SFMA - ECOLI - GREMLIN Contacts

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SFMA - Uncharacterized fimbrial-like protein SfmA

UniProt:	P0ABW5	Sequences: MKLRFISSALAAALFAATGSYAAVVDGGTIHFEGELVNAACSVNTDSADQVVTLGQYRTDIFNAVGNTSALIPFTIQLNDCDPVVAANAAVAFSGQADAINDNLLAIASSTNTTTATGVGIEILDNTSAILKPDGNSFSTNQNLIPGTNVLHFSARYKGTGTSASAGQANADATFIMRYE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13881
Length:	180 (163)
Sequences:	3514 (2761)
Seq/√Len:	216.2

ECOLI - SFMA YCBU FIMI FIMA1 FIMF YDES YBGD YCBV YGIL SFMF ELFA YDER YFCV FIMG YRAH YADN YFCP FIMH YDEQ YEHD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
104_L	120_G	3.113	1.00
117_T	165_S	3.103	1.00
121_I	155_A	2.928	1.00
64_A	67_N	2.820	1.00
122_E	156_R	2.779	1.00
124_L	156_R	2.756	1.00
42_S	80_D	2.734	1.00
75_T	150_V	2.657	1.00
122_E	158_K	2.632	1.00
89_A	177_M	2.573	1.00
105_L	133_P	2.426	1.00
107_I	169_A	2.390	1.00
77_Q	150_V	2.304	1.00
44_N	79_N	2.282	1.00
63_N	67_N	2.238	1.00
157_Y	169_A	2.233	1.00
118_G	164_A	2.232	1.00
128_S	154_S	2.223	1.00
121_I	171_A	2.096	1.00
115_T	168_Q	2.041	1.00
105_L	173_A	2.036	1.00
125_D	129_A	1.920	1.00
75_T	152_H	1.883	1.00
71_L	156_R	1.814	1.00
122_E	130_I	1.728	1.00
73_P	154_S	1.727	1.00
24_V	27_G	1.714	1.00
95_G	105_L	1.712	1.00
44_N	77_Q	1.659	1.00
104_L	158_K	1.607	1.00
103_N	132_K	1.570	1.00
94_S	134_D	1.533	1.00
68_T	122_E	1.507	1.00
10_L	13_A	1.472	1.00
94_S	176_I	1.457	1.00
57_Y	69_S	1.456	1.00
44_N	47_S	1.435	1.00
55_G	72_I	1.434	1.00
65_V	162_T	1.407	1.00
68_T	156_R	1.376	1.00
45_T	50_Q	1.374	1.00
74_F	123_I	1.358	1.00
55_G	70_A	1.354	1.00
62_F	159_G	1.352	1.00
90_A	178_R	1.351	1.00
47_S	50_Q	1.336	1.00
55_G	169_A	1.323	1.00
35_E	56_Q	1.310	1.00
54_L	157_Y	1.295	1.00
50_Q	76_I	1.283	1.00
64_A	159_G	1.277	1.00
73_P	152_H	1.254	1.00
17_A	21_Y	1.253	1.00
47_S	77_Q	1.241	1.00
68_T	124_L	1.229	1.00
20_S	24_V	1.215	1.00
98_D	160_T	1.208	1.00
144_L	149_N	1.181	1.00
89_A	149_N	1.177	1.00
97_A	103_N	1.176	1.00
104_L	122_E	1.165	1.00
52_V	74_F	1.160	1.00
99_A	120_G	1.151	1.00
123_I	173_A	1.150	1.00
99_A	102_D	1.148	1.00
63_N	159_G	1.137	1.00
159_G	164_A	1.125	1.00
159_G	162_T	1.117	1.00
54_L	169_A	1.095	1.00
62_F	164_A	1.094	1.00
54_L	121_I	1.087	1.00
12_A	15_F	1.086	1.00
13_A	16_A	1.081	1.00
42_S	79_N	1.070	1.00
28_G	32_F	1.066	1.00
91_V	151_L	1.066	1.00
11_A	14_L	1.061	1.00
31_H	172_D	1.060	1.00
71_L	154_S	1.035	1.00
38_N	59_T	1.029	1.00
68_T	158_K	1.024	1.00
76_I	175_F	1.015	1.00
132_K	137_S	1.011	1.00
93_F	153_F	1.005	1.00
62_F	67_N	0.990	1.00
18_T	22_A	0.974	1.00
93_F	123_I	0.964	1.00
18_T	21_Y	0.956	1.00
58_R	61_I	0.955	1.00
124_L	154_S	0.944	1.00
92_A	178_R	0.938	1.00
126_N	152_H	0.937	1.00
88_N	143_N	0.932	0.99
105_L	171_A	0.926	0.99
98_D	102_D	0.924	0.99
61_I	69_S	0.920	0.99
108_A	172_D	0.897	0.99
78_L	149_N	0.889	0.99
17_A	20_S	0.876	0.99
62_F	119_V	0.876	0.99
14_L	17_A	0.871	0.99
57_Y	169_A	0.864	0.99
88_N	141_N	0.862	0.99
28_G	175_F	0.862	0.99
57_Y	62_F	0.858	0.99
114_T	168_Q	0.843	0.99
119_V	157_Y	0.841	0.99
16_A	20_S	0.833	0.99
124_L	130_I	0.831	0.99
16_A	19_G	0.828	0.99
123_I	133_P	0.822	0.99
15_F	18_T	0.818	0.99
19_G	22_A	0.815	0.99
57_Y	157_Y	0.808	0.99
116_A	119_V	0.803	0.98
38_N	82_D	0.802	0.98
53_T	157_Y	0.798	0.98
33_E	51_V	0.795	0.98
95_G	98_D	0.791	0.98
17_A	22_A	0.791	0.98
97_A	133_P	0.786	0.98
50_Q	175_F	0.785	0.98
62_F	160_T	0.784	0.98
10_L	14_L	0.782	0.98
96_Q	106_A	0.775	0.98
23_A	26_D	0.773	0.98
98_D	101_N	0.770	0.98
108_A	170_N	0.765	0.98
14_L	18_T	0.765	0.98
20_S	23_A	0.762	0.98
90_A	141_N	0.762	0.98
36_L	164_A	0.761	0.98
13_A	17_A	0.761	0.98
107_I	114_T	0.746	0.98
65_V	118_G	0.743	0.97
11_A	15_F	0.741	0.97
22_A	26_D	0.737	0.97
54_L	72_I	0.736	0.97
120_G	160_T	0.734	0.97
131_L	153_F	0.732	0.97
12_A	16_A	0.732	0.97
29_T	49_D	0.728	0.97
133_P	171_A	0.727	0.97
54_L	155_A	0.727	0.97
65_V	159_G	0.723	0.97
15_F	19_G	0.716	0.97
119_V	164_A	0.713	0.97
67_N	159_G	0.713	0.97
59_T	164_A	0.712	0.97
121_I	169_A	0.710	0.97
53_T	72_I	0.704	0.96
98_D	120_G	0.702	0.96
19_G	24_V	0.702	0.96
98_D	106_A	0.697	0.96
92_A	138_F	0.696	0.96
13_A	18_T	0.688	0.96
65_V	161_G	0.687	0.96
33_E	53_T	0.686	0.96
139_S	142_Q	0.679	0.96
77_Q	148_T	0.676	0.96
75_T	97_A	0.670	0.95
71_L	124_L	0.668	0.95
23_A	27_G	0.667	0.95
10_L	17_A	0.666	0.95
11_A	16_A	0.664	0.95
45_T	48_A	0.663	0.95
91_V	177_M	0.663	0.95
61_I	70_A	0.658	0.95
21_Y	25_V	0.653	0.95
21_Y	24_V	0.651	0.95
68_T	71_L	0.648	0.94
82_D	124_L	0.647	0.94
36_L	57_Y	0.646	0.94
107_I	170_N	0.639	0.94
40_A	157_Y	0.639	0.94
98_D	161_G	0.638	0.94
101_N	104_L	0.632	0.94
107_I	119_V	0.629	0.94
10_L	19_G	0.629	0.94
118_G	161_G	0.627	0.93
37_V	82_D	0.626	0.93
59_T	166_A	0.626	0.93
139_S	144_L	0.623	0.93
118_G	163_S	0.618	0.93
26_D	29_T	0.611	0.93
82_D	85_V	0.608	0.92
95_G	172_D	0.608	0.92
19_G	23_A	0.606	0.92
13_A	19_G	0.605	0.92
90_A	138_F	0.603	0.92
130_I	133_P	0.600	0.92
38_N	87_A	0.600	0.92
54_L	74_F	0.599	0.92
15_F	21_Y	0.595	0.92
10_L	18_T	0.589	0.91
21_Y	26_D	0.588	0.91
143_N	148_T	0.587	0.91
140_T	143_N	0.584	0.91
133_P	153_F	0.582	0.91
141_N	144_L	0.580	0.90
55_G	170_N	0.580	0.90
14_L	22_A	0.577	0.90
79_N	148_T	0.574	0.90
92_A	134_D	0.571	0.90
69_S	157_Y	0.571	0.90
31_H	51_V	0.570	0.90
93_F	175_F	0.570	0.90
13_A	20_S	0.569	0.90
28_G	34_G	0.565	0.89
83_P	87_A	0.563	0.89
158_K	162_T	0.557	0.89
124_L	158_K	0.556	0.89
108_A	115_T	0.553	0.88
100_I	103_N	0.553	0.88
62_F	66_G	0.552	0.88
36_L	107_I	0.548	0.88
30_I	93_F	0.543	0.87
107_I	116_A	0.542	0.87
94_S	174_T	0.540	0.87
45_T	79_N	0.540	0.87
65_V	164_A	0.536	0.87
15_F	20_S	0.535	0.87
30_I	173_A	0.534	0.87
40_A	82_D	0.534	0.87
11_A	23_A	0.531	0.86
52_V	155_A	0.530	0.86
88_N	146_P	0.530	0.86
124_L	128_S	0.527	0.86
63_N	164_A	0.524	0.85
118_G	160_T	0.521	0.85
39_A	60_D	0.520	0.85
107_I	171_A	0.520	0.85
12_A	18_T	0.517	0.85
83_P	146_P	0.516	0.85
18_T	23_A	0.515	0.85
49_D	175_F	0.509	0.84
12_A	21_Y	0.509	0.84
16_A	21_Y	0.508	0.84
36_L	155_A	0.505	0.83
140_T	144_L	0.504	0.83
144_L	147_G	0.503	0.83
54_L	156_R	0.503	0.83
69_S	156_R	0.502	0.83
53_T	56_Q	0.500	0.83

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
2jtyA	1	0.8778	100	0.23	Contact Map
2jmrA	1	0.85	100	0.233	Contact Map
2xg5B	1	0.7778	100	0.244	Contact Map
2uy6B	2	0.8056	100	0.264	Contact Map
1pdkB	1	0.7833	100	0.274	Contact Map
3bwuF	1	0.7	100	0.328	Contact Map
4dwhB	1	0.7611	100	0.342	Contact Map
2w07B	1	0.65	99.9	0.359	Contact Map
3bfqG	1	0.7222	99.9	0.362	Contact Map
5afoA	1	0.95	99.9	0.37	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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