PAL - ECOLI - GREMLIN Contacts

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PAL - Peptidoglycan-associated lipoprotein

UniProt:	P0A912	Sequences: MQLNKVLKGLMIALPVMAIAACSSNKNASNDGSEGMLGAGTGMDANGGNGNMSSEEQARLQMQQLQQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10684
Length:	173 (151)
Sequences:	8581 (6602)
Seq/√Len:	537.3

ECOLI - PAL YFIB YIAD OMPA MOTB MBHA
BACSU - YTXE MOTB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_D	117_Y	3.597	1.00
74_D	81_R	3.577	1.00
106_E	148_Y	3.324	1.00
122_G	147_S	2.973	1.00
157_G	162_A	2.929	1.00
89_D	136_K	2.756	1.00
120_S	124_R	2.683	1.00
155_V	162_A	2.649	1.00
112_R	163_Y	2.620	1.00
75_L	112_R	2.609	1.00
123_E	127_N	2.569	1.00
108_H	152_K	2.555	1.00
89_D	132_Y	2.525	1.00
88_L	132_Y	2.454	1.00
148_Y	152_K	2.392	1.00
78_Y	124_R	2.379	1.00
119_I	123_E	2.353	1.00
130_K	145_I	2.288	1.00
156_L	162_A	2.139	1.00
115_P	150_K	1.931	1.00
155_V	165_K	1.924	1.00
105_V	169_A	1.825	1.00
159_D	162_A	1.765	1.00
115_P	151_E	1.623	1.00
132_Y	136_K	1.603	1.00
130_K	134_Q	1.554	1.00
119_I	151_E	1.547	1.00
134_Q	143_I	1.532	1.00
127_N	130_K	1.527	1.00
80_I	132_Y	1.500	1.00
104_T	144_S	1.500	1.00
139_S	142_Q	1.469	1.00
74_D	77_K	1.451	1.00
111_E	163_Y	1.421	1.00
157_G	163_Y	1.407	1.00
80_I	84_F	1.378	1.00
117_Y	120_S	1.373	1.00
158_H	162_A	1.365	1.00
130_K	143_I	1.358	1.00
105_V	130_K	1.357	1.00
104_T	146_V	1.331	1.00
127_N	145_I	1.317	1.00
82_S	85_A	1.316	1.00
127_N	131_M	1.314	1.00
85_A	132_Y	1.270	1.00
134_Q	140_A	1.255	1.00
92_A	133_L	1.212	1.00
87_M	90_A	1.150	1.00
138_V	143_I	1.121	1.00
130_K	140_A	1.113	1.00
102_K	144_S	1.111	1.00
106_E	146_V	1.109	1.00
93_N	96_R	1.090	1.00
108_H	153_P	1.087	1.00
103_V	143_I	1.084	1.00
117_Y	150_K	1.078	1.00
92_A	136_K	1.064	1.00
106_E	152_K	1.050	1.00
132_Y	135_G	1.050	1.00
138_V	142_Q	1.042	1.00
80_I	128_A	1.040	1.00
159_D	163_Y	1.035	1.00
156_L	159_D	1.032	1.00
78_Y	121_L	1.017	1.00
34_E	38_G	1.017	1.00
123_E	145_I	1.007	1.00
81_R	84_F	0.995	1.00
75_L	117_Y	0.988	1.00
108_H	170_V	0.982	1.00
153_P	166_N	0.976	1.00
34_E	37_L	0.971	1.00
116_E	120_S	0.971	1.00
31_D	38_G	0.961	1.00
112_R	160_E	0.956	1.00
72_Y	84_F	0.943	1.00
98_N	101_Y	0.942	1.00
94_F	98_N	0.937	1.00
31_D	34_E	0.925	1.00
131_M	135_G	0.923	1.00
111_E	157_G	0.921	1.00
22_C	25_N	0.918	1.00
161_A	165_K	0.916	1.00
86_Q	90_A	0.915	1.00
14_L	18_A	0.910	1.00
89_D	93_N	0.900	1.00
31_D	35_G	0.900	1.00
111_E	158_H	0.898	1.00
75_L	110_D	0.883	1.00
111_E	150_K	0.878	1.00
85_A	89_D	0.871	1.00
28_A	33_S	0.863	1.00
27_N	30_N	0.861	1.00
93_N	97_S	0.856	1.00
154_A	165_K	0.851	1.00
15_P	18_A	0.848	1.00
92_A	96_R	0.846	1.00
110_D	118_N	0.844	1.00
105_V	143_I	0.844	1.00
96_R	138_V	0.844	1.00
16_V	20_A	0.841	1.00
53_S	56_E	0.839	1.00
35_G	38_G	0.837	1.00
153_P	163_Y	0.833	1.00
33_S	37_L	0.823	1.00
28_A	31_D	0.818	1.00
86_Q	89_D	0.817	1.00
114_T	117_Y	0.816	1.00
14_L	17_M	0.813	1.00
129_V	169_A	0.801	1.00
123_E	147_S	0.799	1.00
162_A	165_K	0.790	1.00
126_A	147_S	0.783	1.00
12_I	16_V	0.778	1.00
20_A	23_S	0.772	1.00
113_G	118_N	0.766	1.00
158_H	163_Y	0.765	1.00
26_K	29_S	0.763	1.00
95_L	103_V	0.763	1.00
73_F	169_A	0.763	1.00
78_Y	128_A	0.760	1.00
105_V	126_A	0.760	1.00
75_L	113_G	0.756	1.00
23_S	28_A	0.756	1.00
32_G	35_G	0.751	1.00
29_S	33_S	0.751	1.00
131_M	134_Q	0.750	1.00
10_L	13_A	0.750	1.00
59_R	62_M	0.749	1.00
70_I	170_V	0.743	1.00
91_H	95_L	0.742	1.00
111_E	166_N	0.739	1.00
160_E	163_Y	0.739	1.00
90_A	94_F	0.737	1.00
81_R	164_S	0.731	1.00
117_Y	124_R	0.728	1.00
54_S	58_A	0.725	1.00
88_L	129_V	0.722	1.00
26_K	30_N	0.720	1.00
115_P	119_I	0.720	1.00
108_H	151_E	0.719	1.00
92_A	138_V	0.714	1.00
80_I	85_A	0.712	1.00
111_E	162_A	0.708	1.00
106_E	170_V	0.704	1.00
9_G	13_A	0.692	1.00
29_S	32_G	0.692	1.00
73_F	129_V	0.681	1.00
108_H	148_Y	0.680	1.00
21_A	24_S	0.680	1.00
30_N	37_L	0.679	1.00
58_A	62_M	0.679	1.00
88_L	133_L	0.676	1.00
57_Q	66_Q	0.673	1.00
33_S	36_M	0.668	1.00
68_N	91_H	0.667	1.00
112_R	117_Y	0.666	1.00
15_P	19_I	0.663	1.00
115_P	149_G	0.658	1.00
123_E	146_V	0.653	1.00
112_R	150_K	0.652	1.00
120_S	123_E	0.649	1.00
61_Q	65_L	0.648	1.00
30_N	33_S	0.646	1.00
96_R	139_S	0.646	1.00
90_A	93_N	0.644	1.00
31_D	37_L	0.641	1.00
153_P	157_G	0.637	1.00
29_S	35_G	0.635	1.00
66_Q	170_V	0.628	1.00
84_F	87_M	0.627	1.00
13_A	17_M	0.626	1.00
17_M	20_A	0.624	1.00
124_R	127_N	0.622	1.00
109_A	150_K	0.611	1.00
107_G	169_A	0.600	1.00
128_A	131_M	0.600	1.00
114_T	150_K	0.600	1.00
25_N	30_N	0.598	1.00
155_V	159_D	0.596	1.00
111_E	153_P	0.593	1.00
126_A	145_I	0.592	1.00
19_I	22_C	0.589	1.00
32_G	36_M	0.589	1.00
56_E	60_L	0.588	0.99
94_F	101_Y	0.582	0.99
25_N	28_A	0.580	0.99
30_N	36_M	0.579	0.99
60_L	63_Q	0.579	0.99
61_Q	64_Q	0.577	0.99
159_D	166_N	0.572	0.99
26_K	34_E	0.572	0.99
78_Y	120_S	0.571	0.99
155_V	166_N	0.571	0.99
91_H	171_L	0.565	0.99
13_A	16_V	0.564	0.99
25_N	31_D	0.563	0.99
63_Q	67_Q	0.563	0.99
102_K	142_Q	0.563	0.99
31_D	36_M	0.562	0.99
72_Y	154_A	0.557	0.99
18_A	21_A	0.557	0.99
72_Y	164_S	0.555	0.99
11_M	20_A	0.553	0.99
29_S	34_E	0.548	0.99
29_S	37_L	0.548	0.99
55_E	58_A	0.546	0.99
26_K	32_G	0.542	0.99
60_L	64_Q	0.541	0.99
67_Q	72_Y	0.541	0.99
59_R	63_Q	0.540	0.99
66_Q	69_N	0.537	0.99
30_N	34_E	0.534	0.99
118_N	150_K	0.533	0.99
10_L	14_L	0.531	0.99
115_P	120_S	0.529	0.99
11_M	14_L	0.525	0.99
69_N	87_M	0.524	0.99
63_Q	68_N	0.522	0.99
65_L	69_N	0.518	0.99
24_S	27_N	0.515	0.99
75_L	118_N	0.515	0.99
19_I	25_N	0.515	0.99
11_M	15_P	0.514	0.99
28_A	32_G	0.512	0.99
108_H	168_R	0.502	0.98
57_Q	60_L	0.500	0.98

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
3ldtA	2	0.8035	100	0.239	Contact Map
2k1sA	1	0.7977	100	0.268	Contact Map
2aizP	1	0.7746	100	0.28	Contact Map
2hqsH	1	0.6185	100	0.282	Contact Map
1r1mA	1	0.6705	100	0.286	Contact Map
2l26A	1	0.9884	100	0.291	Contact Map
2kgwA	1	0.7399	100	0.293	Contact Map
4b62A	1	0.7861	100	0.295	Contact Map
3td3A	2	0.6763	100	0.296	Contact Map
4b5cA	1	0.6879	100	0.299	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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