YTRA - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YTRA - HTH-type transcriptional repressor YtrA

UniProt:	O34712	Sequences: MIQIDPRSSTPIYEQIIQQMKELCLKGIMKPGDKLPSVRELATIIIANPNTVSKAYKELEREGIIETLRGRGTYISENAKTTLVEGKMTMIKEQLKQLIIDAHYAGVELEKLHEWIKEISADVKGGKKND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	130 (109)
Sequences:	9772 (7358)
Seq/√Len:	704.8

ECOLI - YEGW YIHL MNGR FRLR PHNF PDHR YIDP YDCR EXUR UXUR GLCC NANR LLDR YIEP FADR YJIR DGOR MCBR YDFH CSIR
BACSU - YTRA YHCF YVOA YYDK YISV YURK YMFC YDFD GMUR TRER YBGA GABR YCBG YHDI YDEL YDEF YCXD YDHC LUTR
SULSO - Q97XX0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_K	33_D	4.067	1.00
23_L	28_I	3.099	1.00
21_K	62_E	3.016	1.00
68_L	71_R	2.855	1.00
38_V	49_P	2.705	1.00
67_T	73_T	2.498	1.00
66_E	76_S	2.460	1.00
10_T	18_Q	2.454	1.00
17_I	58_E	2.149	1.00
19_Q	23_L	2.083	1.00
34_K	74_Y	1.895	1.00
31_P	77_E	1.849	1.00
17_I	62_E	1.844	1.00
35_L	65_I	1.826	1.00
17_I	21_K	1.818	1.00
40_E	44_I	1.785	1.00
71_R	74_Y	1.773	1.00
58_E	61_R	1.752	1.00
21_K	64_I	1.736	1.00
22_E	26_K	1.672	1.00
32_G	66_E	1.606	1.00
53_S	57_K	1.604	1.00
60_E	65_I	1.544	1.00
14_E	18_Q	1.538	1.00
32_G	77_E	1.537	1.00
65_I	73_T	1.513	1.00
16_I	47_A	1.505	1.00
29_M	75_I	1.498	1.00
94_Q	97_Q	1.475	1.00
108_E	111_K	1.427	1.00
57_K	60_E	1.402	1.00
60_E	67_T	1.389	1.00
24_C	75_I	1.305	1.00
57_K	61_R	1.299	1.00
23_L	29_M	1.292	1.00
10_T	14_E	1.276	1.00
13_Y	58_E	1.263	1.00
89_T	93_E	1.253	1.00
95_L	98_L	1.224	1.00
94_Q	101_D	1.181	1.00
40_E	43_T	1.152	1.00
13_Y	54_K	1.147	1.00
45_I	56_Y	1.140	1.00
16_I	55_A	1.125	1.00
50_N	53_S	1.115	1.00
56_Y	65_I	1.083	1.00
19_Q	22_E	1.072	1.00
109_L	113_H	1.068	1.00
95_L	112_L	1.063	1.00
19_Q	45_I	1.058	1.00
37_S	40_E	1.056	1.00
47_A	52_V	1.051	1.00
24_C	64_I	1.031	1.00
90_M	94_Q	1.031	1.00
31_P	78_N	1.022	1.00
98_L	102_A	1.019	1.00
93_E	97_Q	0.998	1.00
54_K	58_E	0.992	1.00
94_Q	98_L	0.983	1.00
21_K	25_L	0.970	1.00
18_Q	22_E	0.962	1.00
16_I	45_I	0.941	1.00
54_K	57_K	0.932	1.00
107_V	111_K	0.930	1.00
58_E	62_E	0.921	1.00
39_R	42_A	0.910	1.00
97_Q	101_D	0.892	1.00
96_K	109_L	0.891	1.00
12_I	48_N	0.872	1.00
66_E	77_E	0.866	1.00
12_I	15_Q	0.850	1.00
50_N	54_K	0.843	1.00
56_Y	73_T	0.840	1.00
25_L	64_I	0.836	1.00
103_H	109_L	0.833	1.00
99_I	112_L	0.828	1.00
20_M	35_L	0.815	1.00
38_V	53_S	0.799	1.00
20_M	29_M	0.798	1.00
41_L	56_Y	0.777	1.00
51_T	54_K	0.772	1.00
41_L	52_V	0.771	1.00
68_L	74_Y	0.765	1.00
97_Q	100_I	0.752	1.00
22_E	25_L	0.747	1.00
29_M	35_L	0.740	1.00
38_V	56_Y	0.739	1.00
27_G	30_K	0.737	1.00
31_P	76_S	0.731	1.00
66_E	74_Y	0.724	1.00
18_Q	21_K	0.723	1.00
48_N	51_T	0.718	1.00
14_E	58_E	0.718	1.00
70_G	73_T	0.714	1.00
15_Q	19_Q	0.706	1.00
20_M	24_C	0.705	1.00
83_L	88_M	0.704	1.00
12_I	51_T	0.700	1.00
37_S	69_R	0.699	1.00
107_V	112_L	0.691	1.00
34_K	72_G	0.688	1.00
53_S	67_T	0.686	1.00
89_T	92_K	0.679	1.00
91_I	102_A	0.663	1.00
38_V	82_T	0.656	1.00
93_E	96_K	0.648	1.00
96_K	103_H	0.648	1.00
11_P	14_E	0.648	1.00
38_V	70_G	0.647	1.00
99_I	103_H	0.644	1.00
38_V	73_T	0.642	1.00
23_L	26_K	0.639	1.00
91_I	98_L	0.633	1.00
49_P	54_K	0.632	1.00
34_K	37_S	0.632	1.00
11_P	15_Q	0.629	1.00
101_D	104_Y	0.627	1.00
100_I	106_G	0.626	1.00
100_I	104_Y	0.625	1.00
60_E	73_T	0.616	1.00
111_K	114_E	0.616	1.00
102_A	107_V	0.614	1.00
14_E	17_I	0.614	1.00
48_N	53_S	0.614	1.00
87_K	90_M	0.613	1.00
42_A	52_V	0.611	1.00
38_V	67_T	0.611	1.00
76_S	79_A	0.609	1.00
16_I	52_V	0.609	1.00
88_M	92_K	0.606	1.00
39_R	56_Y	0.603	1.00
17_I	55_A	0.597	1.00
52_V	56_Y	0.592	1.00
17_I	64_I	0.583	1.00
37_S	70_G	0.578	1.00
53_S	56_Y	0.578	1.00
95_L	114_E	0.571	1.00
65_I	75_I	0.569	1.00
110_E	113_H	0.569	1.00
12_I	47_A	0.568	1.00
32_G	68_L	0.568	1.00
91_I	94_Q	0.565	1.00
20_M	59_L	0.565	1.00
35_L	52_V	0.565	1.00
10_T	15_Q	0.552	1.00
87_K	92_K	0.548	1.00
84_V	88_M	0.540	1.00
37_S	73_T	0.537	1.00
82_T	85_E	0.525	1.00
80_K	84_V	0.524	1.00
23_L	44_I	0.519	1.00
101_D	105_A	0.519	1.00
108_E	112_L	0.519	1.00
86_G	89_T	0.519	1.00
85_E	89_T	0.512	0.99
82_T	87_K	0.511	0.99
50_N	67_T	0.509	0.99
93_E	109_L	0.509	0.99
56_Y	60_E	0.506	0.99
42_A	49_P	0.505	0.99
96_K	100_I	0.505	0.99
92_K	96_K	0.505	0.99
84_V	87_K	0.502	0.99
34_K	40_E	0.500	0.99

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
3neuA	2	0.9154	99.9	0.335	Contact Map
3ic7A	2	0.8692	99.9	0.34	Contact Map
3by6A	2	0.9615	99.9	0.35	Contact Map
4r1hA	2	0.8923	99.9	0.358	Contact Map
2ek5A	4	0.9	99.9	0.366	Contact Map
4u0wA	2	0.9385	99.9	0.369	Contact Map
2ra5A	2	0.2385	99.9	0.376	Contact Map
3tqnA	2	0.8308	99.9	0.391	Contact Map
3f8mA	2	0.8308	99.8	0.41	Contact Map
3eetA	2	0.9154	99.8	0.413	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.

Page generated in 0.006 seconds.