TDCF - ECOLI - GREMLIN Contacts

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TDCF - Putative reactive intermediate deaminase TdcF

UniProt:	P0AGL2	Sequences: MKKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVCPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12757
Length:	129 (115)
Sequences:	6896 (4455)
Seq/√Len:	415.4

ECOLI - TDCF RIDA RUTC YJGH YOAB
BACSU - RIDA
HALSA - Q9HNH7
SULSO - Y3206

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_R	93_Q	3.271	1.00
58_K	68_V	2.994	1.00
66_L	70_D	2.663	1.00
45_D	48_D	2.574	1.00
73_K	122_E	2.535	1.00
47_Q	86_T	2.366	1.00
76_V	87_I	2.064	1.00
51_R	55_E	2.063	1.00
77_F	108_V	2.054	1.00
109_Q	112_R	2.024	1.00
47_Q	89_E	2.021	1.00
55_E	94_F	1.949	1.00
57_V	123_A	1.871	1.00
33_I	117_V	1.823	1.00
49_Q	118_K	1.817	1.00
58_K	62_V	1.748	1.00
61_V	125_A	1.696	1.00
52_L	56_N	1.641	1.00
83_D	118_K	1.635	1.00
51_R	94_F	1.580	1.00
112_R	116_D	1.578	1.00
74_M	123_A	1.559	1.00
27_V	66_L	1.546	1.00
81_L	109_Q	1.538	1.00
23_L	72_I	1.521	1.00
55_E	58_K	1.466	1.00
67_S	70_D	1.436	1.00
78_I	87_I	1.435	1.00
46_V	50_A	1.427	1.00
97_E	101_T	1.380	1.00
34_P	117_V	1.375	1.00
23_L	126_V	1.332	1.00
22_D	25_S	1.324	1.00
28_F	124_I	1.316	1.00
52_L	55_E	1.310	1.00
36_C	40_G	1.308	1.00
36_C	39_T	1.302	1.00
42_I	117_V	1.290	1.00
71_I	123_A	1.283	1.00
78_I	107_C	1.282	1.00
106_S	122_E	1.259	1.00
86_T	89_E	1.242	1.00
88_N	105_R	1.237	1.00
31_G	120_E	1.228	1.00
90_V	93_Q	1.217	1.00
43_P	48_D	1.216	1.00
79_T	83_D	1.155	1.00
41_E	115_K	1.148	1.00
83_D	86_T	1.148	1.00
22_D	27_V	1.132	1.00
27_V	64_A	1.119	1.00
61_V	66_L	1.110	1.00
91_Y	105_R	1.100	1.00
26_M	126_V	1.088	1.00
29_T	60_I	1.084	1.00
77_F	110_V	1.058	1.00
79_T	112_R	1.041	1.00
75_T	122_E	1.041	1.00
22_D	66_L	1.038	1.00
29_T	123_A	1.035	1.00
96_D	102_Y	1.034	1.00
96_D	101_T	1.029	1.00
9_R	62_V	1.025	1.00
51_R	90_V	1.024	1.00
34_P	53_S	1.021	1.00
71_I	95_F	1.009	1.00
10_A	19_Q	0.994	1.00
77_F	106_S	0.992	1.00
50_A	87_I	0.988	1.00
46_V	87_I	0.975	1.00
26_M	72_I	0.970	1.00
62_V	67_S	0.968	1.00
79_T	118_K	0.924	1.00
47_Q	90_V	0.917	1.00
89_E	92_K	0.916	1.00
58_K	94_F	0.912	1.00
79_T	116_D	0.911	1.00
61_V	71_I	0.908	1.00
32_Q	60_I	0.904	1.00
20_G	60_I	0.887	1.00
80_D	83_D	0.871	1.00
97_E	102_Y	0.865	1.00
74_M	91_Y	0.865	1.00
68_V	71_I	0.852	1.00
82_N	112_R	0.843	1.00
34_P	49_Q	0.831	1.00
54_L	94_F	0.822	1.00
84_F	107_C	0.819	1.00
43_P	49_Q	0.807	1.00
54_L	68_V	0.807	1.00
44_A	49_Q	0.804	1.00
79_T	111_A	0.800	1.00
89_E	93_Q	0.799	1.00
46_V	83_D	0.796	1.00
90_V	94_F	0.795	1.00
92_K	102_Y	0.794	1.00
47_Q	51_R	0.789	1.00
59_A	62_V	0.787	1.00
54_L	121_I	0.780	1.00
44_A	48_D	0.762	1.00
37_P	52_L	0.758	1.00
68_V	94_F	0.754	1.00
74_M	95_F	0.742	1.00
79_T	110_V	0.733	1.00
71_I	125_A	0.717	1.00
25_S	126_V	0.714	1.00
69_G	96_D	0.701	1.00
47_Q	93_Q	0.698	1.00
16_P	88_N	0.690	1.00
45_D	118_K	0.684	1.00
54_L	91_Y	0.679	1.00
50_A	119_L	0.678	1.00
46_V	90_V	0.675	1.00
29_T	57_V	0.671	0.99
20_G	27_V	0.669	0.99
53_S	121_I	0.665	0.99
46_V	119_L	0.664	0.99
84_F	114_P	0.657	0.99
76_V	105_R	0.656	0.99
20_G	64_A	0.645	0.99
43_P	118_K	0.644	0.99
48_D	51_R	0.640	0.99
9_R	59_A	0.638	0.99
85_A	89_E	0.634	0.99
35_V	40_G	0.633	0.99
14_I	115_K	0.621	0.99
46_V	86_T	0.621	0.99
76_V	121_I	0.620	0.99
27_V	125_A	0.619	0.99
88_N	91_Y	0.619	0.99
23_L	28_F	0.618	0.99
77_F	122_E	0.617	0.99
19_Q	60_I	0.611	0.99
30_S	104_T	0.611	0.99
24_G	126_V	0.607	0.99
45_D	86_T	0.603	0.99
75_T	106_S	0.588	0.99
66_L	126_V	0.585	0.99
81_L	112_R	0.578	0.99
32_Q	57_V	0.576	0.98
37_P	59_A	0.574	0.98
73_K	106_S	0.569	0.98
69_G	97_E	0.568	0.98
23_L	26_M	0.568	0.98
26_M	124_I	0.567	0.98
21_V	72_I	0.566	0.98
78_I	81_L	0.564	0.98
78_I	83_D	0.560	0.98
61_V	68_V	0.554	0.98
80_D	118_K	0.552	0.98
60_I	63_A	0.549	0.98
66_L	125_A	0.547	0.98
39_T	42_I	0.546	0.98
55_E	59_A	0.546	0.98
22_D	64_A	0.543	0.98
61_V	123_A	0.540	0.98
79_T	109_Q	0.534	0.98
18_V	21_V	0.530	0.97
14_I	17_Y	0.528	0.97
29_T	106_S	0.524	0.97
83_D	109_Q	0.523	0.97
33_I	115_K	0.521	0.97
53_S	119_L	0.521	0.97
84_F	88_N	0.519	0.97
71_I	74_M	0.517	0.97
76_V	119_L	0.513	0.97
34_P	44_A	0.508	0.97
53_S	57_V	0.507	0.97
73_K	104_T	0.507	0.97
74_M	121_I	0.507	0.97
36_C	41_E	0.504	0.96
34_P	42_I	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
3vczA	5	0.9535	100	0.134	Contact Map
2b33A	3	0.969	100	0.137	Contact Map
2dyyA	3	0.969	100	0.139	Contact Map
1xrgA	3	0.9612	100	0.144	Contact Map
1qu9A	3	0.9845	100	0.147	Contact Map
2cvlA	3	0.9612	100	0.151	Contact Map
3k0tA	3	0.9612	100	0.153	Contact Map
1x25A	3	0.969	100	0.157	Contact Map
3l7qA	3	0.9535	100	0.158	Contact Map
3r0pA	5	0.9612	100	0.163	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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