DUF2141 - PFAM28P - GREMLIN Contacts

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DUF2141 - Uncharacterized protein conserved in bacteria (DUF2141)

PFAM:	PF09912	Sequences: VTVTGLRNDKGQVRVALYDSEEGFPKKGGKAVRGAVVPIKAGTATVTFEDLPPGTYAVAVFHDENGNGKLDTNFLGIPKEGYGFSNNARGRFGPPSFEDAKFEVGGGDTTIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	112 (108)
Sequences:	14177 (11045)
Seq/√Len:	1062.8
META:	0.92

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_T	101_K	3.987	1.00
12_Q	66_G	3.497	1.00
55_T	103_E	3.373	1.00
65_N	71_D	3.137	1.00
15_V	46_V	2.707	1.00
67_N	71_D	2.681	1.00
6_L	13_V	2.595	1.00
64_E	81_G	2.383	1.00
61_F	70_L	2.135	1.00
14_R	61_F	2.131	1.00
2_T	45_T	2.125	1.00
7_R	81_G	2.080	1.00
20_S	23_G	1.857	1.00
14_R	36_V	1.816	1.00
73_N	77_I	1.723	1.00
2_T	43_T	1.720	1.00
57_A	100_A	1.711	1.00
62_H	81_G	1.700	1.00
73_N	79_K	1.698	1.00
3_V	60_V	1.685	1.00
12_Q	36_V	1.567	1.00
53_P	106_G	1.467	1.00
8_N	64_E	1.413	1.00
18_Y	59_A	1.410	1.00
73_N	76_G	1.386	1.00
96_S	99_D	1.364	1.00
97_F	101_K	1.363	1.00
25_P	59_A	1.337	1.00
9_D	42_G	1.298	1.00
67_N	80_E	1.262	1.00
16_A	59_A	1.231	1.00
105_G	108_D	1.218	1.00
85_S	102_F	1.211	1.00
18_Y	23_G	1.198	1.00
4_T	43_T	1.196	1.00
53_P	105_G	1.179	1.00
35_A	46_V	1.171	1.00
93_G	99_D	1.163	1.00
65_N	80_E	1.150	1.00
24_F	100_A	1.147	1.00
24_F	57_A	1.136	1.00
53_P	104_V	1.125	1.00
98_E	101_K	1.120	1.00
53_P	107_G	1.117	1.00
70_L	82_Y	1.107	1.00
17_L	48_F	1.079	1.00
60_V	83_G	1.077	1.00
11_G	62_H	1.065	1.00
17_L	51_L	1.061	1.00
17_L	58_V	1.057	1.00
82_Y	90_G	1.052	1.00
72_T	76_G	1.045	1.00
19_D	23_G	1.041	1.00
84_F	100_A	1.035	1.00
13_V	44_A	1.023	1.00
27_K	30_K	1.008	1.00
14_R	68_G	0.998	1.00
74_F	79_K	0.950	1.00
9_D	39_I	0.938	1.00
71_D	80_E	0.932	1.00
19_D	52_P	0.921	1.00
31_A	34_G	0.912	1.00
64_E	80_E	0.903	1.00
12_Q	68_G	0.901	1.00
39_I	44_A	0.897	1.00
12_Q	38_P	0.883	1.00
10_K	64_E	0.866	1.00
6_L	39_I	0.855	1.00
63_D	67_N	0.851	1.00
35_A	38_P	0.844	1.00
21_E	98_E	0.843	1.00
15_V	48_F	0.842	1.00
41_A	44_A	0.825	1.00
58_V	83_G	0.825	1.00
28_G	31_A	0.823	1.00
47_T	50_D	0.819	1.00
17_L	56_Y	0.809	1.00
3_V	13_V	0.809	1.00
84_F	88_A	0.808	1.00
15_V	35_A	0.799	1.00
3_V	6_L	0.796	1.00
88_A	99_D	0.791	1.00
9_D	41_A	0.779	1.00
37_V	46_V	0.779	1.00
7_R	64_E	0.773	1.00
83_G	87_N	0.772	1.00
6_L	44_A	0.771	1.00
18_Y	31_A	0.763	1.00
35_A	48_F	0.759	1.00
36_V	39_I	0.745	1.00
72_T	75_L	0.745	1.00
20_S	24_F	0.741	1.00
1_V	58_V	0.735	1.00
93_G	96_S	0.730	1.00
95_P	100_A	0.726	1.00
15_V	60_V	0.713	1.00
94_P	100_A	0.707	1.00
8_N	62_H	0.704	1.00
23_G	29_G	0.700	1.00
71_D	79_K	0.697	1.00
16_A	34_G	0.695	1.00
3_V	15_V	0.694	1.00
21_E	25_P	0.692	1.00
63_D	68_G	0.692	1.00
1_V	48_F	0.691	1.00
9_D	40_K	0.688	1.00
37_V	44_A	0.685	1.00
70_L	80_E	0.684	1.00
88_A	100_A	0.683	1.00
59_A	84_F	0.660	1.00
19_D	32_V	0.656	1.00
51_L	54_G	0.653	1.00
35_A	49_E	0.650	1.00
104_V	107_G	0.643	1.00
70_L	79_K	0.641	1.00
34_G	37_V	0.626	1.00
55_T	97_F	0.625	1.00
23_G	30_K	0.623	1.00
90_G	93_G	0.619	1.00
40_K	44_A	0.617	1.00
51_L	56_Y	0.615	1.00
48_F	51_L	0.613	1.00
59_A	82_Y	0.608	1.00
6_L	81_G	0.607	1.00
87_N	90_G	0.603	1.00
57_A	85_S	0.603	1.00
61_F	81_G	0.601	1.00
77_I	82_Y	0.594	1.00
17_L	50_D	0.593	1.00
16_A	61_F	0.590	1.00
36_V	68_G	0.588	1.00
90_G	99_D	0.586	1.00
51_L	104_V	0.585	1.00
82_Y	87_N	0.584	1.00
19_D	56_Y	0.582	1.00
86_N	101_K	0.581	1.00
84_F	99_D	0.579	1.00
6_L	60_V	0.569	1.00
70_L	78_P	0.557	1.00
20_S	97_F	0.556	1.00
27_K	31_A	0.556	1.00
46_V	49_E	0.553	1.00
72_T	77_I	0.550	1.00
58_V	102_F	0.549	1.00
8_N	42_G	0.548	1.00
24_F	59_A	0.541	1.00
84_F	90_G	0.540	1.00
23_G	31_A	0.539	1.00
7_R	10_K	0.529	1.00
55_T	98_E	0.529	1.00
12_Q	35_A	0.523	1.00
18_Y	30_K	0.522	1.00
30_K	38_P	0.522	1.00
8_N	39_I	0.522	1.00
6_L	62_H	0.521	1.00
6_L	9_D	0.517	1.00
52_P	55_T	0.511	1.00
9_D	44_A	0.511	1.00
56_Y	102_F	0.505	1.00
13_V	60_V	0.503	1.00
57_A	97_F	0.501	1.00
53_P	108_D	0.500	1.00

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
3ghpA	1	0.8661	16.3	0.898	Contact Map
2xwxA	2	0.6607	10.2	0.907	Contact Map
3gf8A	1	0.9554	9.5	0.908	Contact Map
1nqjA	1	0.5804	8.5	0.91	Contact Map
3iduA	1	0.6607	8.3	0.911	Contact Map
4m29A	1	0.7321	7.3	0.913	Contact Map
3payA	4	0.8482	6.9	0.914	Contact Map
3jqwA	1	0.6071	6.6	0.914	Contact Map
4qtqA	1	0.9196	6.5	0.915	Contact Map
3vnyA	3	0.8304	5.8	0.917	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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