RseC_MucC - PFAM28P - GREMLIN Contacts

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RseC_MucC - Positive regulator of sigma(E), RseC/MucC

PFAM:	PF04246	Sequences: VVSIEGGTAWVEIERSSACGSCAAKGGCKLASGSKEKEIEVPNPLGAKVGDRVEVGIPESALLKAALLVYLLPLLLLLAGALLGSALAGGSELLAALGGLLGLALGFLILRLFRRRLKKKFRFQPVILR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (125)
Sequences:	10008 (8298)
Seq/√Len:	742.2
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_T	40_E	3.500	1.00
80_G	102_G	3.295	1.00
3_S	10_W	3.228	1.00
10_W	40_E	3.216	1.00
2_V	12_E	2.917	1.00
84_G	98_G	2.768	1.00
43_N	47_A	2.662	1.00
12_E	36_E	2.594	1.00
10_W	38_E	2.365	1.00
106_G	110_L	2.299	1.00
77_L	99_G	2.193	1.00
43_N	46_G	2.162	1.00
80_G	84_G	2.155	1.00
76_L	106_G	2.137	1.00
12_E	38_E	2.104	1.00
48_K	51_D	2.053	1.00
4_I	49_V	1.843	1.00
111_R	114_R	1.829	1.00
81_A	99_G	1.824	1.00
76_L	102_G	1.814	1.00
109_I	113_F	1.773	1.00
63_L	66_A	1.753	1.00
5_E	10_W	1.662	1.00
67_L	71_L	1.628	1.00
15_R	37_K	1.588	1.00
108_L	112_L	1.536	1.00
96_A	100_L	1.526	1.00
76_L	80_G	1.523	1.00
62_L	66_A	1.519	1.00
102_G	106_G	1.508	1.00
13_I	55_V	1.489	1.00
3_S	49_V	1.476	1.00
111_R	115_R	1.462	1.00
81_A	95_A	1.452	1.00
2_V	38_E	1.417	1.00
80_G	98_G	1.413	1.00
62_L	70_Y	1.375	1.00
95_A	99_G	1.370	1.00
98_G	102_G	1.328	1.00
59_E	63_L	1.321	1.00
4_I	9_A	1.270	1.00
9_A	47_A	1.228	1.00
1_V	47_A	1.217	1.00
8_T	42_P	1.210	1.00
85_S	95_A	1.198	1.00
114_R	118_K	1.180	1.00
61_A	64_K	1.170	1.00
82_L	86_A	1.158	1.00
84_G	88_A	1.110	1.00
1_V	4_I	1.058	1.00
103_L	107_F	1.056	1.00
103_L	106_G	1.045	1.00
94_L	98_G	1.038	1.00
68_L	72_L	1.029	1.00
7_G	42_P	1.013	1.00
110_L	114_R	0.992	1.00
92_E	95_A	0.989	1.00
9_A	43_N	0.980	1.00
93_L	97_L	0.980	1.00
68_L	110_L	0.977	1.00
5_E	8_T	0.974	1.00
5_E	40_E	0.969	1.00
74_L	78_L	0.925	1.00
15_R	18_A	0.924	1.00
78_L	82_L	0.921	1.00
90_G	94_L	0.919	1.00
91_S	94_L	0.900	1.00
100_L	103_L	0.899	1.00
104_A	108_L	0.888	1.00
84_G	90_G	0.882	1.00
37_K	41_V	0.876	1.00
84_G	89_G	0.876	1.00
95_A	98_G	0.873	1.00
64_K	120_K	0.873	1.00
34_S	37_K	0.867	1.00
92_E	96_A	0.867	1.00
57_I	62_L	0.838	1.00
31_A	37_K	0.838	1.00
31_A	35_K	0.837	1.00
44_P	47_A	0.837	1.00
84_G	95_A	0.833	1.00
63_L	67_L	0.831	1.00
47_A	51_D	0.831	1.00
72_L	76_L	0.831	1.00
108_L	111_R	0.829	1.00
57_I	61_A	0.822	1.00
65_A	69_V	0.810	1.00
117_L	120_K	0.804	1.00
21_S	25_K	0.803	1.00
2_V	10_W	0.801	1.00
66_A	70_Y	0.798	1.00
14_E	36_E	0.797	1.00
93_L	96_A	0.786	1.00
29_K	32_S	0.776	1.00
17_S	20_G	0.774	1.00
77_L	103_L	0.769	1.00
18_A	21_S	0.757	1.00
58_P	61_A	0.751	1.00
32_S	37_K	0.746	1.00
115_R	118_K	0.740	1.00
20_G	25_K	0.738	1.00
89_G	94_L	0.737	1.00
23_A	26_G	0.736	1.00
67_L	75_L	0.729	1.00
57_I	70_Y	0.727	1.00
113_F	117_L	0.722	1.00
32_S	35_K	0.722	1.00
7_G	43_N	0.716	1.00
3_S	38_E	0.716	1.00
23_A	27_G	0.714	1.00
79_A	83_L	0.697	1.00
24_A	27_G	0.694	1.00
83_L	87_L	0.691	1.00
56_G	59_E	0.687	1.00
79_A	82_L	0.685	1.00
100_L	104_A	0.681	1.00
112_L	116_R	0.679	1.00
116_R	119_K	0.678	1.00
17_S	21_S	0.677	1.00
107_F	110_L	0.673	1.00
67_L	72_L	0.664	1.00
109_I	112_L	0.661	1.00
9_A	45_L	0.660	1.00
84_G	94_L	0.655	1.00
107_F	111_R	0.650	1.00
68_L	113_F	0.649	1.00
64_K	122_R	0.649	1.00
112_L	115_R	0.649	1.00
21_S	24_A	0.646	1.00
9_A	41_V	0.643	1.00
84_G	102_G	0.643	1.00
42_P	124_Q	0.639	1.00
60_S	122_R	0.636	1.00
114_R	117_L	0.629	1.00
10_W	13_I	0.627	1.00
71_L	75_L	0.623	1.00
116_R	120_K	0.614	1.00
60_S	64_K	0.610	1.00
113_F	116_R	0.605	1.00
20_G	23_A	0.604	1.00
27_G	31_A	0.603	1.00
99_G	103_L	0.601	1.00
11_V	55_V	0.598	1.00
76_L	110_L	0.598	1.00
74_L	81_A	0.597	1.00
69_V	107_F	0.597	1.00
66_A	74_L	0.593	1.00
85_S	92_E	0.591	1.00
24_A	70_Y	0.585	1.00
66_A	69_V	0.585	1.00
47_A	53_V	0.584	1.00
56_G	61_A	0.584	1.00
72_L	109_I	0.579	1.00
14_E	52_R	0.579	1.00
71_L	74_L	0.578	1.00
15_R	57_I	0.576	1.00
4_I	7_G	0.571	1.00
63_L	71_L	0.571	1.00
88_A	94_L	0.568	1.00
105_L	109_I	0.564	1.00
9_A	125_P	0.563	1.00
33_G	37_K	0.560	1.00
121_F	124_Q	0.559	1.00
122_R	125_P	0.556	1.00
85_S	91_S	0.553	1.00
92_E	99_G	0.550	1.00
101_L	104_A	0.549	1.00
69_V	110_L	0.546	1.00
13_I	62_L	0.545	1.00
13_I	37_K	0.528	1.00
69_V	73_P	0.527	1.00
72_L	106_G	0.525	1.00
89_G	98_G	0.525	1.00
105_L	108_L	0.525	1.00
21_S	26_G	0.524	1.00
90_G	93_L	0.522	1.00
17_S	23_A	0.521	1.00
62_L	81_A	0.521	1.00
70_Y	78_L	0.520	1.00
41_V	45_L	0.520	1.00
104_A	107_F	0.518	1.00
88_A	92_E	0.518	1.00
77_L	81_A	0.515	1.00
81_A	96_A	0.508	1.00
30_L	34_S	0.504	1.00
102_G	105_L	0.500	1.00
41_V	53_V	0.500	1.00
17_S	33_G	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
1vehA	1	0.4186	13.9	0.897	Contact Map
1kg2A	1	0.3411	12.1	0.899	Contact Map
2m5oA	1	0.4031	9.8	0.903	Contact Map
4ql5A	4	0.4574	9.2	0.904	Contact Map
3i4oA	1	0.4574	8.1	0.907	Contact Map
4toiA	2	0.3488	7.9	0.907	Contact Map
1xhjA	1	0.4419	7.3	0.909	Contact Map
2d9rA	1	0.4574	7.1	0.909	Contact Map
1oruA	2	0.4264	6.4	0.911	Contact Map
3pjyA	1	0.4109	6.3	0.912	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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