NLPC - ECOLI - GREMLIN Contacts

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NLPC - Probable endopeptidase NlpC

UniProt:	P23898	Sequences: MRFCLILITALLLAGCSHHKAPPPNARLSDSITVIAGLNDQLQSWHGTPYRYGGMTRRGVDCSGFVVVTMRDRFDLQLPRETKQQASIGTQIDKDELLPGDLVFFKTGSGQNGLHVGIYDTNNQFIHASTSKGVMRSSLDNVYWQKNFWQARRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11133
Length:	154 (126)
Sequences:	5728 (3973)
Seq/√Len:	353.9

ECOLI - NLPC MEPS YAFL MEPH
BACSU - LYTF YDDH YKFC CWLO LYTE CWLS PGDS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_D	136_R	3.163	1.00
79_P	88_I	2.646	1.00
60_V	68_V	2.542	1.00
148_F	151_A	2.387	1.00
42_L	126_I	2.362	1.00
97_L	151_A	2.330	1.00
41_Q	74_F	2.244	1.00
127_H	137_S	2.184	1.00
54_G	59_G	2.056	1.00
89_G	152_R	2.027	1.00
45_W	48_T	2.013	1.00
86_A	150_Q	1.959	1.00
43_Q	136_R	1.958	1.00
66_V	118_I	1.952	1.00
129_S	133_G	1.938	1.00
66_V	85_Q	1.906	1.00
124_Q	138_S	1.890	1.00
102_L	116_V	1.829	1.00
36_A	99_P	1.811	1.00
129_S	132_K	1.772	1.00
91_Q	152_R	1.767	1.00
55_M	80_R	1.734	1.00
81_E	84_Q	1.666	1.00
56_T	59_G	1.618	1.00
113_G	149_W	1.613	1.00
117_G	125_F	1.602	1.00
41_Q	45_W	1.569	1.00
43_Q	126_I	1.525	1.00
35_I	39_N	1.499	1.00
65_F	69_T	1.482	1.00
67_V	71_R	1.481	1.00
62_C	115_H	1.448	1.00
82_T	86_A	1.421	1.00
119_Y	123_N	1.354	1.00
66_V	78_L	1.341	1.00
66_V	116_V	1.340	1.00
48_T	134_V	1.310	1.00
41_Q	69_T	1.282	1.00
86_A	113_G	1.280	1.00
67_V	85_Q	1.265	1.00
105_F	117_G	1.255	1.00
125_F	139_L	1.255	1.00
55_M	67_V	1.240	1.00
41_Q	44_S	1.220	1.00
39_N	120_D	1.194	1.00
129_S	135_M	1.184	1.00
48_T	59_G	1.178	1.00
93_D	96_E	1.177	1.00
38_L	74_F	1.175	1.00
107_T	114_L	1.174	1.00
41_Q	73_R	1.168	1.00
124_Q	136_R	1.163	1.00
70_M	78_L	1.161	1.00
66_V	102_L	1.137	1.00
97_L	119_Y	1.120	1.00
71_R	77_Q	1.111	1.00
67_V	80_R	1.099	1.00
104_F	116_V	1.098	1.00
57_R	60_V	1.069	1.00
94_K	97_L	1.068	1.00
46_H	126_I	1.066	1.00
82_T	113_G	1.065	1.00
84_Q	87_S	1.059	1.00
69_T	74_F	1.054	1.00
105_F	125_F	1.033	1.00
60_V	64_G	1.028	1.00
123_N	140_D	1.026	1.00
115_H	127_H	0.982	1.00
103_V	148_F	0.961	1.00
106_K	114_L	0.959	1.00
45_W	68_V	0.951	1.00
36_A	40_D	0.937	1.00
137_S	141_N	0.929	1.00
130_T	133_G	0.927	1.00
68_V	73_R	0.927	1.00
107_T	147_N	0.924	1.00
49_P	59_G	0.923	1.00
80_R	84_Q	0.920	1.00
126_I	136_R	0.917	1.00
40_D	43_Q	0.907	1.00
48_T	56_T	0.904	1.00
106_K	149_W	0.902	1.00
39_N	126_I	0.899	1.00
132_K	135_M	0.891	1.00
119_Y	122_N	0.890	1.00
38_L	70_M	0.884	1.00
91_Q	150_Q	0.868	1.00
48_T	54_G	0.858	1.00
69_T	118_I	0.849	1.00
106_K	112_N	0.842	1.00
103_V	151_A	0.830	1.00
85_Q	116_V	0.824	1.00
78_L	85_Q	0.823	1.00
108_G	114_L	0.820	1.00
41_Q	68_V	0.813	1.00
94_K	145_Q	0.804	1.00
35_I	99_P	0.802	1.00
52_Y	81_E	0.801	1.00
125_F	144_W	0.800	1.00
50_Y	62_C	0.799	1.00
80_R	88_I	0.799	1.00
38_L	69_T	0.796	1.00
51_R	59_G	0.792	1.00
66_V	70_M	0.791	1.00
43_Q	46_H	0.789	1.00
43_Q	120_D	0.786	1.00
83_K	87_S	0.786	1.00
50_Y	128_A	0.769	1.00
108_G	113_G	0.768	1.00
106_K	113_G	0.763	1.00
97_L	103_V	0.755	1.00
103_V	117_G	0.754	1.00
33_T	36_A	0.753	1.00
45_W	60_V	0.751	1.00
127_H	135_M	0.750	1.00
48_T	60_V	0.750	1.00
60_V	134_V	0.749	1.00
99_P	120_D	0.741	1.00
46_H	133_G	0.739	1.00
89_G	92_I	0.738	1.00
103_V	139_L	0.737	1.00
52_Y	64_G	0.736	1.00
34_V	37_G	0.736	1.00
86_A	89_G	0.726	0.99
106_K	111_Q	0.723	0.99
35_I	38_L	0.717	0.99
142_V	146_K	0.715	0.99
79_P	84_Q	0.710	0.99
39_N	42_L	0.705	0.99
54_G	64_G	0.694	0.99
141_N	145_Q	0.687	0.99
108_G	111_Q	0.682	0.99
42_L	118_I	0.670	0.99
103_V	125_F	0.668	0.99
39_N	43_Q	0.659	0.99
46_H	136_R	0.659	0.99
86_A	149_W	0.658	0.99
94_K	148_F	0.658	0.99
117_G	127_H	0.655	0.99
45_W	56_T	0.653	0.99
65_F	126_I	0.651	0.99
92_I	153_R	0.649	0.99
83_K	86_A	0.644	0.99
31_S	34_V	0.636	0.99
68_V	71_R	0.635	0.99
37_G	74_F	0.630	0.99
25_N	30_D	0.622	0.98
82_T	116_V	0.614	0.98
125_F	140_D	0.609	0.98
140_D	145_Q	0.607	0.98
142_V	145_Q	0.606	0.98
94_K	140_D	0.604	0.98
45_W	69_T	0.597	0.98
94_K	151_A	0.592	0.98
48_T	57_R	0.592	0.98
108_G	147_N	0.588	0.98
125_F	137_S	0.586	0.98
129_S	137_S	0.586	0.98
38_L	65_F	0.585	0.98
64_G	67_V	0.581	0.98
59_G	64_G	0.570	0.97
70_M	118_I	0.569	0.97
55_M	64_G	0.567	0.97
82_T	85_Q	0.560	0.97
120_D	124_Q	0.553	0.97
50_Y	115_H	0.543	0.96
94_K	103_V	0.541	0.96
97_L	139_L	0.541	0.96
97_L	148_F	0.540	0.96
25_N	28_L	0.540	0.96
42_L	69_T	0.538	0.96
26_A	29_S	0.536	0.96
108_G	112_N	0.535	0.96
34_V	38_L	0.534	0.96
86_A	104_F	0.533	0.96
114_L	147_N	0.530	0.96
37_G	40_D	0.527	0.96
30_D	34_V	0.524	0.96
45_W	65_F	0.522	0.95
33_T	37_G	0.522	0.95
70_M	76_L	0.514	0.95
56_T	60_V	0.513	0.95
62_C	82_T	0.512	0.95
67_V	77_Q	0.512	0.95
144_W	147_N	0.511	0.95
64_G	128_A	0.511	0.95
55_M	68_V	0.504	0.95
102_L	118_I	0.503	0.94
121_T	124_Q	0.500	0.94

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
2k1gA	1	0.7987	100	0.259	Contact Map
3npfA	2	0.974	100	0.275	Contact Map
3h41A	1	0.9935	100	0.279	Contact Map
4hpeA	1	0.961	100	0.282	Contact Map
4q4gX	1	0.9481	100	0.283	Contact Map
4xcmA	2	0.9221	100	0.287	Contact Map
4fdyA	1	0.9221	100	0.293	Contact Map
2hbwA	1	0.9481	100	0.299	Contact Map
3pbiA	1	0.9156	100	0.311	Contact Map
3m1uA	2	0.9545	100	0.331	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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