YYDG - BACSU - GREMLIN Contacts

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YYDG - Putative peptide biosynthesis protein YydG

UniProt:	Q45595	Sequences: MYNKTVSINLDSRCNASCDHCCFSSSPTSTTRMEKEYIRELVTEFAKNKTIQVISFTGGEVFLDYKFLKELMEIIKPYEKQITLISNGFWGLSKKKVQEYFHDMNSLNVIALTISYDEYHAPFVKSSSIKNILEHSRKYPDIDISLNMAVTKDKMSNHILEELGDSILGVKITKFPMISVGAAKTRIKQENIHKFYSLEDEDSLHCPGYDIVYHHDGEIYPCCSPAIFETKITLREEYNQSFERTVEKLNSNLLLFILRKEGFKWFLNILKENNKIEEFDIPYEFSSICGVCGSLFNSAEKINYFYPYMEKYYNENFKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	319 (267)
Sequences:	7562 (6048)
Seq/√Len:	370.1

ECOLI - ASLB YDEM MOAA
BACSU - YYDG ALBA SKFB MOAA
HALSA - Q9HQF5 MOAA
SULSO - Q97XA7 Q7LXV3 Q97XZ2 Q97XS7 Q97XS8 Q97XA6 Q97WK5 Q980E0 Q97Y04 MOAA Q97WC3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_H	124_V	4.256	1.00
16_A	89_F	3.920	1.00
118_E	124_V	3.503	1.00
39_R	74_I	3.346	1.00
121_A	124_V	3.326	1.00
15_N	87_N	2.930	1.00
102_H	139_Y	2.930	1.00
37_Y	238_Y	2.928	1.00
218_E	236_E	2.893	1.00
43_T	74_I	2.854	1.00
134_E	166_S	2.807	1.00
93_S	135_H	2.786	1.00
34_E	37_Y	2.771	1.00
40_E	44_E	2.601	1.00
64_D	67_F	2.454	1.00
69_K	103_D	2.440	1.00
218_E	233_T	2.345	1.00
43_T	78_Y	2.330	1.00
204_L	222_C	2.328	1.00
289_C	292_C	2.285	1.00
126_S	162_E	2.267	1.00
35_K	70_E	2.168	1.00
6_V	45_F	2.158	1.00
155_M	158_H	2.151	1.00
241_S	244_R	2.134	1.00
13_R	32_R	2.106	1.00
120_H	123_F	2.061	1.00
88_G	114_I	1.990	1.00
236_E	239_N	1.990	1.00
240_Q	244_R	1.940	1.00
38_I	71_L	1.937	1.00
135_H	138_K	1.921	1.00
118_E	123_F	1.863	1.00
74_I	77_P	1.833	1.00
76_K	110_I	1.827	1.00
261_E	267_L	1.747	1.00
120_H	127_S	1.713	1.00
39_R	70_E	1.711	1.00
214_H	218_E	1.706	1.00
35_K	39_R	1.682	1.00
37_Y	40_E	1.648	1.00
35_K	67_F	1.635	1.00
73_E	103_D	1.634	1.00
102_H	106_S	1.627	1.00
33_M	37_Y	1.600	1.00
73_E	77_P	1.600	1.00
103_D	107_L	1.569	1.00
44_E	241_S	1.545	1.00
67_F	70_E	1.539	1.00
93_S	138_K	1.534	1.00
74_I	78_Y	1.530	1.00
39_R	43_T	1.529	1.00
119_Y	124_V	1.523	1.00
15_N	90_W	1.520	1.00
128_S	131_N	1.517	1.00
46_A	78_Y	1.510	1.00
251_S	255_L	1.486	1.00
161_E	165_D	1.482	1.00
131_N	135_H	1.479	1.00
85_I	113_T	1.463	1.00
56_F	82_I	1.461	1.00
64_D	71_L	1.461	1.00
101_F	135_H	1.461	1.00
33_M	38_I	1.459	1.00
32_R	64_D	1.453	1.00
214_H	220_Y	1.452	1.00
134_E	138_K	1.451	1.00
163_L	166_S	1.447	1.00
105_N	139_Y	1.435	1.00
20_H	117_D	1.428	1.00
219_I	245_T	1.392	1.00
127_S	131_N	1.381	1.00
93_S	139_Y	1.375	1.00
62_F	84_L	1.360	1.00
131_N	134_E	1.359	1.00
114_I	133_L	1.340	1.00
162_E	166_S	1.335	1.00
158_H	161_E	1.308	1.00
118_E	121_A	1.301	1.00
103_D	106_S	1.281	1.00
8_I	38_I	1.276	1.00
261_E	264_K	1.273	1.00
76_K	107_L	1.258	1.00
70_E	73_E	1.256	1.00
134_E	137_R	1.253	1.00
243_E	247_E	1.253	1.00
190_E	202_D	1.245	1.00
264_K	267_L	1.243	1.00
75_I	82_I	1.238	1.00
42_V	75_I	1.238	1.00
252_N	255_L	1.219	1.00
72_M	109_V	1.217	1.00
112_L	136_S	1.216	1.00
120_H	155_M	1.205	1.00
129_I	132_I	1.192	1.00
12_S	215_H	1.187	1.00
222_C	274_N	1.186	1.00
146_L	163_L	1.174	1.00
119_Y	123_F	1.172	1.00
220_Y	233_T	1.172	1.00
76_K	82_I	1.166	1.00
135_H	139_Y	1.154	1.00
114_I	136_S	1.151	1.00
100_Y	104_M	1.147	1.00
15_N	60_E	1.146	1.00
72_M	107_L	1.137	1.00
114_I	132_I	1.129	1.00
244_R	248_K	1.128	1.00
252_N	256_F	1.113	1.00
130_K	134_E	1.112	1.00
11_D	32_R	1.109	1.00
68_L	72_M	1.099	1.00
62_F	90_W	1.093	1.00
10_L	56_F	1.089	1.00
45_F	54_I	1.086	1.00
54_I	75_I	1.085	1.00
92_L	100_Y	1.072	1.00
15_N	89_F	1.061	1.00
126_S	130_K	1.061	1.00
40_E	238_Y	1.061	1.00
73_E	107_L	1.059	1.00
84_L	104_M	1.054	1.00
91_G	101_F	1.047	1.00
146_L	169_G	1.044	1.00
6_V	211_I	1.041	1.00
66_K	69_K	1.040	1.00
49_K	52_Q	1.039	1.00
22_C	57_T	1.028	1.00
41_L	213_Y	1.028	1.00
67_F	71_L	1.026	1.00
148_M	159_I	1.017	1.00
93_S	102_H	1.015	1.00
60_E	87_N	1.015	1.00
116_Y	146_L	1.012	1.00
62_F	68_L	1.009	1.00
148_M	172_I	1.004	1.00
113_T	147_N	1.003	1.00
123_F	155_M	0.989	1.00
132_I	136_S	0.988	1.00
56_F	75_I	0.985	1.00
101_F	139_Y	0.979	1.00
94_K	102_H	0.978	1.00
240_Q	245_T	0.976	1.00
16_A	125_K	0.968	1.00
69_K	73_E	0.964	1.00
249_L	253_L	0.963	1.00
240_Q	248_K	0.950	1.00
9_N	215_H	0.946	1.00
161_E	164_G	0.941	1.00
10_L	64_D	0.941	1.00
115_S	149_A	0.939	1.00
69_K	106_S	0.938	1.00
255_L	258_L	0.936	1.00
160_L	164_G	0.927	1.00
203_S	207_P	0.917	1.00
211_I	242_F	0.917	1.00
44_E	243_E	0.912	1.00
128_S	132_I	0.909	1.00
263_F	267_L	0.904	1.00
53_V	83_T	0.900	1.00
42_V	78_Y	0.896	1.00
82_I	109_V	0.893	1.00
235_R	245_T	0.893	1.00
130_K	166_S	0.888	1.00
259_R	262_G	0.887	1.00
130_K	162_E	0.884	1.00
246_V	255_L	0.880	1.00
8_I	41_L	0.876	1.00
31_T	216_D	0.876	1.00
11_D	64_D	0.871	1.00
261_E	270_L	0.869	1.00
250_N	253_L	0.859	1.00
279_F	282_P	0.859	1.00
137_R	168_L	0.857	1.00
84_L	112_L	0.855	1.00
157_N	161_E	0.854	1.00
203_S	209_Y	0.847	1.00
9_N	57_T	0.839	1.00
40_E	43_T	0.836	1.00
118_E	155_M	0.830	1.00
105_N	142_I	0.827	1.00
119_Y	122_P	0.816	1.00
31_T	215_H	0.815	1.00
33_M	41_L	0.813	1.00
65_Y	100_Y	0.804	1.00
10_L	71_L	0.803	1.00
285_F	289_C	0.801	1.00
70_E	74_I	0.799	1.00
75_I	78_Y	0.796	1.00
151_T	154_K	0.795	1.00
35_K	64_D	0.790	1.00
137_R	144_I	0.789	1.00
112_L	142_I	0.785	1.00
57_T	223_C	0.784	1.00
53_V	81_Q	0.782	1.00
116_Y	126_S	0.780	1.00
132_I	135_H	0.778	1.00
101_F	132_I	0.778	1.00
57_T	85_I	0.777	1.00
258_L	264_K	0.774	1.00
121_A	127_S	0.773	1.00
35_K	71_L	0.772	1.00
183_A	186_R	0.771	1.00
254_L	258_L	0.768	1.00
146_L	172_I	0.768	1.00
69_K	72_M	0.767	1.00
177_M	183_A	0.765	1.00
254_L	257_I	0.763	1.00
116_Y	129_I	0.763	1.00
267_L	273_N	0.761	1.00
87_N	90_W	0.761	1.00
242_F	246_V	0.759	1.00
15_N	63_L	0.757	1.00
235_R	240_Q	0.755	1.00
44_E	47_K	0.754	1.00
211_I	246_V	0.752	1.00
9_N	212_V	0.749	1.00
249_L	252_N	0.745	1.00
261_E	266_F	0.742	1.00
119_Y	155_M	0.742	1.00
105_N	141_D	0.740	1.00
101_F	136_S	0.739	1.00
85_I	147_N	0.738	1.00
101_F	105_N	0.738	1.00
7_S	210_D	0.737	1.00
71_L	75_I	0.735	1.00
137_R	170_V	0.734	1.00
39_R	78_Y	0.733	1.00
273_N	276_I	0.733	1.00
10_L	68_L	0.732	1.00
175_F	178_I	0.730	1.00
267_L	271_K	0.730	1.00
133_L	144_I	0.727	1.00
253_L	256_F	0.727	1.00
69_K	107_L	0.725	1.00
278_E	289_C	0.724	1.00
124_V	129_I	0.723	1.00
122_P	153_D	0.719	1.00
259_R	263_F	0.719	1.00
60_E	63_L	0.718	1.00
46_A	80_K	0.718	1.00
136_S	142_I	0.717	1.00
143_D	170_V	0.714	1.00
162_E	165_D	0.712	0.99
125_K	129_I	0.711	0.99
219_I	242_F	0.709	0.99
60_E	86_S	0.708	0.99
111_A	145_S	0.705	0.99
14_C	21_C	0.702	0.99
288_I	292_C	0.698	0.99
18_C	21_C	0.697	0.99
43_T	47_K	0.696	0.99
65_Y	69_K	0.694	0.99
11_D	59_G	0.694	0.99
133_L	146_L	0.692	0.99
55_S	85_I	0.692	0.99
155_M	159_I	0.690	0.99
205_H	209_Y	0.688	0.99
116_Y	130_K	0.685	0.99
72_M	103_D	0.685	0.99
264_K	273_N	0.683	0.99
262_G	267_L	0.682	0.99
14_C	18_C	0.681	0.99
260_K	263_F	0.678	0.99
35_K	74_I	0.675	0.99
230_T	233_T	0.674	0.99
55_S	83_T	0.672	0.99
166_S	169_G	0.671	0.99
118_E	122_P	0.669	0.99
102_H	105_N	0.668	0.99
37_Y	41_L	0.666	0.99
136_S	144_I	0.663	0.99
204_L	207_P	0.658	0.99
89_F	132_I	0.658	0.99
6_V	213_Y	0.658	0.99
54_I	82_I	0.658	0.99
13_R	30_T	0.656	0.99
206_C	222_C	0.652	0.99
253_L	257_I	0.652	0.99
181_G	184_K	0.651	0.99
38_I	64_D	0.650	0.99
265_W	268_N	0.649	0.99
42_V	54_I	0.647	0.99
62_F	100_Y	0.647	0.99
76_K	108_N	0.646	0.99
42_V	80_K	0.646	0.99
68_L	84_L	0.645	0.99
248_K	252_N	0.645	0.99
113_T	145_S	0.644	0.99
119_Y	162_E	0.643	0.99
39_R	77_P	0.641	0.99
139_Y	142_I	0.638	0.99
282_P	287_S	0.638	0.99
62_F	132_I	0.636	0.99
159_I	163_L	0.636	0.99
286_S	289_C	0.633	0.99
64_D	70_E	0.631	0.99
9_N	23_F	0.630	0.99
91_G	132_I	0.629	0.99
217_G	237_E	0.624	0.99
64_D	68_L	0.624	0.99
36_E	39_R	0.614	0.99
288_I	291_V	0.613	0.99
16_A	117_D	0.613	0.99
221_P	232_I	0.612	0.98
250_N	254_L	0.611	0.98
133_L	169_G	0.610	0.98
127_S	130_K	0.609	0.98
51_I	80_K	0.605	0.98
275_K	278_E	0.605	0.98
284_E	287_S	0.602	0.98
213_Y	219_I	0.602	0.98
86_S	114_I	0.601	0.98
36_E	40_E	0.601	0.98
94_K	103_D	0.598	0.98
9_N	214_H	0.597	0.98
287_S	290_G	0.595	0.98
23_F	57_T	0.593	0.98
221_P	234_L	0.590	0.98
282_P	285_F	0.586	0.98
85_I	224_S	0.586	0.98
91_G	104_M	0.585	0.98
213_Y	237_E	0.583	0.98
85_I	223_C	0.580	0.98
150_V	174_K	0.575	0.98
281_I	285_F	0.573	0.98
60_E	88_G	0.572	0.98
217_G	236_E	0.571	0.98
9_N	12_S	0.570	0.98
20_H	23_F	0.569	0.98
246_V	249_L	0.569	0.98
89_F	128_S	0.566	0.98
233_T	236_E	0.566	0.98
278_E	282_P	0.563	0.97
212_V	223_C	0.560	0.97
221_P	225_P	0.560	0.97
246_V	250_N	0.559	0.97
7_S	223_C	0.557	0.97
58_G	212_V	0.557	0.97
238_Y	241_S	0.556	0.97
58_G	61_V	0.555	0.97
251_S	254_L	0.554	0.97
91_G	114_I	0.553	0.97
241_S	245_T	0.553	0.97
38_I	42_V	0.552	0.97
122_P	155_M	0.551	0.97
156_S	160_L	0.551	0.97
25_S	182_A	0.551	0.97
10_L	38_I	0.550	0.97
56_F	71_L	0.549	0.97
83_T	111_A	0.549	0.97
117_D	148_M	0.548	0.97
117_D	149_A	0.545	0.97
84_L	109_V	0.545	0.97
20_H	57_T	0.544	0.97
35_K	38_I	0.543	0.97
263_F	266_F	0.542	0.97
42_V	56_F	0.539	0.97
44_E	238_Y	0.538	0.97
42_V	74_I	0.537	0.97
17_S	24_S	0.536	0.97
44_E	48_N	0.532	0.96
23_F	212_V	0.532	0.96
46_A	79_E	0.531	0.96
180_V	183_A	0.531	0.96
38_I	41_L	0.531	0.96
38_I	56_F	0.530	0.96
57_T	113_T	0.529	0.96
45_F	51_I	0.529	0.96
285_F	288_I	0.527	0.96
123_F	151_T	0.526	0.96
54_I	80_K	0.526	0.96
47_K	243_E	0.526	0.96
132_I	137_R	0.525	0.96
72_M	82_I	0.524	0.96
137_R	169_G	0.524	0.96
266_F	270_L	0.524	0.96
221_P	224_S	0.523	0.96
41_L	237_E	0.522	0.96
147_N	175_F	0.521	0.96
75_I	80_K	0.519	0.96
248_K	251_S	0.518	0.96
72_M	75_I	0.516	0.96
114_I	129_I	0.512	0.96
56_F	72_M	0.512	0.96
203_S	208_G	0.509	0.95
73_E	76_K	0.509	0.95
206_C	209_Y	0.507	0.95
90_W	132_I	0.505	0.95
234_L	251_S	0.505	0.95
91_G	136_S	0.504	0.95
66_K	71_L	0.504	0.95
253_L	258_L	0.503	0.95
41_L	45_F	0.502	0.95
8_I	33_M	0.502	0.95
85_I	117_D	0.501	0.95
174_K	177_M	0.501	0.95
57_T	147_N	0.501	0.95
52_Q	81_Q	0.500	0.95
147_N	223_C	0.500	0.95

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
4k36A	1	0.9498	100	0.368	Contact Map
4m7tA	1	0.7241	100	0.44	Contact Map
1tv8A	2	0.7774	100	0.517	Contact Map
4rtbA	2	0.8621	99.9	0.597	Contact Map
3c8fA	1	0.6301	99.9	0.604	Contact Map
4wcxA	1	0.9467	99.9	0.639	Contact Map
2a5hA	4	0.8809	99.9	0.64	Contact Map
2yx0A	1	0.6991	99.9	0.643	Contact Map
2z2uA	1	0.6238	99.9	0.654	Contact Map
3rfaA	1	0.6646	99.9	0.658	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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