DUF2183 - PFAM28P - GREMLIN Contacts

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DUF2183 - Uncharacterized conserved protein (DUF2183)

PFAM:	PF09949	Sequences: FFYVSSSPWNLYDPLEEFLRRNGFPAGPLLLRDWGPTLDGLFRSGSGREHKLAAIRRLLETFPDLRFILIGDSGQHDPEIYAEIAREFPGRVLAIYIRDV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	100 (99)
Sequences:	6460 (4145)
Seq/√Len:	416.6
META:	0.845

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_R	87_E	3.800	1.00
66_R	93_L	3.036	1.00
85_A	95_I	2.947	1.00
3_Y	27_G	2.716	1.00
83_E	87_E	2.496	1.00
59_L	84_I	2.460	1.00
82_A	86_R	2.447	1.00
52_L	83_E	2.434	1.00
73_S	97_I	2.407	1.00
5_S	31_L	2.400	1.00
60_E	88_F	2.173	1.00
56_R	88_F	2.154	1.00
56_R	60_E	2.065	1.00
6_S	47_G	1.944	1.00
19_L	29_L	1.893	1.00
59_L	91_R	1.893	1.00
59_L	92_V	1.835	1.00
57_R	61_T	1.774	1.00
73_S	99_D	1.691	1.00
37_T	40_G	1.676	1.00
6_S	50_H	1.571	1.00
4_V	55_I	1.525	1.00
2_F	30_L	1.519	1.00
68_I	94_A	1.516	1.00
52_L	56_R	1.472	1.00
48_R	76_H	1.419	1.00
83_E	86_R	1.353	1.00
59_L	67_F	1.320	1.00
19_L	24_F	1.305	1.00
40_G	43_R	1.283	1.00
52_L	87_E	1.262	1.00
2_F	28_P	1.217	1.00
69_L	92_V	1.205	1.00
30_L	54_A	1.203	1.00
20_R	26_A	1.171	1.00
6_S	75_Q	1.099	1.00
79_E	82_A	1.075	1.00
82_A	85_A	1.068	1.00
55_I	84_I	1.054	1.00
2_F	62_F	1.043	1.00
38_L	41_L	1.040	1.00
50_H	54_A	1.039	1.00
17_E	21_R	1.032	1.00
16_E	20_R	1.031	1.00
7_S	15_L	1.022	1.00
52_L	80_I	1.021	1.00
53_A	57_R	1.007	1.00
57_R	60_E	1.005	1.00
58_L	67_F	1.004	1.00
8_P	11_L	0.994	1.00
46_S	49_E	0.993	1.00
2_F	58_L	0.988	1.00
54_A	57_R	0.971	1.00
71_G	77_D	0.956	1.00
55_I	59_L	0.940	1.00
15_L	29_L	0.910	1.00
11_L	14_P	0.907	1.00
6_S	48_R	0.906	1.00
52_L	84_I	0.885	1.00
49_E	53_A	0.882	1.00
16_E	26_A	0.874	1.00
28_P	65_L	0.862	1.00
7_S	10_N	0.855	1.00
58_L	61_T	0.847	1.00
47_G	50_H	0.842	1.00
12_Y	16_E	0.842	1.00
67_F	91_R	0.834	1.00
81_Y	97_I	0.832	1.00
55_I	80_I	0.822	1.00
7_S	11_L	0.820	1.00
88_F	91_R	0.816	1.00
40_G	44_S	0.779	1.00
66_R	90_G	0.777	1.00
8_P	75_Q	0.772	1.00
76_H	79_E	0.769	1.00
36_P	40_G	0.767	1.00
48_R	80_I	0.759	1.00
36_P	41_L	0.757	1.00
2_F	65_L	0.753	1.00
48_R	52_L	0.750	1.00
1_F	24_F	0.734	1.00
51_K	77_D	0.732	1.00
51_K	72_D	0.710	1.00
68_I	96_Y	0.706	1.00
35_G	38_L	0.705	1.00
9_W	12_Y	0.701	1.00
18_F	22_N	0.698	1.00
62_F	65_L	0.696	1.00
14_P	17_E	0.689	1.00
14_P	21_R	0.687	1.00
15_L	31_L	0.686	1.00
20_R	23_G	0.684	1.00
37_T	43_R	0.684	1.00
50_H	80_I	0.677	1.00
32_R	43_R	0.667	0.99
39_D	42_F	0.660	0.99
8_P	32_R	0.654	0.99
50_H	53_A	0.652	0.99
4_V	30_L	0.642	0.99
6_S	9_W	0.637	0.99
53_A	56_R	0.633	0.99
70_I	74_G	0.632	0.99
13_D	17_E	0.627	0.99
7_S	32_R	0.621	0.99
78_P	82_A	0.616	0.99
76_H	80_I	0.616	0.99
36_P	42_F	0.614	0.99
3_Y	25_P	0.604	0.99
37_T	42_F	0.603	0.99
9_W	31_L	0.601	0.99
39_D	46_S	0.599	0.99
84_I	88_F	0.594	0.99
65_L	73_S	0.593	0.99
32_R	75_Q	0.592	0.99
47_G	52_L	0.591	0.99
47_G	76_H	0.588	0.99
47_G	75_Q	0.582	0.99
4_V	58_L	0.579	0.99
41_L	45_G	0.560	0.98
77_D	97_I	0.560	0.98
56_R	84_I	0.559	0.98
16_E	19_L	0.558	0.98
32_R	47_G	0.553	0.98
59_L	69_L	0.549	0.98
3_Y	24_F	0.543	0.98
17_E	20_R	0.543	0.98
59_L	88_F	0.541	0.98
32_R	50_H	0.536	0.98
60_E	64_D	0.533	0.98
66_R	91_R	0.531	0.97
42_F	45_G	0.529	0.97
41_L	44_S	0.528	0.97
7_S	31_L	0.527	0.97
5_S	9_W	0.526	0.97
43_R	47_G	0.525	0.97
38_L	43_R	0.523	0.97
40_G	45_G	0.521	0.97
47_G	80_I	0.517	0.97
10_N	14_P	0.513	0.97
78_P	95_I	0.512	0.97
4_V	74_G	0.511	0.97
35_G	40_G	0.508	0.97
24_F	85_A	0.507	0.97
44_S	47_G	0.507	0.97
79_E	83_E	0.505	0.97
46_S	50_H	0.504	0.97
30_L	58_L	0.503	0.96
9_W	34_W	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
2i33A	2	0.83	71.5	0.854	Contact Map
4xrpA	2	0.86	47.9	0.874	Contact Map
4gxtA	1	0.92	45	0.876	Contact Map
3zvlA	1	0.9	42.7	0.878	Contact Map
3pctA	2	0.83	40	0.88	Contact Map
2o2xA	1	0.99	37.7	0.882	Contact Map
4fypA	2	0.82	34.4	0.884	Contact Map
2gmwA	1	0.99	30.2	0.887	Contact Map
4ovyA	2	0.93	30	0.887	Contact Map
2wm8A	1	0.78	28.7	0.888	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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