RcpC - PFAM28P - GREMLIN Contacts

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RcpC - Flp pilus assembly protein RcpC/CpaB

PFAM:	PF16976	Sequences: GGLAAVLPPGMRAVSVPVDDVSGVAGFILPGDRVDVLLTGGAGGGGGGGGTVTRTVLQNVRVLAVGQATAATTADDDGGKPVVAKTASTVTLEVTPEQAEKLALAQSEGTLSLALR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (108)
Sequences:	31530 (20243)
Seq/√Len:	1947.9
META:	0.931

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_R	59_N	4.117	1.00
61_R	93_E	2.886	1.00
95_T	98_Q	2.818	1.00
11_M	93_E	2.778	1.00
12_R	35_D	2.716	1.00
8_P	93_E	2.305	1.00
33_R	61_R	2.210	1.00
37_L	55_T	2.060	1.00
39_T	53_T	2.017	1.00
13_A	63_L	1.988	1.00
11_M	95_T	1.877	1.00
107_S	110_T	1.839	1.00
57_L	60_V	1.675	1.00
90_V	113_L	1.662	1.00
94_V	102_L	1.654	1.00
15_S	91_T	1.654	1.00
19_D	22_S	1.649	1.00
104_L	108_E	1.648	1.00
8_P	11_M	1.629	1.00
60_V	94_V	1.603	1.00
17_P	21_V	1.587	1.00
13_A	91_T	1.584	1.00
56_V	105_A	1.569	1.00
28_I	62_V	1.527	1.00
106_Q	112_S	1.524	1.00
38_L	109_G	1.498	1.00
4_A	32_D	1.490	1.00
99_A	114_A	1.426	1.00
53_T	104_L	1.366	1.00
57_L	102_L	1.359	1.00
36_V	113_L	1.356	1.00
31_G	61_R	1.306	1.00
37_L	53_T	1.289	1.00
65_V	90_V	1.275	1.00
55_T	100_E	1.253	1.00
97_E	101_K	1.249	1.00
98_Q	101_K	1.240	1.00
15_S	89_T	1.227	1.00
63_L	93_E	1.226	1.00
103_A	112_S	1.221	1.00
38_L	105_A	1.211	1.00
29_L	32_D	1.183	1.00
27_F	64_A	1.162	1.00
36_V	102_L	1.160	1.00
37_L	114_A	1.154	1.00
57_L	98_Q	1.140	1.00
94_V	99_A	1.125	1.00
30_P	64_A	1.109	1.00
38_L	56_V	1.100	1.00
12_R	96_P	1.085	1.00
11_M	98_Q	1.060	1.00
17_P	106_Q	1.033	1.00
36_V	60_V	1.030	1.00
95_T	99_A	1.028	1.00
37_L	100_E	1.010	1.00
8_P	61_R	0.991	1.00
60_V	98_Q	0.989	1.00
75_D	78_G	0.977	1.00
34_V	113_L	0.968	1.00
73_T	76_D	0.968	1.00
11_M	61_R	0.956	1.00
28_I	90_V	0.948	1.00
66_G	91_T	0.947	1.00
14_V	94_V	0.939	1.00
35_D	58_Q	0.934	1.00
55_T	58_Q	0.932	1.00
76_D	79_G	0.922	1.00
72_T	75_D	0.917	1.00
12_R	114_A	0.884	1.00
18_V	23_G	0.876	1.00
41_G	44_G	0.864	1.00
16_V	92_L	0.861	1.00
39_T	103_A	0.858	1.00
7_L	11_M	0.855	1.00
18_V	22_S	0.846	1.00
17_P	20_D	0.844	1.00
57_L	94_V	0.842	1.00
20_D	66_G	0.841	1.00
55_T	114_A	0.841	1.00
39_T	112_S	0.838	1.00
20_D	88_S	0.837	1.00
14_V	103_A	0.835	1.00
51_T	108_E	0.829	1.00
100_E	104_L	0.819	1.00
38_L	108_E	0.815	1.00
35_D	116_R	0.810	1.00
14_V	102_L	0.809	1.00
83_V	86_T	0.802	1.00
58_Q	96_P	0.802	1.00
15_S	24_V	0.784	1.00
103_A	106_Q	0.778	1.00
15_S	25_A	0.765	1.00
7_L	93_E	0.757	1.00
36_V	92_L	0.757	1.00
30_P	65_V	0.751	1.00
19_D	110_T	0.746	1.00
105_A	111_L	0.739	1.00
38_L	54_R	0.729	1.00
46_G	49_G	0.729	1.00
54_R	100_E	0.724	1.00
28_I	32_D	0.722	1.00
34_V	92_L	0.719	1.00
35_D	55_T	0.718	1.00
62_V	90_V	0.715	1.00
60_V	92_L	0.711	1.00
20_D	23_G	0.700	1.00
45_G	48_G	0.699	1.00
17_P	89_T	0.690	1.00
35_D	59_N	0.686	1.00
39_T	104_L	0.684	1.00
107_S	112_S	0.684	1.00
14_V	99_A	0.673	1.00
57_L	101_K	0.659	1.00
22_S	112_S	0.658	1.00
72_T	82_V	0.652	1.00
64_A	91_T	0.643	1.00
74_A	80_K	0.627	1.00
42_A	45_G	0.624	1.00
74_A	77_D	0.623	1.00
75_D	79_G	0.621	1.00
55_T	96_P	0.620	1.00
103_A	107_S	0.620	1.00
25_A	89_T	0.614	1.00
16_V	102_L	0.613	1.00
86_T	89_T	0.608	1.00
81_P	84_A	0.608	1.00
28_I	65_V	0.605	1.00
82_V	85_K	0.601	1.00
73_T	78_G	0.592	1.00
51_T	107_S	0.584	1.00
80_K	83_V	0.581	1.00
73_T	82_V	0.576	1.00
37_L	103_A	0.574	1.00
72_T	76_D	0.574	1.00
24_V	28_I	0.573	1.00
66_G	88_S	0.565	1.00
43_G	46_G	0.565	1.00
79_G	82_V	0.561	1.00
73_T	77_D	0.559	1.00
96_P	100_E	0.557	1.00
92_L	102_L	0.549	1.00
42_A	50_G	0.547	1.00
22_S	107_S	0.544	1.00
37_L	99_A	0.543	1.00
47_G	50_G	0.540	1.00
72_T	77_D	0.539	1.00
77_D	80_K	0.537	1.00
76_D	80_K	0.534	1.00
18_V	90_V	0.533	1.00
72_T	79_G	0.530	1.00
41_G	49_G	0.522	1.00
41_G	45_G	0.520	1.00
39_T	108_E	0.520	1.00
43_G	49_G	0.517	1.00
36_V	56_V	0.517	1.00
42_A	49_G	0.514	1.00
73_T	80_K	0.511	1.00
66_G	89_T	0.509	1.00
97_E	100_E	0.508	1.00
72_T	78_G	0.505	1.00
39_T	107_S	0.502	1.00
53_T	103_A	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
1ltlA	4	0.5431	76.8	0.807	Contact Map
4pofA	3	0.5603	67	0.82	Contact Map
4me3A	1	0.5172	65.5	0.822	Contact Map
3ja87	1	0.8534	59.1	0.829	Contact Map
4fdgB	1	0.8534	57.8	0.83	Contact Map
3ja85	1	0.8621	56.1	0.832	Contact Map
4r7yA	3	0.8448	49.9	0.838	Contact Map
3ja82	1	0.7759	44.9	0.843	Contact Map
3ja83	1	0.8448	43.6	0.844	Contact Map
3ja84	1	0.9914	33.5	0.854	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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