OPENSEQ.org - CCME - ECOLI GREMLIN

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CCME - Cytochrome c-type biogenesis protein CcmE

UniProt:	P69490	Sequence MNIRRKNRLWIACAVLAGLALTIGLVLYALRSNIDLFYTPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGILPDLFREGQGVVVQGELEKGNHILAKEVLAKHDENYTPPEVEKAMEANHRRPASVYKDPAS	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12055
Length:	159 (142)
Sequences:	556
Seq/Len:	3.92

CCME
Paralog alert: 0.03 [within 20: 0.00] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
67_M	83_T	2.868	1.00
79_K	96_E	2.867	1.00
42_E	47_K	2.591	1.00
84_I	109_V	2.338	1.00
67_M	90_S	2.265	1.00
112_Q	125_E	2.06	1.00
3_I	6_K	2.014	1.00
65_M	87_A	1.914	1.00
139_V	142_A	1.821	1.00
104_R	107_Q	1.776	0.99
43_I	60_L	1.721	0.99
83_T	90_S	1.662	0.99
140_E	144_E	1.621	0.99
25_L	29_A	1.568	0.98
144_E	147_H	1.554	0.98
60_L	121_I	1.51	0.98
93_V	109_V	1.506	0.98
116_E	120_H	1.487	0.97
30_L	34_I	1.437	0.96
99_L	126_V	1.435	0.96
94_S	120_H	1.402	0.96
116_E	122_L	1.396	0.96
72_Q	81_T	1.393	0.96
21_L	31_R	1.369	0.95
30_L	35_D	1.342	0.94
104_R	109_V	1.325	0.94
20_A	24_G	1.305	0.93
37_F	108_G	1.301	0.93
141_K	144_E	1.298	0.93
63_G	130_H	1.295	0.93
139_V	143_M	1.241	0.91
17_A	21_L	1.219	0.90
40_P	130_H	1.213	0.89
65_M	143_M	1.207	0.89
30_L	78_L	1.202	0.89
108_G	137_P	1.196	0.88
102_L	130_H	1.19	0.88
7_N	32_S	1.174	0.87
31_R	135_T	1.161	0.86
47_K	54_P	1.152	0.86
41_G	62_V	1.151	0.86
80_V	99_L	1.148	0.85
59_R	124_K	1.147	0.85
19_L	24_G	1.142	0.85
2_N	145_A	1.134	0.84
40_P	63_G	1.131	0.84
81_T	120_H	1.116	0.83
40_P	102_L	1.112	0.83
21_L	44_L	1.109	0.83
107_Q	133_N	1.094	0.81
36_L	112_Q	1.088	0.81
44_L	119_N	1.084	0.81
19_L	35_D	1.077	0.80
28_Y	36_L	1.073	0.80
74_D	77_S	1.072	0.80
116_E	119_N	1.07	0.79
1_M	5_R	1.069	0.79
30_L	36_L	1.067	0.79
102_L	132_E	1.065	0.79
41_G	45_Y	1.049	0.77
27_L	104_R	1.036	0.76
30_L	33_N	1.032	0.76
128_A	136_P	1.028	0.75
37_F	105_E	1.028	0.75
28_Y	35_D	1.023	0.75
41_G	88_E	1.018	0.74
81_T	92_D	1.015	0.74
29_A	126_V	1.013	0.74
63_G	132_E	1.011	0.74
40_P	131_D	1.01	0.74
79_K	94_S	1.008	0.73
138_E	142_A	1.006	0.73
2_N	39_T	1.006	0.73
93_V	137_P	1.003	0.73

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
1sr3A	1	0.8176	100	0.255	Contact Map	0.506
1j6qA	1	0.8428	100	0.263	Contact Map	0.533
2kctA	1	0.566	100	0.516	Contact Map	0.643
4hl0A	2	0.4591	26.4	0.945	Contact Map	0.191
1n9wA	2	0.6667	23.3	0.946	Contact Map	0.303
4gn4B	1	0.5283	18.7	0.949	Contact Map	0.552
1o7iA	2	0.6792	17.4	0.949	Contact Map	0.378
2lxjA	1	0.3962	16.7	0.95	Contact Map	0.141
3camA	2	0.3962	16.5	0.95	Contact Map	0.166
2xgtA	2	0.6667	16.1	0.95	Contact Map	0.479

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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