SINR - BACSU - GREMLIN Contacts

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SINR - HTH-type transcriptional regulator SinR

UniProt:	P06533	Sequences: MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDEKHETEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	111 (102)
Sequences:	1192 (1057)
Seq/√Len:	104.6

ECOLI - DICA YDCN PUUR
BACSU - SINR SLRR ANSR YQAE YONR YOBD XRE RGHR RGHRB IMMR 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
18_S	22_E	3.334	1.00
20_L	31_L	3.313	1.00
52_A	64_E	2.880	1.00
18_S	28_K	2.793	1.00
10_R	35_E	2.542	1.00
15_Y	53_V	2.505	1.00
12_E	68_T	2.319	1.00
3_G	37_N	2.291	1.00
2_I	6_I	2.250	1.00
29_S	33_S	2.232	1.00
27_A	30_Y	2.157	1.00
23_K	53_V	2.142	1.00
26_V	31_L	2.039	1.00
58_V	62_L	1.955	1.00
41_N	44_I	1.853	1.00
36_R	39_Q	1.817	1.00
33_S	40_T	1.812	1.00
9_Y	54_L	1.749	1.00
33_S	39_Q	1.743	1.00
20_L	54_L	1.672	1.00
5_R	60_T	1.604	1.00
28_K	32_S	1.567	1.00
59_H	64_E	1.487	1.00
65_K	68_T	1.467	1.00
33_S	36_R	1.462	1.00
27_A	33_S	1.408	1.00
90_V	95_F	1.383	1.00
29_S	32_S	1.379	1.00
30_Y	33_S	1.362	1.00
91_S	94_Q	1.344	0.99
97_E	104_W	1.343	0.99
44_I	47_L	1.301	0.99
98_F	101_Y	1.256	0.99
20_L	50_V	1.247	0.99
19_E	22_E	1.241	0.99
26_V	30_Y	1.241	0.99
51_S	64_E	1.234	0.99
4_Q	37_N	1.218	0.99
15_Y	23_K	1.193	0.99
32_S	36_R	1.187	0.99
2_I	44_I	1.170	0.99
88_S	91_S	1.170	0.99
17_L	28_K	1.127	0.98
98_F	102_Q	1.058	0.97
101_Y	104_W	1.057	0.97
87_T	90_V	1.024	0.97
34_I	40_T	1.018	0.96
99_L	103_K	1.002	0.96
91_S	95_F	0.992	0.96
6_I	31_L	0.980	0.96
87_T	91_S	0.976	0.95
100_D	104_W	0.964	0.95
80_K	83_R	0.951	0.95
92_K	95_F	0.920	0.94
9_Y	56_V	0.918	0.94
25_G	49_K	0.912	0.93
17_L	31_L	0.891	0.93
24_A	54_L	0.886	0.92
13_K	23_K	0.883	0.92
21_A	33_S	0.879	0.92
43_S	46_F	0.859	0.91
5_R	66_H	0.854	0.91
82_V	85_A	0.852	0.91
26_V	46_F	0.851	0.91
34_I	46_F	0.836	0.90
90_V	94_Q	0.830	0.90
47_L	62_L	0.822	0.89
74_L	85_A	0.815	0.89
28_K	31_L	0.809	0.89
96_R	99_L	0.803	0.88
21_A	31_L	0.790	0.87
28_K	36_R	0.783	0.87
5_R	8_Q	0.780	0.87
98_F	103_K	0.779	0.87
28_K	43_S	0.777	0.86
28_K	33_S	0.766	0.86
94_Q	97_E	0.765	0.86
6_I	20_L	0.760	0.85
20_L	24_A	0.757	0.85
20_L	53_V	0.756	0.85
24_A	50_V	0.756	0.85
76_S	79_E	0.751	0.85
78_W	82_V	0.749	0.84
79_E	82_V	0.744	0.84
41_N	46_F	0.738	0.84
74_L	78_W	0.736	0.83
81_L	85_A	0.735	0.83
18_S	32_S	0.725	0.82
56_V	60_T	0.721	0.82
87_T	93_K	0.717	0.82
97_E	101_Y	0.712	0.81
95_F	98_F	0.701	0.80
5_R	63_D	0.700	0.80
9_Y	60_T	0.692	0.79
75_D	85_A	0.690	0.79
80_K	84_D	0.687	0.79
92_K	98_F	0.686	0.79
15_Y	19_E	0.685	0.79
28_K	39_Q	0.683	0.79
34_I	43_S	0.683	0.79
86_M	100_D	0.680	0.78
46_F	49_K	0.677	0.78
47_L	58_V	0.672	0.77
94_Q	101_Y	0.659	0.76
78_W	81_L	0.644	0.74
26_V	33_S	0.643	0.74
71_D	74_L	0.642	0.74
29_S	40_T	0.634	0.73
8_Q	12_E	0.634	0.73
88_S	100_D	0.627	0.72
2_I	54_L	0.626	0.72
77_E	81_L	0.626	0.72
55_D	69_E	0.624	0.72
17_L	21_A	0.618	0.71
24_A	53_V	0.618	0.71
91_S	98_F	0.610	0.70
27_A	40_T	0.608	0.70
47_L	59_H	0.608	0.70
30_Y	41_N	0.607	0.70
78_W	85_A	0.606	0.70
60_T	65_K	0.598	0.69
40_T	43_S	0.596	0.69
98_F	104_W	0.594	0.68
95_F	99_L	0.593	0.68
24_A	46_F	0.587	0.67
42_P	59_H	0.586	0.67
27_A	32_S	0.586	0.67
36_R	41_N	0.578	0.66
16_S	19_E	0.570	0.65
5_R	64_E	0.563	0.64
29_S	36_R	0.561	0.64
16_S	29_S	0.561	0.64
3_G	6_I	0.555	0.63
41_N	45_Q	0.545	0.62
91_S	104_W	0.533	0.60
27_A	39_Q	0.531	0.60
12_E	48_E	0.531	0.60
21_A	29_S	0.525	0.59
29_S	39_Q	0.524	0.59
30_Y	40_T	0.524	0.59
30_Y	34_I	0.523	0.59
32_S	42_P	0.523	0.59
78_W	89_G	0.522	0.58
91_S	97_E	0.521	0.58
21_A	28_K	0.519	0.58
8_Q	22_E	0.515	0.57
97_E	103_K	0.513	0.57
57_S	60_T	0.511	0.57
32_S	40_T	0.507	0.56
26_V	29_S	0.504	0.56
75_D	83_R	0.503	0.56
77_E	85_A	0.503	0.56
26_V	34_I	0.500	0.55

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
1b0nA	2	0.9279	99.8	0.31	Contact Map
4ndwA	2	0.973	99.8	0.358	Contact Map
3r1fA	2	0.973	99.7	0.37	Contact Map
4o8bA	2	0.8739	99.7	0.381	Contact Map
4jcyA	2	0.7928	99.7	0.393	Contact Map
3qwgA	2	0.6577	99.7	0.396	Contact Map
3op9A	4	0.9369	99.7	0.4	Contact Map
3ivpA	2	0.9369	99.6	0.418	Contact Map
2ebyA	2	0.8559	99.6	0.431	Contact Map
2p5tA	2	0.3694	99.6	0.432	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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