Tad_C - PFAM28P - GREMLIN Contacts

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Tad_C - Putative Tad-like Flp pilus-assembly

PFAM:	PF09977	Sequences: AGAAALADASANTAAARAAAAAAAALNGVDAAGGNSADVEFGYWDPDPTTATTRTFTPGATPPNAVRVTVRRTVPLFFARIFGISSVTVSATATA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	95 (90)
Sequences:	7243 (6477)
Seq/√Len:	682.7
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_R	92_T	3.123	1.00
40_E	67_R	2.748	1.00
17_R	21_A	2.682	1.00
76_L	87_V	2.627	1.00
18_A	22_A	2.301	1.00
69_T	92_T	2.299	1.00
19_A	22_A	2.264	1.00
76_L	79_A	1.963	1.00
65_A	94_T	1.883	1.00
23_A	26_L	1.729	1.00
22_A	26_L	1.701	1.00
13_T	17_R	1.696	1.00
15_A	19_A	1.690	1.00
5_A	8_D	1.659	1.00
14_A	18_A	1.658	1.00
80_R	85_S	1.611	1.00
53_T	56_F	1.605	1.00
67_R	94_T	1.590	1.00
6_L	10_S	1.544	1.00
19_A	23_A	1.542	1.00
31_A	34_G	1.504	1.00
73_T	88_T	1.498	1.00
52_T	55_T	1.427	1.00
71_R	90_S	1.411	1.00
38_D	71_R	1.332	1.00
79_A	82_F	1.309	1.00
7_A	11_A	1.300	1.00
16_A	20_A	1.299	1.00
41_F	44_W	1.276	1.00
4_A	8_D	1.264	1.00
76_L	80_R	1.259	1.00
4_A	7_A	1.255	1.00
51_A	56_F	1.239	1.00
54_R	57_T	1.210	1.00
5_A	10_S	1.184	1.00
24_A	29_V	1.173	1.00
23_A	27_N	1.170	1.00
21_A	25_A	1.157	1.00
38_D	41_F	1.153	1.00
5_A	9_A	1.122	1.00
69_T	90_S	1.116	1.00
48_P	51_A	1.108	1.00
84_I	87_V	1.085	1.00
18_A	21_A	1.075	1.00
70_V	91_A	1.072	1.00
24_A	28_G	1.021	1.00
76_L	84_I	1.007	1.00
6_L	11_A	1.005	1.00
6_L	9_A	1.001	1.00
71_R	88_T	1.001	1.00
39_V	42_G	0.980	1.00
4_A	11_A	0.961	1.00
41_F	45_D	0.957	1.00
7_A	10_S	0.956	1.00
49_T	53_T	0.953	1.00
40_E	69_T	0.944	1.00
24_A	27_N	0.933	1.00
43_Y	46_P	0.932	1.00
37_A	41_F	0.916	1.00
57_T	60_A	0.908	1.00
40_E	58_P	0.873	1.00
74_V	87_V	0.865	1.00
80_R	84_I	0.865	1.00
50_T	53_T	0.864	1.00
16_A	27_N	0.864	1.00
59_G	62_P	0.862	1.00
43_Y	64_N	0.862	1.00
43_Y	62_P	0.857	1.00
51_A	54_R	0.855	1.00
5_A	19_A	0.848	1.00
64_N	74_V	0.839	1.00
51_A	55_T	0.829	1.00
21_A	24_A	0.822	1.00
43_Y	63_P	0.817	1.00
44_W	65_A	0.816	1.00
4_A	10_S	0.812	1.00
42_G	45_D	0.796	1.00
48_P	55_T	0.794	1.00
15_A	18_A	0.791	1.00
56_F	59_G	0.790	1.00
49_T	52_T	0.772	1.00
37_A	40_E	0.758	1.00
26_L	29_V	0.745	1.00
79_A	87_V	0.727	1.00
36_S	39_V	0.727	1.00
23_A	29_V	0.723	1.00
50_T	54_R	0.696	1.00
50_T	57_T	0.685	1.00
64_N	70_V	0.673	1.00
70_V	74_V	0.664	1.00
73_T	86_S	0.662	1.00
8_D	11_A	0.654	1.00
14_A	17_R	0.654	1.00
21_A	27_N	0.652	1.00
22_A	27_N	0.648	1.00
36_S	41_F	0.647	1.00
55_T	58_P	0.646	1.00
51_A	57_T	0.645	1.00
52_T	56_F	0.645	1.00
36_S	40_E	0.645	1.00
75_P	80_R	0.622	1.00
39_V	45_D	0.617	1.00
42_G	46_P	0.610	1.00
32_A	35_N	0.606	1.00
20_A	24_A	0.595	1.00
55_T	59_G	0.590	1.00
48_P	54_R	0.585	1.00
20_A	68_V	0.585	1.00
48_P	53_T	0.577	1.00
51_A	58_P	0.572	1.00
41_F	66_V	0.571	1.00
4_A	9_A	0.570	1.00
59_G	63_P	0.566	1.00
29_V	70_V	0.565	1.00
77_F	80_R	0.564	1.00
56_F	60_A	0.550	1.00
31_A	37_A	0.541	1.00
40_E	43_Y	0.540	1.00
50_T	55_T	0.539	1.00
76_L	83_G	0.537	1.00
53_T	57_T	0.535	1.00
24_A	70_V	0.535	1.00
33_G	37_A	0.534	1.00
9_A	15_A	0.522	1.00
14_A	27_N	0.521	0.99
17_R	41_F	0.521	0.99
23_A	28_G	0.515	0.99
40_E	45_D	0.514	0.99
77_F	82_F	0.510	0.99
19_A	26_L	0.510	0.99
77_F	81_I	0.503	0.99
49_T	56_F	0.501	0.99
54_R	60_A	0.501	0.99
65_A	77_F	0.500	0.99
13_T	16_A	0.500	0.99

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
2rmgA	1	0.2947	1.2	0.906	Contact Map
2pjvA	1	0.2526	1.1	0.907	Contact Map
2rmhA	1	0.2947	0.8	0.915	Contact Map
2h9uA	2	0.3789	0.7	0.918	Contact Map
4ui9T	1	0.2105	0.7	0.919	Contact Map
4nnoA	1	0.3263	0.7	0.92	Contact Map
3mfqA	1	0.3368	0.6	0.922	Contact Map
4cl2A	1	0.3263	0.6	0.922	Contact Map
1pq4A	1	0.3368	0.6	0.924	Contact Map
2bkyA	2	0.3368	0.6	0.925	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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