CZRA - BACSU - GREMLIN Contacts

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CZRA - HTH-type transcriptional repressor CzrA

UniProt:	O31844	Sequences: MTEFRETEQSAADLDEETLFLVAQTFKALSDPTRIRILHLLSQGEHAVNGIAEKLNLLQSTVSHQLRFLKNLRLVKSRREGTSIYYSPEDEHVLDVLQQMIHHTQHD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	107 (88)
Sequences:	5311 (3488)
Seq/√Len:	371.8

ECOLI - ARSR YGAV
BACSU - CZRA ARSR ASER SDPR YBZH YCEK
HALSA - ARSR2
SULSO - Q97VE0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_E	78_R	3.304	1.00
77_S	84_I	3.016	1.00
76_K	87_S	2.958	1.00
79_R	84_I	2.334	1.00
76_K	89_E	2.261	1.00
28_A	72_L	2.153	1.00
20_F	32_P	1.888	1.00
70_K	77_S	1.870	1.00
57_L	62_V	1.843	1.00
45_E	87_S	1.820	1.00
95_D	99_Q	1.783	1.00
40_L	54_K	1.703	1.00
24_Q	71_N	1.601	1.00
67_R	71_N	1.591	1.00
38_L	74_L	1.578	1.00
45_E	85_Y	1.552	1.00
23_A	32_P	1.534	1.00
47_A	83_S	1.525	1.00
40_L	46_H	1.454	1.00
66_L	75_V	1.369	1.00
57_L	61_T	1.356	1.00
28_A	68_F	1.349	1.00
37_I	51_I	1.346	1.00
15_D	18_T	1.346	1.00
31_D	64_H	1.315	1.00
42_S	94_L	1.291	1.00
52_A	59_Q	1.271	1.00
46_H	50_G	1.266	1.00
16_E	36_R	1.265	1.00
41_L	75_V	1.254	1.00
47_A	50_G	1.251	1.00
61_T	64_H	1.246	1.00
48_V	66_L	1.245	1.00
26_F	96_V	1.235	1.00
26_F	100_M	1.223	1.00
33_T	62_V	1.212	1.00
94_L	98_Q	1.199	1.00
68_F	72_L	1.195	1.00
58_L	61_T	1.183	1.00
22_V	100_M	1.163	1.00
98_Q	102_H	1.131	1.00
46_H	54_K	1.117	1.00
45_E	80_E	1.093	1.00
55_L	62_V	1.069	1.00
64_H	82_T	1.069	1.00
51_I	62_V	1.066	1.00
42_S	98_Q	1.065	1.00
95_D	102_H	1.057	1.00
73_R	89_E	1.040	1.00
49_N	83_S	1.038	1.00
66_L	70_K	1.015	1.00
38_L	88_P	1.003	1.00
68_F	71_N	1.002	1.00
50_G	53_E	0.995	1.00
33_T	57_L	0.978	1.00
19_L	36_R	0.972	1.00
25_T	74_L	0.952	1.00
18_T	21_L	0.944	1.00
41_L	46_H	0.943	1.00
52_A	62_V	0.938	1.00
91_E	94_L	0.905	1.00
20_F	24_Q	0.895	1.00
95_D	98_Q	0.891	1.00
80_E	83_S	0.887	1.00
17_E	20_F	0.881	1.00
70_K	84_I	0.867	1.00
26_F	29_L	0.860	1.00
16_E	20_F	0.851	1.00
23_A	30_S	0.837	1.00
19_L	39_H	0.817	1.00
37_I	41_L	0.815	1.00
90_D	93_V	0.802	1.00
92_H	96_V	0.785	1.00
26_F	30_S	0.782	1.00
69_L	75_V	0.782	1.00
91_E	95_D	0.774	1.00
64_H	68_F	0.753	1.00
36_R	40_L	0.744	1.00
48_V	70_K	0.731	1.00
23_A	35_I	0.731	1.00
58_L	64_H	0.725	1.00
38_L	97_L	0.717	1.00
15_D	19_L	0.711	1.00
93_V	97_L	0.701	0.99
46_H	51_I	0.682	0.99
25_T	96_V	0.675	0.99
33_T	36_R	0.672	0.99
47_A	85_Y	0.672	0.99
79_R	82_T	0.672	0.99
61_T	65_Q	0.671	0.99
76_K	90_D	0.664	0.99
21_L	24_Q	0.661	0.99
40_L	55_L	0.647	0.99
40_L	51_I	0.642	0.99
49_N	53_E	0.634	0.99
29_L	32_P	0.634	0.99
43_Q	46_H	0.618	0.99
28_A	74_L	0.613	0.99
70_K	79_R	0.612	0.99
31_D	61_T	0.608	0.98
21_L	73_R	0.608	0.98
52_A	56_N	0.607	0.98
64_H	67_R	0.598	0.98
80_E	85_Y	0.583	0.98
39_H	97_L	0.582	0.98
96_V	100_M	0.579	0.98
33_T	65_Q	0.579	0.98
32_P	36_R	0.579	0.98
27_K	30_S	0.576	0.98
67_R	70_K	0.570	0.98
31_D	65_Q	0.568	0.98
58_L	82_T	0.557	0.97
52_A	55_L	0.553	0.97
60_S	64_H	0.550	0.97
99_Q	102_H	0.548	0.97
25_T	92_H	0.548	0.97
39_H	43_Q	0.548	0.97
17_E	91_E	0.544	0.97
21_L	95_D	0.544	0.97
50_G	54_K	0.541	0.97
26_F	35_I	0.534	0.97
89_E	92_H	0.531	0.96
92_H	100_M	0.526	0.96
16_E	19_L	0.522	0.96
48_V	63_S	0.521	0.96
36_R	39_H	0.517	0.96
44_G	50_G	0.510	0.95
22_V	101_I	0.510	0.95
22_V	92_H	0.509	0.95
39_H	42_S	0.508	0.95
58_L	65_Q	0.501	0.95
21_L	92_H	0.500	0.95

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
1r1tA	2	0.9159	99.7	0.49	Contact Map
1u2wA	2	1	99.7	0.491	Contact Map
1r1uA	2	0.8972	99.7	0.505	Contact Map
2kkoA	2	0.9346	99.7	0.507	Contact Map
2jscA	2	0.8131	99.6	0.528	Contact Map
4k2eA	2	0.8879	99.6	0.532	Contact Map
3pqkA	2	0.9065	99.6	0.534	Contact Map
1q1hA	1	0.7477	99.6	0.541	Contact Map
3f6vA	2	0.8037	99.6	0.541	Contact Map
2vxzA	1	0.7664	99.6	0.545	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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