DUF2877 - PFAM28P - GREMLIN Contacts

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DUF2877 - Protein of unknown function (DUF2877)

PFAM:	PF11392	Sequences: LIGLGPGLTPSGDDFLAGLLAALRALGRPAAAAALAAAALLAAAAGRTTAISAALLRAAARGEASEPLHALLAALAAGDPDALAAALARLLAIGHTSGADLLAGLLLGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	109 (108)
Sequences:	5316 (4171)
Seq/√Len:	401.4
META:	0.916

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_A	64_A	5.244	1.00
11_S	100_D	4.115	1.00
15_F	107_L	3.488	1.00
22_A	105_L	2.879	1.00
91_L	99_A	2.723	1.00
68_L	105_L	2.311	1.00
68_L	101_L	2.280	1.00
8_L	51_I	2.091	1.00
54_A	58_A	2.054	1.00
64_A	69_H	2.009	1.00
90_L	102_L	2.003	1.00
19_L	108_G	1.846	1.00
70_A	89_R	1.843	1.00
17_A	59_A	1.833	1.00
45_A	53_A	1.821	1.00
22_A	108_G	1.757	1.00
65_S	101_L	1.714	1.00
65_S	93_I	1.630	1.00
67_P	93_I	1.611	1.00
87_L	102_L	1.592	1.00
53_A	57_R	1.552	1.00
72_L	105_L	1.527	1.00
58_A	63_E	1.517	1.00
9_T	14_D	1.477	1.00
15_F	103_A	1.437	1.00
1_L	12_G	1.333	1.00
6_P	11_S	1.311	1.00
37_A	41_L	1.303	1.00
44_A	53_A	1.275	1.00
11_S	96_T	1.247	1.00
21_A	68_L	1.244	1.00
69_H	73_A	1.235	1.00
51_I	55_L	1.235	1.00
79_D	82_A	1.204	1.00
35_L	39_A	1.191	1.00
46_G	53_A	1.187	1.00
17_A	21_A	1.177	1.00
56_L	59_A	1.170	1.00
79_D	83_L	1.103	1.00
20_L	60_A	1.099	1.00
17_A	55_L	1.094	1.00
71_L	90_L	1.084	1.00
18_G	22_A	1.082	1.00
17_A	64_A	1.079	1.00
74_A	86_A	1.074	1.00
45_A	57_R	1.057	1.00
66_E	70_A	1.054	1.00
49_T	53_A	1.050	1.00
55_L	58_A	1.038	1.00
57_R	61_R	1.030	1.00
36_A	41_L	1.017	1.00
48_T	52_S	0.994	1.00
58_A	61_R	0.994	1.00
90_L	93_I	0.993	1.00
36_A	40_L	0.986	1.00
38_A	42_A	0.984	1.00
33_A	36_A	0.961	1.00
43_A	46_G	0.957	1.00
33_A	37_A	0.947	1.00
14_D	97_S	0.944	1.00
37_A	40_L	0.941	1.00
47_R	53_A	0.926	1.00
14_D	94_G	0.909	1.00
55_L	65_S	0.897	1.00
101_L	105_L	0.896	1.00
71_L	105_L	0.894	1.00
17_A	101_L	0.886	1.00
22_A	26_L	0.884	1.00
21_A	69_H	0.881	1.00
55_L	101_L	0.855	1.00
3_G	7_G	0.852	1.00
6_P	100_D	0.852	1.00
30_A	33_A	0.837	1.00
64_A	68_L	0.836	1.00
15_F	19_L	0.825	1.00
71_L	102_L	0.822	1.00
86_A	89_R	0.820	1.00
2_I	56_L	0.817	1.00
15_F	100_D	0.811	1.00
74_A	83_L	0.804	1.00
25_A	72_L	0.797	1.00
94_G	97_S	0.789	1.00
68_L	90_L	0.787	1.00
18_G	101_L	0.779	1.00
50_A	54_A	0.777	1.00
52_S	56_L	0.752	1.00
21_A	72_L	0.746	1.00
11_S	15_F	0.741	1.00
6_P	96_T	0.740	1.00
88_A	92_A	0.740	1.00
80_P	89_R	0.735	1.00
70_A	86_A	0.731	1.00
33_A	39_A	0.731	1.00
21_A	59_A	0.730	1.00
50_A	53_A	0.728	1.00
2_I	46_G	0.725	1.00
52_S	55_L	0.720	1.00
81_D	85_A	0.719	1.00
20_L	24_R	0.711	1.00
39_A	42_A	0.710	1.00
103_A	107_L	0.706	1.00
25_A	73_A	0.703	1.00
9_T	52_S	0.703	1.00
84_A	88_A	0.699	1.00
55_L	68_L	0.690	1.00
17_A	68_L	0.687	1.00
19_L	69_H	0.686	1.00
9_T	94_G	0.685	1.00
9_T	97_S	0.676	0.99
87_L	91_L	0.674	0.99
85_A	89_R	0.654	0.99
89_R	92_A	0.651	0.99
55_L	63_E	0.650	0.99
24_R	64_A	0.643	0.99
94_G	98_G	0.631	0.99
51_I	64_A	0.629	0.99
22_A	100_D	0.628	0.99
17_A	56_L	0.623	0.99
4_L	55_L	0.621	0.99
21_A	105_L	0.618	0.99
54_A	57_R	0.617	0.99
75_L	78_G	0.615	0.99
38_A	41_L	0.615	0.99
8_L	93_I	0.615	0.99
66_E	69_H	0.606	0.99
26_L	76_A	0.606	0.99
25_A	69_H	0.599	0.99
64_A	101_L	0.597	0.99
19_L	23_L	0.591	0.99
24_R	62_G	0.591	0.99
93_I	96_T	0.586	0.98
7_G	10_P	0.581	0.98
22_A	72_L	0.578	0.98
2_I	45_A	0.578	0.98
25_A	29_P	0.576	0.98
2_I	68_L	0.572	0.98
47_R	50_A	0.571	0.98
28_R	31_A	0.570	0.98
100_D	103_A	0.567	0.98
36_A	39_A	0.565	0.98
84_A	87_L	0.561	0.98
11_S	99_A	0.556	0.98
73_A	77_A	0.553	0.98
96_T	100_D	0.553	0.98
77_A	82_A	0.549	0.98
82_A	86_A	0.548	0.98
8_L	49_T	0.548	0.98
6_P	16_L	0.539	0.97
71_L	86_A	0.539	0.97
65_S	90_L	0.538	0.97
45_A	60_A	0.532	0.97
51_I	54_A	0.530	0.97
32_A	36_A	0.529	0.97
34_A	38_A	0.528	0.97
85_A	92_A	0.526	0.97
23_L	34_A	0.524	0.97
81_D	84_A	0.524	0.97
68_L	102_L	0.523	0.97
73_A	88_A	0.523	0.97
60_A	63_E	0.507	0.96
51_I	100_D	0.500	0.96
11_S	95_H	0.500	0.96

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
3e1hA	2	0.9174	25.4	0.897	Contact Map
1ee0A	2	0.9541	25	0.897	Contact Map
2p0uA	2	0.9358	24.2	0.897	Contact Map
3awkA	2	0.9358	20.5	0.901	Contact Map
3a5rA	2	0.9725	18	0.903	Contact Map
3wxyA	2	0.9633	17.8	0.903	Contact Map
4jaqD	2	0.9817	17.4	0.904	Contact Map
3wd8A	2	0.9358	16.9	0.905	Contact Map
1xesA	2	0.945	16.7	0.905	Contact Map
3euoA	2	0.9174	16.4	0.905	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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