YJCK - BACSU - GREMLIN Contacts

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YJCK - Putative ribosomal-protein-alanine acetyltransferase

UniProt:	O31633	Sequences: MLKGKTIYVRPLEVTDAEENLGLQSENRDFFEQFSMIRADDYYTVEGQRKRITEYQERLEKDEEYHFGIFTASDDRLIGTVSLFQIIRGALQTAFIGYFLDKAHNGKGIMTEAVRLVVDYAFHELKLHRIEAGVMPRNLGSMRVLEKAGFHKEGIARKNVKINGVWEDHQVLAILNPDDEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	181 (165)
Sequences:	20056 (15340)
Seq/√Len:	1194.2

ECOLI - RIMJ ATDA RIML YHHY MNAT
BACSU - YJCK YDAF YOAA YOKL YNAD YKKB YJDG YWNH
HALSA - Q9HMZ2 Q9HRY6 Q9HNJ3 Q9HRY5 Q9HSL3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_T	147_K	2.674	1.00
132_A	145_L	2.617	1.00
10_R	70_F	2.559	1.00
71_T	74_D	2.396	1.00
10_R	16_D	2.366	1.00
94_A	127_L	2.189	1.00
134_V	142_M	2.159	1.00
3_K	72_A	2.159	1.00
152_K	170_Q	2.155	1.00
153_E	173_A	2.130	1.00
152_K	155_I	2.116	1.00
83_L	121_A	2.092	1.00
6_T	112_E	2.060	1.00
4_G	116_L	2.013	1.00
143_R	146_E	1.950	1.00
134_V	145_L	1.937	1.00
28_R	102_K	1.915	1.00
142_M	146_E	1.900	1.00
119_D	123_H	1.899	1.00
96_I	114_V	1.853	1.00
118_V	150_F	1.797	1.00
68_G	77_L	1.790	1.00
4_G	112_E	1.748	1.00
12_L	68_G	1.707	1.00
155_I	170_Q	1.696	1.00
128_H	158_K	1.687	1.00
18_E	45_V	1.678	1.00
19_E	77_L	1.663	1.00
101_D	104_H	1.653	1.00
118_V	130_I	1.641	1.00
142_M	170_Q	1.627	1.00
114_V	148_A	1.620	1.00
81_V	113_A	1.606	1.00
26_E	102_K	1.604	1.00
17_A	49_R	1.603	1.00
100_L	110_M	1.534	1.00
45_V	49_R	1.529	1.00
8_Y	72_A	1.515	1.00
70_F	75_D	1.507	1.00
44_T	47_G	1.499	1.00
136_P	168_D	1.491	1.00
51_R	55_Y	1.480	1.00
142_M	152_K	1.479	1.00
116_L	119_D	1.460	1.00
69_I	100_L	1.417	1.00
139_L	142_M	1.405	1.00
146_E	152_K	1.358	1.00
14_V	53_T	1.353	1.00
120_Y	124_E	1.344	1.00
128_H	166_W	1.339	1.00
81_V	117_V	1.310	1.00
129_R	173_A	1.290	1.00
3_K	8_Y	1.285	1.00
111_T	144_V	1.281	1.00
8_Y	70_F	1.280	1.00
161_K	166_W	1.275	1.00
21_L	45_V	1.241	1.00
136_P	155_I	1.237	1.00
78_I	104_H	1.237	1.00
159_N	169_H	1.227	1.00
142_M	172_L	1.224	1.00
69_I	113_A	1.211	1.00
19_E	76_R	1.208	1.00
137_R	167_E	1.205	1.00
156_A	171_V	1.203	1.00
98_Y	145_L	1.188	1.00
17_A	52_I	1.157	1.00
110_M	144_V	1.150	1.00
76_R	103_A	1.146	1.00
121_A	130_I	1.144	1.00
76_R	104_H	1.124	1.00
71_T	78_I	1.113	1.00
17_A	45_V	1.097	1.00
49_R	53_T	1.094	1.00
80_T	99_F	1.081	1.00
67_F	117_V	1.072	1.00
105_N	140_G	1.064	1.00
102_K	105_N	1.058	1.00
121_A	125_L	1.058	1.00
134_V	172_L	1.057	1.00
129_R	153_E	1.053	1.00
111_T	115_R	1.045	1.00
98_Y	141_S	1.043	1.00
23_L	99_F	1.034	1.00
87_I	91_L	1.032	1.00
152_K	172_L	1.024	1.00
14_V	49_R	1.021	1.00
95_F	133_G	1.014	1.00
23_L	101_D	1.011	1.00
158_K	168_D	1.007	1.00
157_R	173_A	1.007	1.00
43_Y	47_G	1.003	1.00
19_E	22_G	0.998	1.00
155_I	168_D	0.995	1.00
4_G	7_I	0.993	1.00
93_T	131_E	0.992	1.00
120_Y	125_L	0.992	1.00
67_F	120_Y	0.966	1.00
132_A	150_F	0.941	1.00
118_V	148_A	0.937	1.00
136_P	170_Q	0.936	1.00
118_V	174_I	0.932	1.00
157_R	168_D	0.930	1.00
144_V	148_A	0.930	1.00
21_L	25_S	0.929	1.00
139_L	143_R	0.927	1.00
26_E	101_D	0.919	1.00
22_G	101_D	0.915	1.00
70_F	77_L	0.908	1.00
71_T	109_I	0.906	1.00
26_E	103_A	0.896	1.00
71_T	76_R	0.893	1.00
83_L	117_V	0.893	1.00
135_M	167_E	0.888	1.00
12_L	80_T	0.886	1.00
115_R	119_D	0.886	1.00
14_V	56_Q	0.885	1.00
121_A	127_L	0.885	1.00
106_G	140_G	0.885	1.00
111_T	148_A	0.885	1.00
50_K	54_E	0.884	1.00
93_T	129_R	0.877	1.00
8_Y	75_D	0.876	1.00
145_L	150_F	0.875	1.00
150_F	174_I	0.861	1.00
32_E	35_S	0.857	1.00
16_D	70_F	0.857	1.00
100_L	109_I	0.852	1.00
115_R	148_A	0.851	1.00
161_K	165_V	0.847	1.00
17_A	21_L	0.846	1.00
58_R	63_E	0.845	1.00
7_I	109_I	0.840	1.00
76_R	101_D	0.839	1.00
71_T	107_K	0.837	1.00
42_Y	48_Q	0.826	1.00
19_E	101_D	0.812	1.00
21_L	48_Q	0.809	1.00
7_I	113_A	0.809	1.00
156_A	159_N	0.804	1.00
112_E	116_L	0.804	1.00
14_V	17_A	0.804	1.00
58_R	64_E	0.798	1.00
71_T	104_H	0.797	1.00
92_Q	166_W	0.796	1.00
24_Q	99_F	0.785	1.00
104_H	107_K	0.776	1.00
93_T	159_N	0.771	1.00
153_E	157_R	0.763	1.00
98_Y	110_M	0.755	1.00
161_K	164_G	0.753	1.00
4_G	9_V	0.748	1.00
10_R	68_G	0.744	1.00
141_S	145_L	0.742	1.00
95_F	131_E	0.742	1.00
18_E	22_G	0.741	1.00
50_K	53_T	0.740	1.00
22_G	26_E	0.732	1.00
69_I	81_V	0.729	1.00
22_G	76_R	0.725	1.00
158_K	166_W	0.723	1.00
46_E	49_R	0.723	1.00
133_G	169_H	0.721	1.00
139_L	146_E	0.719	1.00
34_F	137_R	0.713	1.00
66_H	82_S	0.710	1.00
106_G	111_T	0.709	1.00
28_R	33_Q	0.707	1.00
6_T	108_G	0.690	1.00
83_L	94_A	0.690	1.00
133_G	156_A	0.683	1.00
55_Y	66_H	0.682	1.00
22_G	103_A	0.682	1.00
31_F	35_S	0.676	1.00
106_G	143_R	0.662	1.00
32_E	37_I	0.651	1.00
98_Y	114_V	0.650	1.00
47_G	50_K	0.649	1.00
23_L	77_L	0.644	1.00
100_L	105_N	0.642	1.00
69_I	79_G	0.639	1.00
11_P	59_L	0.639	1.00
69_I	109_I	0.635	1.00
46_E	50_K	0.632	1.00
34_F	135_M	0.632	1.00
134_V	141_S	0.631	1.00
134_V	170_Q	0.628	1.00
137_R	165_V	0.623	1.00
114_V	144_V	0.623	1.00
84_F	95_F	0.619	1.00
143_R	147_K	0.618	1.00
31_F	105_N	0.618	1.00
111_T	140_G	0.616	1.00
140_G	143_R	0.615	1.00
146_E	172_L	0.614	1.00
31_F	34_F	0.613	1.00
160_V	169_H	0.607	1.00
13_E	16_D	0.607	1.00
43_Y	48_Q	0.605	1.00
98_Y	144_V	0.605	1.00
78_I	109_I	0.601	1.00
94_A	121_A	0.596	1.00
48_Q	52_I	0.593	1.00
162_I	165_V	0.592	1.00
26_E	105_N	0.587	1.00
11_P	56_Q	0.586	1.00
132_A	141_S	0.583	1.00
77_L	80_T	0.582	1.00
5_K	112_E	0.579	1.00
10_R	13_E	0.574	1.00
136_P	142_M	0.574	1.00
162_I	167_E	0.567	1.00
31_F	99_F	0.565	1.00
86_I	94_A	0.565	1.00
92_Q	161_K	0.564	1.00
148_A	174_I	0.564	1.00
133_G	171_V	0.558	1.00
122_F	174_I	0.557	1.00
118_V	122_F	0.556	1.00
131_E	156_A	0.551	1.00
81_V	114_V	0.549	1.00
48_Q	51_R	0.548	1.00
100_L	104_H	0.546	1.00
131_E	159_N	0.543	1.00
85_Q	94_A	0.542	1.00
109_I	112_E	0.542	1.00
35_S	99_F	0.542	1.00
92_Q	128_H	0.541	1.00
28_R	105_N	0.540	1.00
96_I	130_I	0.537	1.00
156_A	173_A	0.536	1.00
9_V	116_L	0.531	1.00
151_H	157_R	0.531	1.00
7_I	112_E	0.526	1.00
82_S	97_G	0.525	1.00
135_M	162_I	0.521	1.00
24_Q	80_T	0.518	1.00
106_G	144_V	0.516	1.00
56_Q	59_L	0.515	1.00
45_V	48_Q	0.512	1.00
69_I	110_M	0.511	1.00
19_E	70_F	0.509	1.00
114_V	118_V	0.507	1.00
56_Q	60_E	0.506	1.00
110_M	114_V	0.505	1.00
129_R	159_N	0.504	1.00
18_E	21_L	0.504	1.00
73_S	109_I	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
3pzjA	2	0.9558	100	0.277	Contact Map
2vzyA	3	0.8729	100	0.285	Contact Map
1nslA	3	0.9669	100	0.295	Contact Map
1yreA	2	0.9337	100	0.299	Contact Map
3igrA	2	1	100	0.299	Contact Map
3r9fA	1	0.9503	100	0.301	Contact Map
2fckA	2	0.9282	100	0.304	Contact Map
2z10A	2	0.9448	100	0.318	Contact Map
3tcvA	2	0.9558	100	0.329	Contact Map
3fbuA	2	0.9171	100	0.33	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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