GTA_holin_3TM - PFAM28P - GREMLIN Contacts

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

GTA_holin_3TM - Holin of 3TMs, for gene-transfer release

PFAM:	PF11351	Sequences: GALIGPVGKLLDKFIPDKDEKAKAKLELELAKLQQAGEFAQLDAELELAKAQLEINKAEAASGSWFVAGWRPAIGWVCGAALAYNFILQPLLAWALALGGALLPEELWTLLGGMLGLYFGGRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (107)
Sequences:	6770 (4396)
Seq/√Len:	425.0
META:	0.941

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_E	57_K	3.933	1.00
58_A	61_A	3.505	1.00
73_A	79_G	3.331	1.00
47_E	50_K	3.312	1.00
29_E	32_K	3.196	1.00
20_E	23_K	3.010	1.00
70_W	75_G	2.997	1.00
74_I	79_G	2.290	1.00
31_A	34_Q	2.083	1.00
64_S	69_G	1.906	1.00
62_S	67_V	1.891	1.00
77_V	83_A	1.846	1.00
17_D	20_E	1.749	1.00
32_K	36_A	1.743	1.00
73_A	76_W	1.673	1.00
109_T	112_G	1.580	1.00
66_F	73_A	1.568	1.00
18_K	21_K	1.538	1.00
22_A	25_K	1.534	1.00
19_D	23_K	1.529	1.00
64_S	68_A	1.524	1.00
65_W	69_G	1.493	1.00
21_K	25_K	1.365	1.00
51_A	54_E	1.312	1.00
11_L	15_I	1.303	1.00
5_G	9_K	1.296	1.00
84_Y	89_Q	1.294	1.00
9_K	12_D	1.232	1.00
84_Y	91_L	1.217	1.00
18_K	22_A	1.205	1.00
113_G	117_L	1.204	1.00
106_E	109_T	1.199	1.00
13_K	16_P	1.189	1.00
74_I	111_L	1.179	1.00
57_K	61_A	1.178	1.00
95_A	99_G	1.145	1.00
50_K	54_E	1.139	1.00
12_D	25_K	1.101	1.00
101_A	104_P	1.094	1.00
59_E	70_W	1.090	1.00
89_Q	93_A	1.087	1.00
66_F	76_W	1.083	1.00
23_K	29_E	1.078	1.00
19_D	22_A	1.074	1.00
16_P	22_A	1.074	1.00
5_G	8_G	1.068	1.00
20_E	24_A	1.067	1.00
15_I	18_K	1.065	1.00
63_G	68_A	1.043	1.00
7_V	10_L	1.019	1.00
30_L	34_Q	1.019	1.00
85_N	89_Q	1.010	1.00
21_K	24_A	0.998	1.00
62_S	65_W	0.995	1.00
78_C	111_L	0.977	1.00
96_L	100_G	0.975	1.00
108_W	112_G	0.963	1.00
80_A	83_A	0.950	1.00
4_I	7_V	0.946	1.00
114_M	117_L	0.935	1.00
81_A	86_F	0.921	1.00
109_T	113_G	0.919	1.00
63_G	67_V	0.918	1.00
15_I	20_E	0.917	1.00
45_E	48_L	0.891	1.00
66_F	69_G	0.890	1.00
16_P	21_K	0.882	1.00
93_A	96_L	0.877	1.00
45_E	49_A	0.872	1.00
10_L	14_F	0.865	1.00
32_K	35_Q	0.862	1.00
3_L	6_P	0.861	1.00
62_S	68_A	0.861	1.00
15_I	24_A	0.857	1.00
6_P	10_L	0.854	1.00
12_D	21_K	0.852	1.00
65_W	68_A	0.851	1.00
17_D	23_K	0.848	1.00
6_P	9_K	0.848	1.00
30_L	33_L	0.844	1.00
59_E	75_G	0.834	1.00
8_G	12_D	0.823	1.00
84_Y	88_L	0.822	1.00
22_A	26_L	0.819	1.00
101_A	105_E	0.813	1.00
31_A	35_Q	0.801	1.00
16_P	19_D	0.795	1.00
11_L	21_K	0.793	1.00
96_L	99_G	0.777	1.00
64_S	67_V	0.771	1.00
75_G	114_M	0.769	1.00
51_A	57_K	0.760	1.00
94_W	98_L	0.760	1.00
73_A	80_A	0.746	1.00
95_A	100_G	0.744	1.00
106_E	112_G	0.720	1.00
49_A	53_L	0.718	1.00
52_Q	55_I	0.717	1.00
81_A	85_N	0.715	1.00
69_G	76_W	0.706	1.00
44_A	48_L	0.706	1.00
17_D	21_K	0.704	1.00
85_N	106_E	0.701	1.00
74_I	78_C	0.698	1.00
16_P	20_E	0.691	1.00
46_L	50_K	0.689	1.00
53_L	57_K	0.687	1.00
84_Y	92_L	0.682	1.00
69_G	73_A	0.675	1.00
8_G	13_K	0.674	1.00
15_I	21_K	0.671	1.00
23_K	26_L	0.654	0.99
59_E	67_V	0.644	0.99
82_L	110_L	0.644	0.99
48_L	52_Q	0.643	0.99
4_I	8_G	0.630	0.99
15_I	19_D	0.625	0.99
93_A	97_A	0.624	0.99
112_G	117_L	0.624	0.99
11_L	14_F	0.619	0.99
94_W	97_A	0.614	0.99
11_L	16_P	0.611	0.99
85_N	109_T	0.610	0.99
92_L	95_A	0.603	0.99
51_A	55_I	0.603	0.99
35_Q	44_A	0.601	0.99
82_L	111_L	0.600	0.99
56_N	60_A	0.593	0.99
82_L	85_N	0.591	0.99
86_F	106_E	0.590	0.99
30_L	36_A	0.580	0.99
82_L	108_W	0.577	0.99
12_D	16_P	0.577	0.99
81_A	84_Y	0.577	0.99
19_D	24_A	0.574	0.99
89_Q	92_L	0.571	0.99
25_K	31_A	0.568	0.98
86_F	110_L	0.568	0.98
89_Q	96_L	0.565	0.98
29_E	34_Q	0.562	0.98
77_V	81_A	0.560	0.98
54_E	58_A	0.559	0.98
4_I	9_K	0.556	0.98
33_L	36_A	0.556	0.98
92_L	96_L	0.555	0.98
13_K	17_D	0.549	0.98
26_L	29_E	0.542	0.98
91_L	94_W	0.541	0.98
30_L	35_Q	0.538	0.98
80_A	84_Y	0.533	0.98
8_G	11_L	0.533	0.98
82_L	107_L	0.533	0.98
55_I	59_E	0.532	0.98
108_W	111_L	0.530	0.98
19_D	26_L	0.520	0.97
75_G	78_C	0.517	0.97
6_P	16_P	0.517	0.97
16_P	23_K	0.509	0.97
10_L	15_I	0.501	0.97
81_A	108_W	0.500	0.97

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
1j6rA	1	0.8455	16.4	0.899	Contact Map
4wd8A	3	0.4146	13.5	0.903	Contact Map
3bulA	1	0.9106	10.2	0.908	Contact Map
1mskA	1	0.9106	8.2	0.912	Contact Map
2m8rA	1	0.7805	6.5	0.916	Contact Map
4rdqA	5	0.6016	5.8	0.918	Contact Map
3fewX	1	0.9837	5.4	0.919	Contact Map
2i88A	1	0.9593	5.3	0.92	Contact Map
1rh1A	1	0.9431	5.2	0.92	Contact Map
1a87A	1	0.9919	4.4	0.922	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 0.0052 seconds.