FIME - ECOLI - GREMLIN Contacts

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FIME - Type 1 fimbriae regulatory protein FimE

UniProt:	P0ADH7	Sequences: MSKRRYLTGKEVQAMMQAVCYGATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDEREAVERWTQERANWKGADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAGLWERNNLINEKLKREEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10312
Length:	198 (175)
Sequences:	28719 (22054)
Seq/√Len:	1667.1

ECOLI - FIME FIMB XERC INTQ INTR INTD XERD INTF INTB INTZ INTA INTS INTE
BACSU - YOEC XERC XERD INT YOPP YOMM
HALSA - Q9HR66 Q9HQV5 O52010 O54590 Q9HSI7
SULSO - Q980D9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
143_G	160_L	4.657	1.00
71_T	161_G	3.047	1.00
50_Y	87_T	2.981	1.00
142_C	159_Y	2.683	1.00
134_H	137_M	2.675	1.00
35_A	135_P	2.265	1.00
35_A	45_L	2.204	1.00
61_N	72_V	2.183	1.00
49_H	101_A	2.148	1.00
39_G	142_C	2.116	1.00
42_I	136_H	2.090	1.00
58_G	80_R	2.088	1.00
49_H	110_R	2.083	1.00
154_R	157_Q	2.016	1.00
140_H	173_A	1.923	1.00
37_R	76_R	1.866	1.00
59_R	72_V	1.852	1.00
66_K	69_F	1.813	1.00
80_R	84_E	1.813	1.00
12_V	36_Y	1.803	1.00
30_C	86_W	1.797	1.00
33_L	82_A	1.720	1.00
147_A	156_I	1.719	1.00
152_D	155_L	1.708	1.00
69_F	163_R	1.693	1.00
146_L	151_A	1.690	1.00
162_H	168_T	1.659	1.00
75_L	80_R	1.647	1.00
28_D	119_I	1.623	1.00
160_L	168_T	1.620	1.00
154_R	158_D	1.610	1.00
148_E	178_R	1.591	1.00
54_D	57_E	1.547	1.00
74_P	159_Y	1.517	1.00
43_S	47_D	1.486	1.00
44_E	71_T	1.477	1.00
19_V	123_A	1.460	1.00
8_T	11_E	1.455	1.00
42_I	113_R	1.445	1.00
40_M	62_I	1.436	1.00
42_I	46_L	1.418	1.00
20_C	29_Y	1.404	1.00
29_Y	33_L	1.384	1.00
9_G	145_E	1.375	1.00
12_V	145_E	1.371	1.00
31_L	116_A	1.370	1.00
49_H	52_D	1.366	1.00
157_Q	165_I	1.342	1.00
124_G	133_T	1.340	1.00
40_M	45_L	1.340	1.00
36_Y	145_E	1.339	1.00
147_A	172_T	1.308	1.00
146_L	156_I	1.298	1.00
54_D	59_R	1.287	1.00
167_H	170_R	1.273	1.00
113_R	117_Y	1.273	1.00
55_L	84_E	1.265	1.00
119_I	122_D	1.243	1.00
101_A	110_R	1.240	1.00
142_C	146_L	1.233	1.00
144_Y	173_A	1.233	1.00
148_E	175_N	1.224	1.00
63_R	70_S	1.223	1.00
52_D	63_R	1.222	1.00
37_R	79_E	1.204	1.00
18_A	126_E	1.202	1.00
115_Q	118_R	1.199	1.00
49_H	100_D	1.198	1.00
7_L	141_A	1.181	1.00
51_Q	100_D	1.180	1.00
36_Y	138_L	1.180	1.00
166_R	169_V	1.175	1.00
7_L	133_T	1.164	1.00
9_G	149_R	1.159	1.00
30_C	82_A	1.154	1.00
153_T	169_V	1.146	1.00
7_L	15_M	1.142	1.00
50_Y	102_I	1.136	1.00
31_L	45_L	1.135	1.00
36_Y	141_A	1.132	1.00
165_I	169_V	1.115	1.00
48_L	60_I	1.103	1.00
16_M	33_L	1.099	1.00
120_I	124_G	1.089	1.00
11_E	14_A	1.088	1.00
114_Q	117_Y	1.085	1.00
29_Y	82_A	1.085	1.00
155_L	182_L	1.079	1.00
145_E	148_E	1.072	1.00
31_L	103_F	1.061	1.00
18_A	127_A	1.048	1.00
112_S	115_Q	1.046	1.00
61_N	70_S	1.046	1.00
37_R	78_D	1.036	1.00
158_D	179_F	1.035	1.00
58_G	77_F	1.020	1.00
141_A	145_E	1.007	1.00
42_I	117_Y	1.005	1.00
42_I	116_A	1.000	1.00
14_A	18_A	0.999	1.00
50_Y	90_R	0.998	1.00
117_Y	121_R	0.990	1.00
30_C	85_R	0.988	1.00
101_A	104_I	0.988	1.00
19_V	32_I	0.979	1.00
55_L	80_R	0.970	1.00
51_Q	99_T	0.965	1.00
121_R	132_Q	0.959	1.00
26_A	89_E	0.957	1.00
46_L	116_A	0.948	1.00
13_Q	17_Q	0.939	1.00
30_C	103_F	0.928	1.00
76_R	79_E	0.927	1.00
178_R	181_G	0.918	1.00
6_Y	141_A	0.905	1.00
117_Y	135_P	0.903	1.00
86_W	90_R	0.899	1.00
77_F	81_E	0.898	1.00
34_L	103_F	0.896	1.00
164_N	167_H	0.895	1.00
123_A	126_E	0.895	1.00
181_G	185_R	0.893	1.00
157_Q	168_T	0.893	1.00
38_H	73_H	0.890	1.00
63_R	68_G	0.890	1.00
105_S	109_S	0.887	1.00
15_M	32_I	0.876	1.00
122_D	126_E	0.865	1.00
159_Y	179_F	0.865	1.00
154_R	169_V	0.863	1.00
9_G	13_Q	0.855	1.00
120_I	138_L	0.851	1.00
180_A	184_E	0.846	1.00
33_L	78_D	0.840	1.00
90_R	104_I	0.840	1.00
142_C	160_L	0.833	1.00
41_R	136_H	0.824	1.00
79_E	82_A	0.820	1.00
34_L	60_I	0.818	1.00
26_A	85_R	0.812	1.00
148_E	177_A	0.808	1.00
75_L	79_E	0.800	1.00
85_R	89_E	0.791	1.00
7_L	11_E	0.781	1.00
5_R	137_M	0.778	1.00
119_I	123_A	0.772	1.00
115_Q	119_I	0.771	1.00
9_G	148_E	0.771	1.00
19_V	29_Y	0.767	1.00
35_A	138_L	0.766	1.00
120_I	135_P	0.763	1.00
18_A	123_A	0.761	1.00
82_A	85_R	0.759	1.00
157_Q	169_V	0.758	1.00
74_P	180_A	0.751	1.00
30_C	79_E	0.748	1.00
6_Y	173_A	0.747	1.00
153_T	165_I	0.741	1.00
151_A	155_L	0.740	1.00
54_D	61_N	0.733	1.00
33_L	37_R	0.730	1.00
34_L	79_E	0.722	1.00
78_D	81_E	0.721	1.00
34_L	40_M	0.717	1.00
176_A	179_F	0.717	1.00
12_V	16_M	0.711	1.00
33_L	79_E	0.710	1.00
183_W	186_N	0.705	1.00
121_R	125_I	0.700	1.00
42_I	135_P	0.694	1.00
143_G	156_I	0.685	1.00
47_D	110_R	0.682	1.00
40_M	60_I	0.680	1.00
151_A	182_L	0.678	1.00
116_A	135_P	0.678	1.00
46_L	113_R	0.676	1.00
133_T	137_M	0.675	1.00
147_A	175_N	0.669	1.00
137_M	140_H	0.663	1.00
182_L	185_R	0.661	1.00
34_L	45_L	0.660	1.00
175_N	178_R	0.659	1.00
27_R	111_L	0.659	1.00
30_C	34_L	0.659	1.00
143_G	172_T	0.652	1.00
118_R	122_D	0.652	1.00
53_L	102_I	0.650	1.00
54_D	58_G	0.648	1.00
177_A	181_G	0.648	1.00
32_I	138_L	0.647	1.00
28_D	123_A	0.646	1.00
30_C	83_V	0.646	1.00
10_K	14_A	0.640	1.00
32_I	120_I	0.629	1.00
87_T	90_R	0.628	1.00
151_A	156_I	0.626	1.00
55_L	58_G	0.625	1.00
26_A	30_C	0.624	1.00
144_Y	172_T	0.622	1.00
59_R	180_A	0.622	1.00
121_R	124_G	0.621	1.00
27_R	86_W	0.615	1.00
86_W	89_E	0.615	1.00
27_R	119_I	0.613	1.00
87_T	91_A	0.611	1.00
114_Q	121_R	0.608	1.00
35_A	42_I	0.606	1.00
16_M	29_Y	0.604	1.00
155_L	159_Y	0.604	1.00
112_S	118_R	0.602	1.00
6_Y	144_Y	0.595	1.00
84_E	88_Q	0.595	1.00
39_G	160_L	0.591	1.00
140_H	170_R	0.589	1.00
38_H	76_R	0.588	1.00
7_L	12_V	0.584	1.00
163_R	167_H	0.582	1.00
16_M	19_V	0.581	1.00
50_Y	91_A	0.580	1.00
115_Q	122_D	0.576	1.00
77_F	184_E	0.575	1.00
34_L	83_V	0.575	1.00
14_A	127_A	0.574	1.00
55_L	75_L	0.573	1.00
181_G	184_E	0.570	1.00
24_T	106_R	0.568	1.00
64_R	71_T	0.566	1.00
83_V	102_I	0.566	1.00
154_R	172_T	0.561	1.00
120_I	133_T	0.560	1.00
44_E	64_R	0.560	1.00
15_M	124_G	0.555	1.00
40_M	44_E	0.554	1.00
156_I	172_T	0.553	1.00
151_A	185_R	0.553	1.00
143_G	162_H	0.551	1.00
165_I	168_T	0.550	1.00
147_A	174_S	0.549	1.00
27_R	30_C	0.548	1.00
117_Y	134_H	0.545	1.00
143_G	168_T	0.543	1.00
152_D	182_L	0.543	1.00
14_A	17_Q	0.538	1.00
7_L	137_M	0.537	1.00
64_R	161_G	0.536	1.00
26_A	29_Y	0.533	1.00
105_S	115_Q	0.531	1.00
81_E	85_R	0.530	1.00
4_R	140_H	0.523	1.00
144_Y	174_S	0.519	1.00
14_A	129_T	0.518	1.00
147_A	152_D	0.513	1.00
124_G	134_H	0.511	1.00
114_Q	118_R	0.510	1.00
157_Q	167_H	0.510	1.00
104_I	108_G	0.509	1.00
164_N	168_T	0.507	1.00
55_L	102_I	0.505	1.00
85_R	88_Q	0.504	1.00
5_R	132_Q	0.503	1.00
28_D	31_L	0.502	1.00
52_D	64_R	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
3nkhA	2	0.9697	100	0.226	Contact Map
2a3vA	3	0.9293	100	0.235	Contact Map
1a0pA	1	0.8939	100	0.268	Contact Map
4a8eA	2	0.8737	100	0.272	Contact Map
1z19A	3	0.9091	100	0.29	Contact Map
1z1bA	3	0.8939	100	0.29	Contact Map
1xo0A	3	0.9343	100	0.3	Contact Map
1ae9A	4	0.8384	100	0.303	Contact Map
1aihA	2	0.8485	100	0.362	Contact Map
3vcfA	1	0.7929	99.9	0.439	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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