YAJL - ECOLI - GREMLIN Contacts

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YAJL - Chaperone protein YajL

UniProt:	Q46948	Sequences: MSASALVCLAPGSEETEAVTTIDLLVRGGIKVTTASVASDGNLAITCSRGVKLLADAPLVEVADGEYDVIVLPGGIKGAECFRDSTLLVETVKQFHRSGRIVAAICAAPATVLVPHDIFPIGNMTGFPTLKDKIPAEQWLDKRVVWDARVKLLTSQGPGTAIDFGLKIIDLLVGREKAHEVASQLVMAAGIYNYYE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13272
Length:	196 (168)
Sequences:	15185 (10337)
Seq/√Len:	797.5

ECOLI - YAJL YHBO HCHA
BACSU - YOAZ YRAA YDEA GS18
HALSA - Q9HMG4 Q9HRT2
SULSO - Q97Z65

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_W	171_L	2.815	1.00
4_S	31_K	2.717	1.00
6_L	67_Y	2.679	1.00
167_K	170_D	2.533	1.00
6_L	35_A	2.442	1.00
122_G	148_A	2.407	1.00
33_T	67_Y	2.364	1.00
123_N	140_L	2.308	1.00
44_A	54_L	2.200	1.00
122_G	147_D	2.156	1.00
4_S	33_T	2.150	1.00
119_F	124_M	2.103	1.00
123_N	138_Q	2.019	1.00
33_T	57_A	2.013	1.00
175_R	179_H	1.981	1.00
146_W	167_K	1.927	1.00
24_L	169_I	1.868	1.00
28_G	169_I	1.812	1.00
96_H	151_K	1.787	1.00
22_I	26_V	1.735	1.00
122_G	152_L	1.682	1.00
148_A	151_K	1.679	1.00
95_F	100_R	1.622	1.00
170_D	175_R	1.597	1.00
38_A	43_L	1.593	1.00
44_A	52_K	1.587	1.00
13_S	47_C	1.566	1.00
96_H	102_V	1.565	1.00
143_R	163_D	1.554	1.00
131_K	135_P	1.542	1.00
146_W	153_L	1.535	1.00
123_N	147_D	1.519	1.00
177_K	180_E	1.502	1.00
58_P	61_E	1.498	1.00
104_A	154_T	1.495	1.00
101_I	171_L	1.482	1.00
37_V	85_S	1.478	1.00
46_T	52_K	1.455	1.00
173_V	177_K	1.435	1.00
15_E	19_V	1.425	1.00
30_I	172_L	1.397	1.00
91_T	95_F	1.391	1.00
7_V	71_V	1.373	1.00
103_A	168_I	1.366	1.00
60_V	87_L	1.366	1.00
122_G	151_K	1.359	1.00
7_V	22_I	1.337	1.00
90_E	94_Q	1.336	1.00
104_A	113_L	1.318	1.00
167_K	171_L	1.316	1.00
142_K	163_D	1.309	1.00
52_K	56_D	1.305	1.00
89_V	93_K	1.300	1.00
11_P	46_T	1.274	1.00
155_S	160_T	1.267	1.00
25_L	165_G	1.266	1.00
86_T	90_E	1.263	1.00
94_Q	98_S	1.261	1.00
96_H	152_L	1.255	1.00
69_V	101_I	1.236	1.00
103_A	164_F	1.233	1.00
57_A	61_E	1.233	1.00
96_H	118_I	1.230	1.00
90_E	93_K	1.224	1.00
153_L	171_L	1.217	1.00
174_G	177_K	1.212	1.00
13_S	18_A	1.209	1.00
133_K	137_E	1.200	1.00
5_A	69_V	1.199	1.00
87_L	90_E	1.188	1.00
18_A	34_T	1.179	1.00
146_W	151_K	1.178	1.00
23_D	27_R	1.177	1.00
9_L	34_T	1.175	1.00
99_G	102_V	1.153	1.00
99_G	151_K	1.151	1.00
89_V	116_H	1.150	1.00
30_I	173_V	1.142	1.00
63_A	66_E	1.142	1.00
20_T	162_I	1.132	1.00
16_T	20_T	1.131	1.00
84_D	115_P	1.123	1.00
101_I	172_L	1.099	1.00
22_I	34_T	1.092	1.00
117_D	120_P	1.087	1.00
115_P	137_E	1.072	1.00
8_C	88_L	1.071	1.00
94_Q	97_R	1.066	1.00
110_A	133_K	1.049	1.00
36_S	42_N	1.047	1.00
134_I	139_W	1.044	1.00
96_H	99_G	1.044	1.00
9_L	18_A	1.043	1.00
123_N	145_V	1.028	1.00
144_V	167_K	1.026	1.00
71_V	164_F	1.022	1.00
20_T	23_D	1.014	1.00
107_A	130_L	1.009	1.00
20_T	165_G	1.008	1.00
93_K	97_R	0.993	1.00
35_A	57_A	0.989	1.00
127_F	157_G	0.984	1.00
30_I	169_I	0.967	1.00
68_D	100_R	0.964	1.00
7_V	32_V	0.963	1.00
72_L	92_V	0.951	1.00
101_I	151_K	0.951	1.00
153_L	164_F	0.946	1.00
15_E	51_V	0.946	1.00
37_V	87_L	0.939	1.00
155_S	164_F	0.935	1.00
123_N	142_K	0.928	1.00
95_F	98_S	0.925	1.00
83_R	115_P	0.920	1.00
36_S	55_A	0.907	1.00
20_T	161_A	0.900	1.00
38_A	42_N	0.892	1.00
24_L	165_G	0.889	1.00
176_E	180_E	0.885	1.00
57_A	62_V	0.884	1.00
104_A	109_P	0.884	1.00
37_V	59_L	0.881	1.00
72_L	108_A	0.875	1.00
23_D	26_V	0.872	1.00
42_N	58_P	0.871	1.00
69_V	172_L	0.863	1.00
125_T	145_V	0.857	1.00
72_L	112_V	0.855	1.00
153_L	168_I	0.851	1.00
71_V	103_A	0.850	1.00
89_V	115_P	0.843	1.00
130_L	133_K	0.843	1.00
101_I	153_L	0.842	1.00
70_I	95_F	0.839	1.00
156_Q	160_T	0.838	1.00
13_S	53_L	0.833	1.00
170_D	178_A	0.830	1.00
21_T	71_V	0.829	1.00
35_A	62_V	0.828	1.00
132_D	136_A	0.827	1.00
162_I	166_L	0.826	1.00
5_A	30_I	0.819	1.00
33_T	56_D	0.817	1.00
21_T	161_A	0.813	1.00
22_I	32_V	0.808	1.00
109_P	126_G	0.806	1.00
72_L	88_L	0.805	1.00
9_L	13_S	0.791	1.00
24_L	166_L	0.782	1.00
91_T	94_Q	0.778	1.00
67_Y	95_F	0.770	1.00
85_S	88_L	0.760	1.00
153_L	167_K	0.754	1.00
18_A	22_I	0.744	1.00
7_V	18_A	0.744	1.00
133_K	136_A	0.737	1.00
11_P	38_A	0.736	1.00
44_A	55_A	0.729	1.00
25_L	168_I	0.728	1.00
6_L	62_V	0.723	1.00
69_V	168_I	0.721	1.00
131_K	139_W	0.715	1.00
69_V	103_A	0.713	1.00
30_I	69_V	0.706	1.00
15_E	47_C	0.705	1.00
96_H	122_G	0.695	1.00
75_G	78_G	0.692	1.00
105_I	161_A	0.692	1.00
161_A	165_G	0.687	1.00
140_L	145_V	0.687	1.00
46_T	50_G	0.681	1.00
143_R	146_W	0.680	1.00
104_A	108_A	0.677	1.00
77_K	81_C	0.677	1.00
93_K	116_H	0.675	1.00
13_S	73_P	0.674	1.00
26_V	32_V	0.671	1.00
143_R	160_T	0.670	1.00
5_A	25_L	0.664	1.00
12_G	46_T	0.658	1.00
15_E	49_R	0.658	1.00
128_P	157_G	0.650	1.00
101_I	168_I	0.650	1.00
86_T	89_V	0.646	1.00
25_L	30_I	0.644	1.00
7_V	21_T	0.640	1.00
29_G	177_K	0.636	1.00
43_L	54_L	0.633	1.00
43_L	55_A	0.630	1.00
30_I	68_D	0.628	1.00
24_L	27_R	0.626	1.00
35_A	67_Y	0.623	1.00
92_V	116_H	0.623	1.00
163_D	166_L	0.620	1.00
176_E	179_H	0.619	1.00
114_V	119_F	0.614	1.00
114_V	134_I	0.612	1.00
66_E	98_S	0.602	1.00
114_V	124_M	0.600	1.00
89_V	92_V	0.600	1.00
62_V	67_Y	0.599	1.00
63_A	94_Q	0.596	1.00
132_D	135_P	0.596	1.00
126_G	139_W	0.596	1.00
92_V	112_V	0.595	1.00
77_K	80_E	0.594	1.00
4_S	68_D	0.592	1.00
141_D	145_V	0.592	1.00
43_L	46_T	0.586	1.00
8_C	35_A	0.585	1.00
124_M	134_I	0.585	1.00
105_I	164_F	0.582	1.00
24_L	28_G	0.582	1.00
78_G	82_F	0.580	1.00
14_E	23_D	0.573	1.00
8_C	70_I	0.573	1.00
102_V	151_K	0.566	1.00
89_V	112_V	0.564	1.00
102_V	152_L	0.559	1.00
84_D	89_V	0.554	1.00
62_V	91_T	0.553	1.00
28_G	177_K	0.553	1.00
103_A	153_L	0.552	1.00
163_D	167_K	0.552	1.00
57_A	63_A	0.551	1.00
35_A	91_T	0.550	1.00
67_Y	70_I	0.550	1.00
24_L	162_I	0.550	1.00
81_C	84_D	0.548	1.00
102_V	113_L	0.548	1.00
79_A	83_R	0.546	1.00
6_L	33_T	0.545	1.00
93_K	118_I	0.544	1.00
110_A	130_L	0.542	1.00
22_I	51_V	0.542	1.00
17_E	158_P	0.541	1.00
17_E	74_G	0.529	1.00
47_C	51_V	0.527	1.00
38_A	58_P	0.525	1.00
92_V	118_I	0.525	1.00
82_F	85_S	0.525	1.00
14_E	48_S	0.523	1.00
102_V	118_I	0.522	1.00
113_L	116_H	0.516	1.00
6_L	91_T	0.515	1.00
42_N	55_A	0.511	1.00
72_L	113_L	0.504	1.00
19_V	53_L	0.504	1.00
18_A	73_P	0.503	1.00
9_L	45_I	0.502	1.00
71_V	155_S	0.502	1.00
20_T	24_L	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
3ot1A	2	0.9847	100	0.16	Contact Map
2ab0A	2	0.9745	100	0.161	Contact Map
2rk3A	2	0.9286	100	0.177	Contact Map
4k2hA	4	0.9388	100	0.178	Contact Map
4e08A	2	0.9388	100	0.18	Contact Map
3ewnA	2	0.9643	100	0.183	Contact Map
4xllA	2	0.9286	100	0.184	Contact Map
3noqA	2	0.9541	100	0.187	Contact Map
3mgkA	2	0.949	100	0.19	Contact Map
3graA	2	0.8929	100	0.192	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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