OPENSEQ.org - HOLC - ECOLI GREMLIN

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HOLC - DNA polymerase III subunit chi

UniProt:	P28905	Sequence MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11413
Length:	147 (145)
Sequences:	581
Seq/Len:	4.01

HOLC
Paralog alert: 0.01 [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
49_A	82_I	3.109	1.00
29_A	41_I	2.406	1.00
40_L	83_A	2.359	1.00
8_L	143_T	2.335	1.00
32_R	39_V	2.285	1.00
117_V	127_A	2.128	1.00
65_V	80_V	2.09	1.00
115_D	130_R	2.079	1.00
131_Y	135_R	1.907	1.00
115_D	134_Y	1.782	0.99
60_P	63_S	1.725	0.99
96_L	110_F	1.72	0.99
7_Y	24_L	1.583	0.98
5_T	142_N	1.576	0.98
133_A	137_A	1.521	0.98
49_A	69_L	1.51	0.98
21_V	123_L	1.482	0.97
30_A	60_P	1.467	0.97
46_E	50_Y	1.452	0.97
29_A	39_V	1.45	0.97
42_A	96_L	1.418	0.96
129_E	135_R	1.408	0.96
14_T	23_Q	1.378	0.95
31_E	112_E	1.371	0.95
53_D	67_H	1.347	0.95
4_A	139_F	1.325	0.94
73_G	81_E	1.321	0.94
4_A	69_L	1.321	0.94
121_D	125_Q	1.304	0.93
26_C	56_L	1.263	0.92
25_V	29_A	1.25	0.91
112_E	144_A	1.242	0.91
3_N	76_G	1.24	0.91
131_Y	143_T	1.232	0.90
53_D	66_P	1.23	0.90
91_S	144_A	1.229	0.90
48_Q	100_R	1.206	0.89
74_P	77_G	1.199	0.89
68_N	135_R	1.199	0.89
94_D	111_T	1.189	0.88
50_Y	73_G	1.189	0.88
7_Y	28_I	1.173	0.87
3_N	142_N	1.161	0.87
49_A	84_W	1.129	0.85
24_L	27_E	1.123	0.84
127_A	130_R	1.121	0.84
125_Q	129_E	1.121	0.84
61_A	136_V	1.115	0.84
129_E	132_K	1.107	0.83
1_M	146_W	1.103	0.83
68_N	78_A	1.087	0.81
98_S	134_Y	1.08	0.81
118_P	123_L	1.075	0.80
22_E	48_Q	1.066	0.80
42_A	83_A	1.057	0.79
116_F	124_K	1.056	0.79
42_A	106_F	1.053	0.78
10_D	13_T	1.048	0.78
98_S	115_D	1.047	0.78
2_K	139_F	1.046	0.78
95_I	116_F	1.039	0.77
5_T	114_V	1.037	0.77
30_A	63_S	1.032	0.76
52_L	86_Q	1.032	0.76
97_I	114_V	1.029	0.76
134_Y	141_L	1.028	0.76
96_L	104_A	1.015	0.75
22_E	51_R	1.013	0.75
35_S	114_V	1.01	0.74
85_P	89_S	1.007	0.74

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
3sxuA	1	1	100	0.048	Contact Map	0.664
2ocaA	1	1	64.9	0.914	Contact Map	0.603
2eyqA	2	0.9388	35.6	0.928	Contact Map	0.381
4ernA	1	0.9252	30.3	0.931	Contact Map	0.599
1nktA	2	0.9048	28.8	0.931	Contact Map	0.736
1ofdA	2	0.9456	21.6	0.935	Contact Map	0.16
1tf5A	1	0.9456	19.6	0.937	Contact Map	0.62
2ipcA	4	0.9456	17.8	0.938	Contact Map	0.673
2fsfA	2	0.9048	12	0.942	Contact Map	0.689
1hyqA	1	0.9592	11.8	0.943	Contact Map	0.403

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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