RNaseH_like - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

RNaseH_like - Ribonuclease H-like

PFAM:	PF04308	Sequences: EVIEEIKEFIKEEPGPEYKIYIGTDSQVKGKETDFVTAIVVHRVGKGGRYFYRKEKERKIYSLRERILNEVSLSLELALELCELLEKRLGGLADVDLEIHLDINPNGKSNELIKEAVGYIRGMGFEAKIKPDAFAASSVADRHTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	145 (138)
Sequences:	4497 (2860)
Seq/√Len:	243.4
META:	0.927

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_N	73_L	3.115	1.00
64_R	115_E	3.073	1.00
55_E	73_L	3.066	1.00
50_Y	143_H	2.948	1.00
37_T	77_L	2.719	1.00
24_T	74_S	2.629	1.00
62_S	65_E	2.608	1.00
101_L	120_I	2.351	1.00
104_N	107_G	2.343	1.00
108_K	111_E	2.323	1.00
76_E	80_E	2.305	1.00
113_I	129_I	2.135	1.00
69_N	72_S	2.076	1.00
24_T	37_T	2.076	1.00
79_L	125_F	2.029	1.00
67_I	109_S	1.940	1.00
7_K	11_K	1.820	1.00
13_E	16_P	1.819	1.00
67_I	112_L	1.773	1.00
72_S	76_E	1.719	1.00
128_K	132_D	1.687	1.00
19_K	44_V	1.677	1.00
19_K	98_E	1.629	1.00
5_E	49_R	1.614	1.00
21_Y	135_A	1.611	1.00
117_V	129_I	1.548	1.00
32_E	56_K	1.530	1.00
67_I	116_A	1.526	1.00
98_E	128_K	1.523	1.00
22_I	74_S	1.522	1.00
34_D	56_K	1.478	1.00
71_V	101_L	1.451	1.00
8_E	12_E	1.445	1.00
133_A	137_S	1.439	1.00
4_E	8_E	1.436	1.00
109_S	112_L	1.425	1.00
74_S	99_I	1.418	1.00
17_E	44_V	1.392	1.00
34_D	54_K	1.365	1.00
71_V	116_A	1.347	1.00
75_L	120_I	1.337	1.00
72_S	119_Y	1.335	1.00
78_A	125_F	1.313	1.00
4_E	88_R	1.301	1.00
40_V	135_A	1.265	1.00
118_G	122_G	1.260	1.00
28_V	31_K	1.260	1.00
5_E	51_F	1.244	1.00
103_I	116_A	1.243	1.00
75_L	119_Y	1.224	1.00
57_E	60_I	1.221	1.00
9_F	41_V	1.213	1.00
8_E	11_K	1.209	1.00
42_H	48_G	1.189	1.00
67_I	103_I	1.185	1.00
35_F	69_N	1.183	1.00
16_P	46_K	1.159	1.00
100_H	128_K	1.149	1.00
27_Q	144_T	1.134	1.00
101_L	116_A	1.117	1.00
37_T	55_E	1.085	1.00
99_I	102_D	1.085	1.00
26_S	66_R	1.073	1.00
35_F	61_Y	1.058	1.00
74_S	120_I	1.051	1.00
19_K	96_D	1.042	1.00
104_N	110_N	1.017	1.00
60_I	66_R	1.014	1.00
36_V	52_Y	0.999	1.00
117_V	127_A	0.989	1.00
14_P	17_E	0.980	1.00
121_R	127_A	0.966	1.00
113_I	117_V	0.959	1.00
39_I	77_L	0.957	1.00
67_I	70_E	0.953	1.00
78_A	99_I	0.950	1.00
31_K	56_K	0.943	1.00
18_Y	43_R	0.938	1.00
75_L	123_M	0.935	1.00
79_L	83_E	0.932	1.00
33_T	66_R	0.930	1.00
68_L	72_S	0.928	1.00
35_F	73_L	0.925	1.00
20_I	41_V	0.925	1.00
5_E	8_E	0.919	1.00
40_V	139_V	0.916	1.00
68_L	115_E	0.914	1.00
88_R	93_A	0.907	1.00
112_L	116_A	0.899	1.00
41_V	51_F	0.876	0.99
100_H	134_F	0.874	0.99
48_G	139_V	0.869	0.99
50_Y	139_V	0.868	0.99
84_L	87_K	0.858	0.99
57_E	69_N	0.856	0.99
117_V	121_R	0.856	0.99
79_L	82_C	0.850	0.99
81_L	85_L	0.837	0.99
4_E	15_G	0.831	0.99
68_L	116_A	0.826	0.99
110_N	113_I	0.821	0.99
21_Y	134_F	0.817	0.99
114_K	121_R	0.815	0.99
103_I	113_I	0.805	0.99
21_Y	42_H	0.792	0.99
63_L	108_K	0.787	0.99
135_A	138_S	0.774	0.99
104_N	109_S	0.774	0.99
121_R	126_E	0.774	0.99
9_F	13_E	0.774	0.99
14_P	18_Y	0.772	0.99
64_R	111_E	0.767	0.99
28_V	33_T	0.763	0.99
136_A	139_V	0.762	0.99
134_F	138_S	0.761	0.99
22_I	78_A	0.755	0.98
34_D	144_T	0.752	0.98
4_E	7_K	0.748	0.98
68_L	119_Y	0.747	0.98
72_S	123_M	0.743	0.98
33_T	61_Y	0.733	0.98
13_E	18_Y	0.732	0.98
101_L	127_A	0.723	0.98
68_L	71_V	0.722	0.98
72_S	79_L	0.718	0.98
98_E	102_D	0.713	0.98
77_L	80_E	0.709	0.98
66_R	71_V	0.704	0.98
60_I	65_E	0.698	0.97
53_R	76_E	0.697	0.97
73_L	76_E	0.694	0.97
29_K	32_E	0.694	0.97
133_A	138_S	0.685	0.97
76_E	79_L	0.684	0.97
9_F	12_E	0.680	0.97
87_K	93_A	0.677	0.97
96_D	126_E	0.676	0.97
13_E	43_R	0.671	0.97
59_K	62_S	0.670	0.97
119_Y	123_M	0.670	0.97
74_S	78_A	0.667	0.97
64_R	68_L	0.654	0.96
66_R	70_E	0.654	0.96
80_E	84_L	0.643	0.96
137_S	144_T	0.643	0.96
21_Y	40_V	0.642	0.96
75_L	125_F	0.642	0.96
40_V	48_G	0.641	0.96
107_G	110_N	0.640	0.96
65_E	69_N	0.637	0.96
40_V	116_A	0.634	0.95
21_Y	44_V	0.633	0.95
105_P	110_N	0.632	0.95
99_I	120_I	0.631	0.95
13_E	46_K	0.631	0.95
82_C	125_F	0.630	0.95
131_P	136_A	0.623	0.95
100_H	133_A	0.619	0.95
10_I	13_E	0.617	0.95
17_E	96_D	0.615	0.95
9_F	49_R	0.613	0.95
36_V	54_K	0.608	0.94
22_I	81_L	0.606	0.94
109_S	116_A	0.600	0.94
32_E	58_R	0.599	0.94
57_E	73_L	0.596	0.94
37_T	73_L	0.596	0.94
23_G	26_S	0.594	0.94
52_Y	120_I	0.594	0.94
11_K	15_G	0.578	0.93
27_Q	33_T	0.571	0.92
53_R	80_E	0.570	0.92
68_L	112_L	0.565	0.92
52_Y	143_H	0.564	0.92
134_F	139_V	0.563	0.92
10_I	95_V	0.563	0.92
106_N	110_N	0.558	0.91
46_K	123_M	0.556	0.91
4_E	11_K	0.555	0.91
99_I	104_N	0.554	0.91
33_T	57_E	0.550	0.91
64_R	122_G	0.546	0.91
10_I	14_P	0.544	0.90
45_G	48_G	0.542	0.90
134_F	137_S	0.542	0.90
33_T	59_K	0.540	0.90
34_D	66_R	0.539	0.90
70_E	74_S	0.538	0.90
7_K	10_I	0.536	0.90
32_E	92_L	0.536	0.90
28_V	32_E	0.536	0.90
86_E	95_V	0.531	0.89
11_K	17_E	0.524	0.89
112_L	115_E	0.523	0.89
27_Q	142_R	0.523	0.89
9_F	14_P	0.519	0.88
67_I	71_V	0.515	0.88
131_P	135_A	0.514	0.88
117_V	132_D	0.512	0.88
9_F	18_Y	0.510	0.87
114_K	118_G	0.510	0.87
64_R	99_I	0.509	0.87
33_T	60_I	0.508	0.87
58_R	62_S	0.505	0.87
98_E	118_G	0.502	0.86
104_N	144_T	0.502	0.86
49_R	127_A	0.500	0.86

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
1xovA	1	0.5724	54.1	0.92	Contact Map
1rblM	3	0.2828	34.6	0.929	Contact Map
4ol8A	2	0.8621	32	0.93	Contact Map
1svdM	3	0.2759	21	0.936	Contact Map
3czxA	2	0.6	16.5	0.939	Contact Map
3m89A	1	0.4345	13.6	0.941	Contact Map
1gk8I	3	0.269	13	0.942	Contact Map
3o59X	1	0.2414	10.5	0.944	Contact Map
1wddS	3	0.2897	10.4	0.944	Contact Map
1jwqA	1	0.6069	8.3	0.947	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.

Page generated in 0.0061 seconds.