RNHL - BACSU - GREMLIN Contacts

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RNHL - 14.7 kDa ribonuclease H-like protein

UniProt:	P54162	Sequences: MPTEIYVDGASAGNPGPSGIGIFIKHEGKAESFSIPIGVHTNQEAEFLALIEGMKLCATRGYQSVSFRTDSDIVERATELEMVKNITFQPFVEEIIRLKAAFPLFFIKWIPGKQNQKADLLAKEAIRLNEKN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	132 (123)
Sequences:	4057 (2414)
Seq/√Len:	217.6

ECOLI - RNH
BACSU - RNHL YPEP
HALSA - RNH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_D	76_R	3.925	1.00
66_S	108_K	3.699	1.00
99_K	103_P	3.375	1.00
76_R	80_L	3.330	1.00
52_E	55_K	2.985	1.00
5_I	53_G	2.982	1.00
12_A	123_K	2.707	1.00
32_S	117_K	2.692	1.00
50_L	74_V	2.580	1.00
12_A	127_R	2.532	1.00
69_T	75_E	2.380	1.00
55_K	104_L	2.165	1.00
12_A	126_I	2.117	1.00
48_L	52_E	1.948	1.00
68_R	108_K	1.945	1.00
10_A	126_I	1.799	1.00
66_S	106_F	1.726	1.00
10_A	122_A	1.668	1.00
123_K	126_I	1.666	1.00
34_S	124_E	1.626	1.00
7_V	69_T	1.625	1.00
34_S	125_A	1.533	1.00
22_I	33_F	1.525	1.00
50_L	67_F	1.522	1.00
4_E	66_S	1.506	1.00
123_K	127_R	1.476	1.00
44_E	100_A	1.456	1.00
21_G	125_A	1.431	1.00
120_L	124_E	1.422	1.00
111_P	114_Q	1.409	1.00
23_F	118_A	1.398	1.00
77_A	102_F	1.392	1.00
25_K	30_A	1.380	1.00
117_K	120_L	1.358	1.00
4_E	68_R	1.334	1.00
7_V	49_A	1.294	1.00
4_E	25_K	1.280	1.00
6_Y	68_R	1.268	1.00
18_S	40_H	1.244	1.00
72_D	109_W	1.239	1.00
22_I	53_G	1.231	1.00
19_G	126_I	1.200	1.00
98_L	101_A	1.177	1.00
75_E	107_I	1.172	1.00
20_I	37_I	1.164	1.00
20_I	52_E	1.163	1.00
35_I	52_E	1.160	1.00
10_A	123_K	1.160	1.00
37_I	44_E	1.156	1.00
55_K	94_E	1.141	1.00
75_E	79_E	1.110	1.00
118_A	125_A	1.100	1.00
78_T	107_I	1.092	1.00
72_D	75_E	1.089	1.00
34_S	121_L	1.067	1.00
6_Y	25_K	1.050	1.00
40_H	44_E	1.045	1.00
20_I	35_I	1.043	1.00
95_I	98_L	1.019	1.00
47_F	73_I	1.013	1.00
77_A	82_M	1.005	1.00
37_I	45_A	0.991	1.00
95_I	99_K	0.990	1.00
57_C	65_V	0.983	1.00
78_T	82_M	0.971	1.00
94_E	97_R	0.969	1.00
86_I	93_E	0.964	1.00
121_L	125_A	0.961	1.00
77_A	81_E	0.957	1.00
23_F	117_K	0.927	0.99
96_I	99_K	0.908	0.99
7_V	50_L	0.907	0.99
58_A	101_A	0.905	0.99
5_I	67_F	0.905	0.99
30_A	117_K	0.904	0.99
19_G	122_A	0.901	0.99
26_H	63_Q	0.888	0.99
32_S	121_L	0.875	0.99
79_E	107_I	0.873	0.99
93_E	98_L	0.863	0.99
90_P	97_R	0.860	0.99
5_I	65_V	0.843	0.99
92_V	98_L	0.826	0.99
76_R	81_E	0.821	0.99
33_F	56_L	0.813	0.99
21_G	121_L	0.808	0.99
13_G	16_G	0.804	0.99
21_G	118_A	0.791	0.98
47_F	74_V	0.784	0.98
5_I	24_I	0.782	0.98
113_K	116_Q	0.780	0.98
50_L	107_I	0.779	0.98
64_S	106_F	0.766	0.98
89_Q	95_I	0.758	0.98
89_Q	93_E	0.757	0.98
90_P	96_I	0.755	0.98
18_S	45_A	0.755	0.98
57_C	62_Y	0.753	0.98
36_P	125_A	0.751	0.98
24_I	31_E	0.749	0.98
36_P	126_I	0.745	0.98
98_L	102_F	0.738	0.97
120_L	123_K	0.737	0.97
69_T	74_V	0.714	0.97
51_I	104_L	0.710	0.97
24_I	56_L	0.700	0.96
26_H	29_K	0.688	0.96
72_D	82_M	0.681	0.96
47_F	77_A	0.675	0.96
83_V	88_F	0.674	0.96
44_E	48_L	0.666	0.95
57_C	61_G	0.665	0.95
75_E	78_T	0.659	0.95
19_G	23_F	0.652	0.95
79_E	106_F	0.646	0.94
22_I	35_I	0.646	0.94
96_I	103_P	0.643	0.94
96_I	100_A	0.635	0.94
52_E	56_L	0.632	0.94
43_Q	73_I	0.631	0.94
74_V	77_A	0.630	0.94
23_F	32_S	0.627	0.94
21_G	32_S	0.627	0.94
21_G	34_S	0.621	0.93
37_I	48_L	0.617	0.93
109_W	114_Q	0.614	0.93
119_D	123_K	0.614	0.93
72_D	111_P	0.613	0.93
7_V	53_G	0.610	0.93
13_G	126_I	0.609	0.93
3_T	57_C	0.604	0.92
92_V	96_I	0.604	0.92
34_S	123_K	0.602	0.92
90_P	94_E	0.599	0.92
48_L	104_L	0.599	0.92
73_I	77_A	0.599	0.92
40_H	45_A	0.595	0.92
31_E	56_L	0.586	0.91
41_T	73_I	0.583	0.91
62_Y	65_V	0.582	0.91
90_P	93_E	0.578	0.90
92_V	95_I	0.577	0.90
68_R	110_I	0.577	0.90
18_S	44_E	0.573	0.90
99_K	105_F	0.573	0.90
22_I	52_E	0.568	0.90
7_V	67_F	0.567	0.90
10_A	109_W	0.563	0.89
82_M	107_I	0.562	0.89
67_F	105_F	0.562	0.89
11_S	14_N	0.560	0.89
3_T	63_Q	0.555	0.89
8_D	46_E	0.552	0.88
8_D	70_D	0.551	0.88
61_G	64_S	0.551	0.88
57_C	63_Q	0.549	0.88
46_E	70_D	0.548	0.88
88_F	91_F	0.547	0.88
5_I	22_I	0.546	0.88
3_T	24_I	0.543	0.88
21_G	33_F	0.542	0.87
122_A	126_I	0.539	0.87
13_G	123_K	0.537	0.87
14_N	42_N	0.536	0.87
124_E	127_R	0.536	0.87
83_V	92_V	0.535	0.87
51_I	95_I	0.534	0.87
48_L	91_F	0.532	0.86
121_L	124_E	0.524	0.86
53_G	65_V	0.521	0.85
112_G	116_Q	0.520	0.85
89_Q	92_V	0.518	0.85
51_I	55_K	0.517	0.85
45_A	118_A	0.511	0.84
93_E	96_I	0.510	0.84
122_A	125_A	0.509	0.84
63_Q	103_P	0.508	0.84
51_I	98_L	0.507	0.84
118_A	121_L	0.506	0.84
3_T	62_Y	0.505	0.84
34_S	126_I	0.503	0.83
20_I	49_A	0.503	0.83
58_A	62_Y	0.501	0.83
26_H	61_G	0.500	0.83

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
4mh8A	1	0	100	0.302	Contact Map
1jl1A	1	0.9848	100	0.331	Contact Map
3h08A	1	0.9545	100	0.333	Contact Map
2lsnA	1	0.9773	100	0.345	Contact Map
1rilA	1	0.9773	100	0.348	Contact Map
2e4lA	1	0.9848	100	0.35	Contact Map
2qkbA	1	0.9697	100	0.355	Contact Map
3hstB	1	1	100	0.363	Contact Map
3u3gD	1	0.9924	100	0.364	Contact Map
3qioA	1	0.8333	100	0.364	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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