YLBH - BACSU - GREMLIN Contacts

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YLBH - Putative rRNA methyltransferase YlbH

UniProt:	O34331	Sequences: MRVISGSKKGRSLKAVAGTSTRPTTDKVKESIFNMIGPYFDGGRGLDLFAGSGGLGIEALSRGFEHCIFVDRDFKAIQTVKSNLKTLELTKHAQVYRNDAERALHAAAKRETGFRGIFLDPPYKEQKLKALLTLIDEYQMLEEDGFIVAEHDREVELPETVGDLVMTRKETYGLTGVAIYKKRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	184 (177)
Sequences:	4198 (3075)
Seq/√Len:	231.1

ECOLI - RSMD
BACSU - YLBH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_G	69_F	3.262	1.00
57_I	84_L	2.838	1.00
14_K	82_S	2.751	1.00
8_K	89_L	2.616	1.00
3_V	57_I	2.597	1.00
29_K	54_G	2.304	1.00
32_I	177_V	2.287	1.00
11_R	86_T	2.283	1.00
151_H	178_A	2.257	1.00
44_R	66_H	2.239	1.00
74_F	97_R	2.165	1.00
7_S	92_H	2.153	1.00
68_I	114_F	2.118	1.00
141_L	145_G	2.115	1.00
84_L	93_A	2.089	1.00
45_G	55_L	2.074	1.00
50_A	69_F	1.916	1.00
60_L	93_A	1.904	1.00
66_H	94_Q	1.901	1.00
115_R	142_E	1.851	1.00
71_D	77_I	1.845	1.00
30_E	34_N	1.844	1.00
103_A	107_A	1.819	1.00
35_M	179_I	1.804	1.00
60_L	67_C	1.804	1.00
68_I	96_Y	1.779	1.00
77_I	95_V	1.758	1.00
169_K	176_G	1.757	1.00
166_M	180_Y	1.746	1.00
31_S	172_Y	1.694	1.00
46_L	114_F	1.674	1.00
84_L	95_V	1.666	1.00
28_V	175_T	1.659	1.00
21_T	76_A	1.649	1.00
78_Q	82_S	1.584	1.00
48_L	70_V	1.569	1.00
44_R	112_T	1.564	1.00
171_T	176_G	1.543	1.00
11_R	88_E	1.518	1.00
117_I	145_G	1.508	1.00
74_F	78_Q	1.485	1.00
77_I	97_R	1.464	1.00
8_K	87_L	1.463	1.00
49_F	131_L	1.442	1.00
2_R	26_D	1.420	1.00
40_F	43_G	1.416	1.00
56_G	67_C	1.397	1.00
124_K	152_D	1.394	1.00
70_V	103_A	1.376	1.00
85_K	90_T	1.359	1.00
98_N	103_A	1.349	1.00
24_T	150_E	1.341	1.00
166_M	178_A	1.325	1.00
31_S	34_N	1.323	1.00
35_M	168_R	1.315	1.00
166_M	169_K	1.311	1.00
82_S	85_K	1.302	1.00
135_I	145_G	1.288	1.00
127_K	131_L	1.283	1.00
153_R	171_T	1.278	1.00
55_L	118_F	1.275	1.00
66_H	112_T	1.274	1.00
142_E	145_G	1.268	1.00
60_L	69_F	1.263	1.00
45_G	59_A	1.243	1.00
99_D	102_R	1.220	1.00
32_I	55_L	1.204	1.00
117_I	135_I	1.198	1.00
78_Q	81_K	1.169	1.00
127_K	130_A	1.166	1.00
48_L	100_A	1.163	1.00
69_F	93_A	1.162	1.00
71_D	76_A	1.161	1.00
75_K	78_Q	1.155	1.00
133_T	137_E	1.113	1.00
50_A	80_V	1.104	1.00
42_G	65_E	1.099	1.00
136_D	163_D	1.095	1.00
146_F	167_T	1.089	1.00
11_R	87_L	1.089	1.00
107_A	140_M	1.087	1.00
105_H	134_L	1.074	1.00
136_D	164_L	1.066	1.00
113_G	139_Q	1.061	1.00
45_G	64_F	1.058	1.00
40_F	116_G	1.055	1.00
113_G	142_E	1.053	1.00
169_K	178_A	1.046	1.00
82_S	86_T	1.034	1.00
45_G	116_G	1.032	1.00
72_R	99_D	1.029	1.00
7_S	89_L	1.019	1.00
98_N	102_R	1.008	1.00
152_D	174_L	1.007	1.00
45_G	67_C	1.007	1.00
129_K	133_T	1.006	1.00
68_I	103_A	0.987	1.00
4_I	30_E	0.986	1.00
15_A	18_G	0.985	1.00
15_A	52_S	0.978	1.00
167_T	181_K	0.978	1.00
13_L	83_N	0.965	1.00
81_K	97_R	0.964	1.00
134_L	138_Y	0.958	1.00
44_R	113_G	0.957	1.00
130_A	133_T	0.956	1.00
28_V	31_S	0.955	1.00
16_V	79_T	0.951	1.00
50_A	56_G	0.950	1.00
60_L	84_L	0.948	1.00
45_G	118_F	0.948	1.00
24_T	120_D	0.946	1.00
40_F	64_F	0.938	1.00
124_K	154_E	0.931	1.00
119_L	149_A	0.930	1.00
1_M	15_A	0.929	1.00
4_I	26_D	0.927	1.00
77_I	80_V	0.917	1.00
31_S	35_M	0.907	1.00
44_R	114_F	0.906	1.00
68_I	94_Q	0.892	0.99
70_V	98_N	0.892	0.99
8_K	11_R	0.883	0.99
165_V	181_K	0.877	0.99
153_R	176_G	0.877	0.99
128_L	149_A	0.877	0.99
160_T	180_Y	0.873	0.99
119_L	147_I	0.872	0.99
98_N	106_A	0.860	0.99
28_V	177_V	0.859	0.99
35_M	170_E	0.858	0.99
46_L	117_I	0.852	0.99
44_R	68_I	0.850	0.99
44_R	142_E	0.847	0.99
33_F	59_A	0.845	0.99
100_A	131_L	0.844	0.99
17_A	75_K	0.832	0.99
77_I	81_K	0.824	0.99
151_H	155_V	0.822	0.99
44_R	65_E	0.815	0.99
70_V	100_A	0.813	0.99
18_G	21_T	0.809	0.99
172_Y	177_V	0.808	0.99
89_L	92_H	0.805	0.99
152_D	155_V	0.804	0.99
96_Y	103_A	0.804	0.99
126_Q	129_K	0.798	0.99
37_G	62_R	0.796	0.99
117_I	141_L	0.796	0.99
27_K	30_E	0.795	0.99
81_K	85_K	0.793	0.99
79_T	83_N	0.790	0.99
128_L	151_H	0.785	0.99
32_I	148_V	0.779	0.98
68_I	112_T	0.770	0.98
102_R	105_H	0.759	0.98
170_E	177_V	0.753	0.98
46_L	68_I	0.749	0.98
3_V	84_L	0.748	0.98
50_A	71_D	0.747	0.98
151_H	176_G	0.746	0.98
94_Q	112_T	0.746	0.98
49_F	127_K	0.740	0.98
20_S	73_D	0.734	0.98
132_L	147_I	0.730	0.98
25_T	28_V	0.712	0.97
113_G	140_M	0.711	0.97
33_F	118_F	0.711	0.97
57_I	93_A	0.703	0.97
37_G	40_F	0.703	0.97
108_A	138_Y	0.703	0.97
69_F	84_L	0.701	0.97
25_T	175_T	0.694	0.97
36_I	148_V	0.693	0.97
148_V	177_V	0.686	0.97
101_E	130_A	0.679	0.96
71_D	80_V	0.679	0.96
158_P	161_V	0.678	0.96
13_L	87_L	0.673	0.96
104_L	134_L	0.672	0.96
14_K	79_T	0.670	0.96
118_F	148_V	0.665	0.96
3_V	29_K	0.658	0.96
18_G	76_A	0.657	0.96
108_A	140_M	0.655	0.96
134_L	137_E	0.651	0.95
43_G	64_F	0.650	0.95
35_M	177_V	0.648	0.95
55_L	148_V	0.648	0.95
39_Y	168_R	0.641	0.95
29_K	55_L	0.634	0.95
154_E	174_L	0.633	0.95
168_R	179_I	0.630	0.95
38_P	43_G	0.629	0.95
14_K	86_T	0.628	0.95
74_F	77_I	0.623	0.94
105_H	138_Y	0.617	0.94
48_L	119_L	0.615	0.94
25_T	172_Y	0.614	0.94
31_S	177_V	0.612	0.94
18_G	73_D	0.608	0.94
144_D	181_K	0.607	0.93
26_D	30_E	0.606	0.93
5_S	62_R	0.605	0.93
43_G	115_R	0.603	0.93
119_L	131_L	0.603	0.93
100_A	104_L	0.599	0.93
101_E	127_K	0.598	0.93
130_A	134_L	0.596	0.93
5_S	29_K	0.596	0.93
32_I	118_F	0.591	0.93
125_E	155_V	0.590	0.93
27_K	31_S	0.586	0.92
15_A	21_T	0.585	0.92
128_L	155_V	0.584	0.92
24_T	28_V	0.583	0.92
159_E	166_M	0.583	0.92
104_L	140_M	0.583	0.92
64_F	116_G	0.582	0.92
57_I	87_L	0.580	0.92
101_E	134_L	0.580	0.92
131_L	135_I	0.580	0.92
8_K	60_L	0.572	0.91
101_E	131_L	0.572	0.91
103_A	140_M	0.572	0.91
38_P	41_D	0.569	0.91
148_V	179_I	0.568	0.91
24_T	54_G	0.564	0.91
8_K	92_H	0.563	0.91
21_T	79_T	0.562	0.91
128_L	152_D	0.558	0.90
136_D	162_G	0.554	0.90
55_L	179_I	0.549	0.90
158_P	180_Y	0.549	0.90
161_V	180_Y	0.547	0.89
48_L	104_L	0.546	0.89
89_L	93_A	0.545	0.89
57_I	83_N	0.545	0.89
70_V	96_Y	0.543	0.89
39_Y	146_F	0.543	0.89
47_D	56_G	0.540	0.89
73_D	76_A	0.538	0.89
150_E	175_T	0.535	0.88
107_A	138_Y	0.534	0.88
72_R	97_R	0.532	0.88
49_F	100_A	0.532	0.88
83_N	86_T	0.532	0.88
55_L	116_G	0.530	0.88
96_Y	106_A	0.528	0.88
1_M	18_G	0.518	0.87
119_L	128_L	0.515	0.86
107_A	113_G	0.515	0.86
76_A	83_N	0.515	0.86
136_D	165_V	0.514	0.86
7_S	63_G	0.513	0.86
60_L	89_L	0.509	0.86
49_F	99_D	0.509	0.86
128_L	132_L	0.508	0.86
47_D	53_G	0.505	0.85
32_I	179_I	0.505	0.85
24_T	30_E	0.503	0.85
10_G	170_E	0.502	0.85
148_V	172_Y	0.502	0.85
35_M	148_V	0.502	0.85
129_K	157_L	0.501	0.85
67_C	93_A	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
1ws6A	1	0.9185	100	0.54	Contact Map
2fpoA	1	0.9783	100	0.571	Contact Map
2fhpA	1	0.9946	100	0.571	Contact Map
2iftA	1	0.9565	99.9	0.579	Contact Map
4bluA	2	0.9022	99.9	0.595	Contact Map
2oo3A	1	0.9293	99.9	0.601	Contact Map
3x0dA	1	0.8967	99.9	0.613	Contact Map
2esrA	2	0.837	99.9	0.617	Contact Map
3p9nA	1	0.9565	99.9	0.62	Contact Map
4dcmA	1	0.8696	99.8	0.666	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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