YIBN - ECOLI - GREMLIN Contacts

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YIBN - Uncharacterized protein YibN

UniProt:	P0AG27	Sequences: MQEIMQFVGRHPILSIAWIALLVAVLVTTFKSLTSKVKVITRGEATRLINKEDAVVVDLRQRDDFRKGHIAGSINLLPSEIKANNVGELEKHKDKPVIVVDGSGMQCQEPANALTKAGFAQVFVLKEGVAGWAGENLPLVRGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12295
Length:	143 (112)
Sequences:	5214 (3914)
Seq/√Len:	369.8

ECOLI - YIBN YGAP THTM GLPE PSPE YNJE
BACSU - YQHL YRKF YTWF
HALSA - Q9HME4 Q9HMT7 Q9HMT6 O54647
SULSO - Q97VI9 Q97ZB1 Q97XC6 Q7LX53

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_T	44_E	3.077	1.00
96_P	123_F	2.810	1.00
46_T	137_L	2.693	1.00
65_F	69_H	2.304	1.00
64_D	106_Q	2.303	1.00
62_R	75_N	2.178	1.00
129_V	139_L	2.160	1.00
45_A	125_L	2.135	1.00
99_V	114_L	2.098	1.00
40_I	44_E	2.034	1.00
45_A	98_I	1.984	1.00
131_G	135_E	1.982	1.00
55_V	95_K	1.971	1.00
45_A	56_V	1.937	1.00
85_N	88_E	1.839	1.00
44_E	48_L	1.824	1.00
42_R	137_L	1.811	1.00
79_S	82_K	1.740	1.00
107_C	124_V	1.720	1.00
62_R	66_R	1.670	1.00
42_R	131_G	1.666	1.00
68_G	133_A	1.653	1.00
127_E	131_G	1.630	1.00
40_I	45_A	1.619	1.00
42_R	135_E	1.612	1.00
68_G	141_R	1.570	1.00
111_A	122_V	1.493	1.00
96_P	121_Q	1.472	1.00
45_A	54_A	1.332	1.00
59_L	110_P	1.316	1.00
100_V	129_V	1.315	1.00
56_V	100_V	1.277	1.00
99_V	111_A	1.269	1.00
70_I	100_V	1.260	1.00
99_V	122_V	1.250	1.00
39_V	126_K	1.249	1.00
129_V	133_A	1.247	1.00
64_D	102_G	1.241	1.00
48_L	51_K	1.227	1.00
46_T	50_N	1.219	1.00
41_T	126_K	1.216	1.00
111_A	124_V	1.187	1.00
42_R	125_L	1.187	1.00
61_Q	64_D	1.176	1.00
92_H	95_K	1.173	1.00
69_H	100_V	1.165	1.00
97_V	114_L	1.161	1.00
39_V	124_V	1.119	1.00
93_K	119_F	1.118	1.00
70_I	73_S	1.113	1.00
35_S	38_K	1.103	1.00
71_A	140_V	1.097	1.00
40_I	123_F	1.096	1.00
73_S	100_V	1.090	1.00
101_D	106_Q	1.081	1.00
108_Q	124_V	1.071	1.00
42_R	46_T	1.064	1.00
125_L	131_G	1.064	1.00
45_A	48_L	1.059	1.00
48_L	54_A	1.032	1.00
54_A	98_I	1.023	1.00
48_L	96_P	1.017	1.00
112_N	116_K	1.014	1.00
43_G	135_E	1.008	1.00
115_T	120_A	1.001	1.00
60_R	129_V	0.996	1.00
68_G	139_L	0.986	1.00
101_D	104_G	0.981	1.00
44_E	47_R	0.958	1.00
59_L	99_V	0.958	1.00
57_V	99_V	0.949	1.00
102_G	105_M	0.944	1.00
55_V	74_I	0.941	1.00
113_A	117_A	0.939	1.00
61_Q	106_Q	0.930	1.00
48_L	98_I	0.921	1.00
103_S	130_A	0.916	1.00
65_F	75_N	0.907	1.00
101_D	107_C	0.886	1.00
40_I	98_I	0.884	1.00
43_G	47_R	0.874	1.00
43_G	137_L	0.865	1.00
111_A	115_T	0.853	1.00
50_N	53_D	0.842	1.00
125_L	128_G	0.836	1.00
56_V	98_I	0.825	1.00
114_L	119_F	0.810	1.00
70_I	132_W	0.795	1.00
102_G	130_A	0.795	1.00
119_F	122_V	0.786	1.00
46_T	49_I	0.782	1.00
45_A	49_I	0.777	1.00
82_K	113_A	0.773	1.00
130_A	133_A	0.762	1.00
55_V	97_V	0.760	1.00
49_I	56_V	0.758	1.00
98_I	125_L	0.755	1.00
97_V	119_F	0.752	1.00
60_R	68_G	0.750	1.00
78_P	110_P	0.746	1.00
66_R	133_A	0.739	1.00
130_A	134_G	0.737	1.00
38_K	115_T	0.736	1.00
47_R	51_K	0.732	1.00
85_N	89_L	0.731	1.00
29_T	32_S	0.723	1.00
70_I	140_V	0.722	1.00
38_K	123_F	0.700	0.99
115_T	122_V	0.696	0.99
53_D	95_K	0.689	0.99
40_I	48_L	0.679	0.99
64_D	67_K	0.678	0.99
77_L	81_I	0.674	0.99
109_E	112_N	0.671	0.99
57_V	91_K	0.665	0.99
86_V	113_A	0.658	0.99
56_V	73_S	0.657	0.99
80_E	84_N	0.654	0.99
60_R	102_G	0.649	0.99
84_N	88_E	0.638	0.99
87_G	90_E	0.637	0.99
133_A	139_L	0.631	0.99
40_I	54_A	0.622	0.99
49_I	54_A	0.617	0.99
60_R	64_D	0.614	0.99
104_G	124_V	0.614	0.99
54_A	96_P	0.612	0.98
61_Q	77_L	0.604	0.98
58_D	73_S	0.599	0.98
90_E	94_D	0.595	0.98
48_L	52_E	0.585	0.98
102_G	106_Q	0.585	0.98
109_E	113_A	0.584	0.98
57_V	60_R	0.584	0.98
125_L	132_W	0.583	0.98
86_V	114_L	0.580	0.98
64_D	103_S	0.580	0.98
65_F	100_V	0.570	0.98
80_E	85_N	0.563	0.97
78_P	109_E	0.559	0.97
55_V	96_P	0.556	0.97
86_V	110_P	0.552	0.97
100_V	125_L	0.549	0.97
108_Q	111_A	0.541	0.97
52_E	121_Q	0.538	0.97
112_N	115_T	0.536	0.97
87_G	92_H	0.533	0.96
70_I	125_L	0.533	0.96
76_L	85_N	0.533	0.96
55_V	91_K	0.531	0.96
94_D	120_A	0.530	0.96
66_R	139_L	0.527	0.96
63_D	66_R	0.525	0.96
78_P	113_A	0.524	0.96
49_I	72_G	0.523	0.96
69_H	140_V	0.521	0.96
76_L	89_L	0.518	0.96
103_S	106_Q	0.514	0.96
66_R	140_V	0.513	0.96
61_Q	79_S	0.512	0.96
69_H	73_S	0.509	0.95
56_V	70_I	0.506	0.95
67_K	102_G	0.506	0.95
57_V	114_L	0.504	0.95
76_L	110_P	0.502	0.95
90_E	119_F	0.501	0.95
113_A	116_K	0.500	0.95
61_Q	75_N	0.500	0.95

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
1urhA	1	0.7552	99.9	0.326	Contact Map
3aayA	1	0.7692	99.9	0.331	Contact Map
1uarA	1	0.7762	99.9	0.335	Contact Map
1e0cA	1	0.7902	99.9	0.337	Contact Map
3hzuA	2	0.8462	99.9	0.343	Contact Map
1yt8A	1	0.7413	99.9	0.348	Contact Map
2hhgA	2	0.8531	99.9	0.351	Contact Map
1qxnA	2	0.8881	99.9	0.351	Contact Map
3tp9A	2	0.951	99.9	0.353	Contact Map
1rhsA	1	0.7902	99.9	0.355	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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