IMMR - BACSU - GREMLIN Contacts

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IMMR - HTH-type transcriptional regulator ImmR

UniProt:	P96631	Sequences: MSLGKRLKEARQKAGYTQKEAAEKLNIGNNNLSNYERDYRDPDTDTLLKLSNLYNVSTDYLLGKDEVSKKNETDLLNKTINEAIQELKDEDTLLFMNDGEFDEETARLVKKALKNGIKFIDELKKKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	127 (110)
Sequences:	1284 (1179)
Seq/√Len:	112.4

ECOLI - DICA
BACSU - IMMR RGHR YQAE RGHRB ANSR SLRR YOBD YONR SINR XRE YQAF YGZD YAZB
HALSA - O51961 Q9HRZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_L	7_L	3.022	1.00
21_A	32_L	2.959	1.00
16_Y	53_L	2.528	1.00
19_K	29_N	2.465	1.00
19_K	23_E	2.428	1.00
21_A	54_Y	2.378	1.00
4_G	38_D	2.308	1.00
34_N	39_Y	2.260	1.00
52_N	64_K	2.105	1.00
11_R	36_E	2.076	1.00
30_N	34_N	2.055	1.00
24_K	53_L	2.035	1.00
28_G	31_N	2.024	1.00
27_I	32_L	1.999	1.00
58_T	62_L	1.901	1.00
7_L	54_Y	1.841	1.00
10_A	54_Y	1.745	1.00
29_N	33_S	1.709	1.00
31_N	34_N	1.667	1.00
21_A	50_L	1.631	1.00
51_S	64_K	1.621	1.00
34_N	40_R	1.614	1.00
44_T	47_L	1.570	1.00
6_R	60_Y	1.552	1.00
30_N	33_S	1.517	1.00
102_D	105_T	1.491	1.00
35_Y	46_T	1.484	1.00
10_A	56_V	1.417	1.00
6_R	63_G	1.383	1.00
43_D	46_T	1.376	1.00
59_D	64_K	1.368	1.00
56_V	60_Y	1.361	1.00
7_L	32_L	1.351	1.00
27_I	31_N	1.327	1.00
8_K	12_Q	1.319	1.00
20_E	23_E	1.311	1.00
41_D	44_T	1.269	0.99
108_L	112_A	1.267	0.99
35_Y	40_R	1.258	0.99
18_Q	32_L	1.209	0.99
5_K	38_D	1.176	0.99
13_K	68_S	1.175	0.99
32_L	35_Y	1.161	0.99
9_E	13_K	1.157	0.99
16_Y	20_E	1.139	0.99
65_D	68_S	1.130	0.99
25_L	50_L	1.112	0.98
6_R	64_K	1.107	0.98
21_A	53_L	1.095	0.98
47_L	58_T	1.094	0.98
22_A	34_N	1.073	0.98
105_T	108_L	1.071	0.98
28_G	34_N	1.044	0.98
6_R	9_E	1.043	0.98
25_L	53_L	1.029	0.97
34_N	37_R	1.028	0.97
6_R	66_E	1.023	0.97
16_Y	24_K	1.005	0.97
18_Q	22_A	0.983	0.96
3_L	44_T	0.969	0.96
18_Q	29_N	0.946	0.96
22_A	30_N	0.943	0.95
14_A	53_L	0.933	0.95
97_N	100_E	0.926	0.95
105_T	112_A	0.915	0.95
19_K	34_N	0.907	0.94
42_P	59_D	0.903	0.94
107_R	111_K	0.899	0.94
11_R	18_Q	0.899	0.94
7_L	21_A	0.893	0.94
35_Y	43_D	0.891	0.94
20_E	24_K	0.890	0.94
34_N	43_D	0.888	0.94
97_N	101_F	0.882	0.94
10_A	13_K	0.867	0.93
30_N	40_R	0.862	0.93
33_S	40_R	0.837	0.92
33_S	42_P	0.835	0.92
3_L	61_L	0.825	0.91
28_G	39_Y	0.819	0.91
18_Q	36_E	0.814	0.91
108_L	111_K	0.813	0.90
22_A	32_L	0.803	0.90
31_N	37_R	0.802	0.90
28_G	33_S	0.798	0.90
48_L	64_K	0.794	0.89
94_L	99_G	0.791	0.89
14_A	24_K	0.790	0.89
17_T	20_E	0.789	0.89
29_N	46_T	0.784	0.89
51_S	63_G	0.779	0.89
27_I	30_N	0.770	0.88
33_S	37_R	0.768	0.88
14_A	55_N	0.767	0.88
87_L	91_D	0.767	0.88
94_L	97_N	0.762	0.87
21_A	25_L	0.757	0.87
101_F	105_T	0.751	0.87
103_E	106_A	0.750	0.87
22_A	36_E	0.738	0.86
19_K	33_S	0.737	0.86
17_T	29_N	0.736	0.86
33_S	43_D	0.729	0.85
30_N	35_Y	0.707	0.83
60_Y	68_S	0.705	0.83
26_N	49_K	0.698	0.82
105_T	111_K	0.698	0.82
29_N	32_L	0.697	0.82
27_I	35_Y	0.697	0.82
11_R	22_A	0.692	0.82
31_N	35_Y	0.686	0.81
98_D	106_A	0.681	0.81
48_L	51_S	0.678	0.81
3_L	41_D	0.676	0.80
87_L	97_N	0.675	0.80
107_R	110_K	0.667	0.79
81_N	88_K	0.666	0.79
3_L	54_Y	0.663	0.79
102_D	108_L	0.659	0.79
60_Y	66_E	0.654	0.78
26_N	30_N	0.654	0.78
103_E	107_R	0.653	0.78
35_Y	44_T	0.633	0.76
46_T	49_K	0.622	0.75
93_L	110_K	0.617	0.74
80_I	84_I	0.616	0.74
93_L	98_D	0.616	0.74
51_S	58_T	0.615	0.74
28_G	42_P	0.608	0.73
80_I	83_A	0.601	0.72
29_N	39_Y	0.588	0.70
5_K	37_R	0.585	0.70
88_K	97_N	0.578	0.69
17_T	37_R	0.577	0.69
95_F	101_F	0.573	0.68
79_T	82_E	0.572	0.68
82_E	88_K	0.566	0.68
65_D	70_K	0.564	0.67
45_D	48_L	0.563	0.67
92_T	112_A	0.561	0.67
42_P	46_T	0.551	0.65
79_T	83_A	0.551	0.65
40_R	44_T	0.543	0.64
81_N	84_I	0.539	0.64
6_R	10_A	0.537	0.63
19_K	31_N	0.534	0.63
91_D	109_V	0.532	0.63
48_L	52_N	0.532	0.63
48_L	58_T	0.530	0.62
101_F	109_V	0.528	0.62
53_L	56_V	0.528	0.62
47_L	62_L	0.525	0.62
27_I	50_L	0.525	0.62
29_N	43_D	0.523	0.61
49_K	52_N	0.517	0.61
96_M	99_G	0.516	0.60
79_T	84_I	0.516	0.60
47_L	59_D	0.512	0.60
29_N	37_R	0.510	0.60
79_T	92_T	0.510	0.60
8_K	39_Y	0.509	0.59
91_D	96_M	0.504	0.59
46_T	50_L	0.503	0.59
85_Q	89_D	0.502	0.58
10_A	60_Y	0.500	0.58

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
4ndwA	2	0.9134	99.8	0.377	Contact Map
3r1fA	2	0.9213	99.8	0.386	Contact Map
3qwgA	2	0.6378	99.7	0.399	Contact Map
3op9A	4	0.8268	99.7	0.406	Contact Map
4o8bA	2	0.7638	99.7	0.408	Contact Map
3ivpA	2	0.8425	99.7	0.411	Contact Map
1b0nA	2	0.8031	99.7	0.43	Contact Map
3u3wA	2	0.9685	99.7	0.431	Contact Map
4jcyA	2	0.6929	99.7	0.436	Contact Map
4yv9A	3	0.937	99.6	0.46	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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