.869	1.00
172_I	190_C	0.857	1.00
18_D	118_A	0.857	1.00
63_H	66_N	0.851	1.00
183_A	206_Q	0.850	1.00
14_L	162_T	0.849	1.00
103_E	134_A	0.843	1.00
146_G	153_R	0.843	1.00
95_R	192_G	0.838	1.00
34_L	37_E	0.837	1.00
105_L	110_K	0.835	1.00
87_E	90_P	0.833	1.00
17_M	126_K	0.832	1.00
112_R	135_H	0.831	1.00
156_H	166_A	0.831	1.00
105_L	112_R	0.824	1.00
36_P	40_G	0.818	1.00
95_R	98_T	0.817	1.00
200_I	204_Q	0.817	1.00
80_D	83_A	0.803	1.00
164_L	168_R	0.797	1.00
34_L	38_T	0.794	1.00
22_L	130_T	0.793	1.00
118_A	123_L	0.792	1.00
166_A	187_I	0.788	1.00
11_D	110_K	0.787	1.00
22_L	126_K	0.786	1.00
211_L	217_L	0.783	1.00
33_K	37_E	0.782	1.00
84_M	88_M	0.780	1.00
57_Q	60_D	0.774	1.00
45_V	49_E	0.771	1.00
31_W	35_V	0.767	1.00
170_L	188_R	0.766	1.00
66_N	69_C	0.760	1.00
99_I	131_G	0.759	1.00
123_L	126_K	0.756	1.00
117_N	148_P	0.755	1.00
141_S	144_T	0.755	1.00
152_Q	184_Q	0.753	1.00
100_P	104_A	0.750	1.00
180_D	183_A	0.744	1.00
53_Y	56_Q	0.738	1.00
38_T	41_A	0.734	1.00
191_L	210_S	0.732	1.00
155_W	178_I	0.732	1.00
127_L	133_D	0.729	1.00
76_Q	79_L	0.728	1.00
13_V	170_L	0.722	1.00
78_G	81_I	0.719	1.00
190_C	217_L	0.717	1.00
84_M	87_E	0.716	1.00
79_L	83_A	0.713	1.00
10_V	110_K	0.710	1.00
179_L	191_L	0.707	1.00
201_A	204_Q	0.705	1.00
112_R	137_D	0.705	1.00
117_N	150_E	0.704	1.00
89_G	125_V	0.703	1.00
99_I	134_A	0.702	1.00
31_W	36_P	0.700	1.00
60_D	63_H	0.698	1.00
102_L	135_H	0.697	1.00
192_G	214_Y	0.690	1.00
202_E	206_Q	0.689	1.00
11_D	111_Q	0.687	1.00
36_P	41_A	0.682	1.00
66_N	70_L	0.681	1.00
10_V	168_R	0.680	1.00
23_D	93_V	0.680	1.00
194_T	214_Y	0.679	1.00
51_M	54_M	0.663	1.00
111_Q	164_L	0.659	1.00
138_L	158_V	0.658	1.00
74_S	80_D	0.655	1.00
64_T	67_W	0.655	1.00
38_T	83_A	0.655	1.00
52_E	55_R	0.653	1.00
29_Y	32_Q	0.653	1.00
11_D	164_L	0.650	1.00
211_L	214_Y	0.649	1.00
123_L	127_L	0.647	1.00
82_C	85_T	0.647	1.00
124_A	139_L	0.646	1.00
23_D	95_R	0.644	1.00
171_F	181_A	0.643	1.00
118_A	122_N	0.643	1.00
37_E	44_G	0.642	1.00
62_Q	67_W	0.641	1.00
80_D	84_M	0.638	1.00
54_M	58_Y	0.636	1.00
98_T	102_L	0.636	1.00
94_L	130_T	0.635	1.00
172_I	217_L	0.635	1.00
14_L	113_I	0.635	1.00
175_S	178_I	0.634	1.00
40_G	43_N	0.633	1.00
144_T	161_A	0.633	1.00
75_E	78_G	0.622	1.00
159_A	164_L	0.619	1.00
15_L	101_F	0.619	1.00
202_E	205_Y	0.617	1.00
76_Q	81_I	0.616	1.00
178_I	181_A	0.615	1.00
27_D	33_K	0.615	1.00
78_G	82_C	0.615	1.00
52_E	56_Q	0.612	1.00
121_H	125_V	0.610	1.00
74_S	81_I	0.608	1.00
77_L	80_D	0.608	1.00
18_D	126_K	0.606	1.00
20_T	173_D	0.604	1.00
40_G	44_G	0.602	1.00
55_R	58_Y	0.598	1.00
50_A	54_M	0.593	1.00
103_E	106_K	0.590	1.00
142_T	154_L	0.588	1.00
154_L	158_V	0.586	1.00
145_F	154_L	0.585	1.00
26_F	93_V	0.580	1.00
123_L	139_L	0.580	1.00
115_L	171_F	0.580	1.00
156_H	159_A	0.579	1.00
119_H	122_N	0.578	1.00
97_D	101_F	0.575	1.00
166_A	169_T	0.574	1.00
18_D	174_D	0.572	1.00
67_W	70_L	0.572	1.00
171_F	178_I	0.571	1.00
106_K	109_G	0.569	1.00
81_I	85_T	0.566	1.00
159_A	185_F	0.566	1.00
101_F	172_I	0.566	1.00
10_V	13_V	0.566	1.00
36_P	39_W	0.565	1.00
98_T	101_F	0.565	1.00
64_T	68_Y	0.564	1.00
53_Y	57_Q	0.562	1.00
140_L	154_L	0.561	1.00
20_T	192_G	0.559	1.00
19_G	25_A	0.554	1.00
21_L	102_L	0.553	1.00
39_W	43_N	0.552	1.00
24_L	118_A	0.551	1.00
70_L	73_W	0.549	1.00
140_L	162_T	0.545	1.00
136_L	139_L	0.543	1.00
54_M	57_Q	0.541	1.00
176_E	191_L	0.541	1.00
101_F	104_A	0.538	1.00
122_N	126_K	0.535	1.00
117_N	142_T	0.533	1.00
118_A	178_I	0.531	1.00
63_H	67_W	0.528	1.00
118_A	141_S	0.525	1.00
22_L	92_A	0.525	1.00
64_T	69_C	0.523	1.00
118_A	173_D	0.520	1.00
154_L	181_A	0.520	1.00
96_E	215_R	0.520	1.00
138_L	141_S	0.515	1.00
89_G	129_H	0.515	1.00
191_L	202_E	0.507	1.00
13_V	112_R	0.506	1.00
180_D	206_Q	0.502	1.00
159_A	165_K	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
3d6jA	1	0.9414	100	0.324	Contact Map
4uw9A	1	0.8874	100	0.327	Contact Map
3l5kA	1	0.982	100	0.327	Contact Map
3qxgA	3	0.9595	100	0.329	Contact Map
4eekA	2	0.9505	100	0.33	Contact Map
3s6jA	2	0.955	100	0.331	Contact Map
3iruA	4	0.9865	100	0.333	Contact Map
3sd7A	1	0.9414	100	0.333	Contact Map
1swvA	2	0.9505	100	0.336	Contact Map
3mc1A	2	0.9459	100	0.337	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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