YYAT - BACSU - GREMLIN Contacts

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YYAT - Uncharacterized protein YyaT

UniProt:	P37504	Sequences: MNIKRITTEADLHEALKIRRGVFIEEQHVSEADEFDEFDTLQEQCQHILVYHENQPVGTGRARIVGHTAKLERICILKPYRKYGLGKIIVSGLEEIMKEKGLTSYKLHGQTQAAGFYQKLGYQISSQEFMEDGIPHVLMTKEISRNIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	148 (130)
Sequences:	3359 (2583)
Seq/√Len:	226.6

ECOLI - ELAA YIID
BACSU - YYAT YJCF YYBD YITI
HALSA - Q9HPZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_E	122_Y	2.961	1.00
60_G	93_L	2.960	1.00
114_A	124_I	2.639	1.00
108_H	129_F	2.419	1.00
20_R	34_E	2.116	1.00
92_G	95_E	2.101	1.00
111_T	128_E	2.058	1.00
128_E	135_P	2.003	1.00
87_K	120_L	1.958	1.00
18_I	75_C	1.949	1.00
14_E	51_Y	1.845	1.00
18_I	77_L	1.832	1.00
90_V	120_L	1.797	1.00
57_V	80_Y	1.790	1.00
94_E	141_K	1.780	1.00
49_L	56_P	1.777	1.00
114_A	137_V	1.768	1.00
50_V	85_L	1.743	1.00
63_R	72_E	1.735	1.00
125_S	138_L	1.698	1.00
21_G	77_L	1.669	1.00
12_L	16_L	1.665	1.00
71_L	90_V	1.631	1.00
51_Y	56_P	1.622	1.00
58_G	76_I	1.599	1.00
21_G	25_E	1.588	1.00
50_V	58_G	1.582	1.00
125_S	140_T	1.567	1.00
59_T	75_C	1.527	1.00
118_Q	124_I	1.520	1.00
87_K	119_K	1.507	1.00
114_A	118_Q	1.478	1.00
96_I	100_K	1.470	1.00
94_E	105_Y	1.453	1.00
129_F	138_L	1.435	1.00
130_M	133_G	1.395	1.00
87_K	91_S	1.372	1.00
115_G	118_Q	1.348	1.00
130_M	135_P	1.344	1.00
65_V	70_K	1.331	1.00
17_K	21_G	1.330	1.00
15_A	49_L	1.308	1.00
108_H	138_L	1.304	1.00
60_G	74_I	1.296	1.00
29_V	132_D	1.295	1.00
27_Q	110_Q	1.285	1.00
33_D	132_D	1.284	1.00
74_I	90_V	1.283	1.00
126_S	138_L	1.275	1.00
29_V	134_I	1.272	1.00
68_T	106_K	1.271	1.00
20_R	31_E	1.258	1.00
48_I	96_I	1.252	1.00
48_I	93_L	1.248	1.00
96_I	99_E	1.242	1.00
55_Q	79_P	1.240	1.00
108_H	131_E	1.238	1.00
46_Q	96_I	1.227	1.00
106_K	138_L	1.226	1.00
16_L	35_F	1.199	1.00
124_I	137_V	1.173	1.00
88_I	92_G	1.162	1.00
15_A	59_T	1.122	1.00
52_H	80_Y	1.109	1.00
20_R	24_I	1.108	1.00
104_S	140_T	1.098	1.00
21_G	33_D	1.078	1.00
64_I	102_L	1.059	1.00
62_A	97_M	1.047	1.00
70_K	106_K	1.037	1.00
98_K	141_K	1.034	1.00
46_Q	100_K	1.023	1.00
111_T	114_A	1.011	1.00
106_K	140_T	1.000	1.00
71_L	74_I	0.990	1.00
80_Y	83_Y	0.989	1.00
26_E	81_R	0.986	1.00
20_R	35_F	0.981	1.00
110_Q	136_H	0.976	1.00
20_R	25_E	0.967	1.00
24_I	31_E	0.941	1.00
10_A	14_E	0.937	1.00
14_E	17_K	0.926	1.00
13_H	16_L	0.921	1.00
91_S	95_E	0.916	1.00
92_G	96_I	0.907	0.99
97_M	105_Y	0.905	0.99
52_H	57_V	0.894	0.99
69_A	102_L	0.889	0.99
38_F	63_R	0.885	0.99
60_G	89_I	0.877	0.99
58_G	89_I	0.868	0.99
95_E	99_E	0.865	0.99
86_G	116_F	0.861	0.99
109_G	139_M	0.852	0.99
37_E	43_E	0.850	0.99
113_A	116_F	0.842	0.99
68_T	104_S	0.838	0.99
63_R	70_K	0.837	0.99
71_L	93_L	0.832	0.99
48_I	60_G	0.822	0.99
57_V	85_L	0.818	0.99
9_E	13_H	0.818	0.99
70_K	107_L	0.807	0.99
30_S	33_D	0.802	0.99
51_Y	54_N	0.797	0.99
88_I	91_S	0.796	0.99
25_E	30_S	0.794	0.99
45_C	63_R	0.791	0.99
111_T	135_P	0.778	0.98
58_G	85_L	0.770	0.98
70_K	108_H	0.759	0.98
52_H	83_Y	0.757	0.98
11_D	49_L	0.757	0.98
77_L	80_Y	0.756	0.98
17_K	37_E	0.753	0.98
55_Q	77_L	0.753	0.98
16_L	20_R	0.751	0.98
91_S	120_L	0.747	0.98
18_I	56_P	0.744	0.98
21_G	79_P	0.734	0.98
62_A	96_I	0.715	0.97
97_M	102_L	0.706	0.97
122_Y	141_K	0.705	0.97
45_C	64_I	0.693	0.97
84_G	87_K	0.692	0.97
123_Q	142_E	0.685	0.96
111_T	137_V	0.681	0.96
105_Y	122_Y	0.679	0.96
114_A	128_E	0.668	0.96
23_F	26_E	0.667	0.96
85_L	88_I	0.667	0.96
71_L	122_Y	0.660	0.96
18_I	59_T	0.656	0.95
30_S	34_E	0.652	0.95
29_V	131_E	0.650	0.95
11_D	15_A	0.650	0.95
23_F	110_Q	0.642	0.95
71_L	105_Y	0.642	0.95
26_E	78_K	0.639	0.95
124_I	128_E	0.639	0.95
50_V	88_I	0.637	0.95
24_I	34_E	0.636	0.95
107_L	117_Y	0.634	0.94
47_H	59_T	0.632	0.94
39_D	72_E	0.625	0.94
20_R	30_S	0.623	0.94
95_E	98_K	0.623	0.94
48_I	92_G	0.619	0.94
94_E	120_L	0.615	0.94
22_V	81_R	0.610	0.93
71_L	107_L	0.610	0.93
36_D	61_R	0.607	0.93
23_F	27_Q	0.596	0.92
50_V	57_V	0.596	0.92
61_R	73_R	0.591	0.92
89_I	92_G	0.588	0.92
83_Y	86_G	0.580	0.91
13_H	35_F	0.580	0.91
48_I	62_A	0.580	0.91
72_E	110_Q	0.579	0.91
69_A	97_M	0.577	0.91
131_E	134_I	0.576	0.91
127_Q	137_V	0.569	0.91
118_Q	123_Q	0.568	0.91
33_D	131_E	0.565	0.90
104_S	142_E	0.565	0.90
128_E	137_V	0.564	0.90
58_G	86_G	0.560	0.90
82_K	87_K	0.559	0.90
76_I	85_L	0.557	0.90
37_E	44_Q	0.556	0.90
80_Y	85_L	0.553	0.89
13_H	37_E	0.548	0.89
27_Q	136_H	0.543	0.89
13_H	17_K	0.541	0.88
10_A	43_E	0.540	0.88
63_R	69_A	0.536	0.88
112_Q	134_I	0.535	0.88
69_A	101_G	0.525	0.87
38_F	44_Q	0.524	0.87
26_E	110_Q	0.523	0.87
107_L	139_M	0.520	0.86
66_G	70_K	0.518	0.86
52_H	55_Q	0.511	0.85
26_E	73_R	0.510	0.85
26_E	132_D	0.510	0.85
12_L	39_D	0.509	0.85
65_V	72_E	0.506	0.85
107_L	113_A	0.506	0.85
27_Q	73_R	0.506	0.85
23_F	73_R	0.505	0.85
24_I	30_S	0.504	0.85
74_I	120_L	0.501	0.84
21_G	78_K	0.500	0.84

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
2g0bA	4	0.9865	99.9	0.404	Contact Map
1q2yA	1	0.9392	99.9	0.416	Contact Map
1kzfA	1	0.9054	99.9	0.429	Contact Map
3p2hA	1	0.9324	99.9	0.434	Contact Map
2jdcA	1	0.9257	99.9	0.439	Contact Map
1ro5A	5	0.9865	99.9	0.447	Contact Map
1xebA	2	0.9459	99.9	0.448	Contact Map
3efaA	2	0.9527	99.9	0.449	Contact Map
1y9wA	2	0.9324	99.8	0.564	Contact Map
1yvkA	3	0.9189	99.7	0.585	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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