SLYA - ECOLI - GREMLIN Contacts

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SLYA - Transcriptional regulator SlyA

UniProt:	P0A8W2	Sequences: MESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEMEAVINKTRAEILHGISAEELEQLITLIAKLEHNIIELQAKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13408
Length:	144 (130)
Sequences:	23301 (17337)
Seq/√Len:	1520.6

ECOLI - SLYA MPRA MARR
BACSU - YFIV YUSO YCGE YSMB YWAE YETL MHQR YYBA YXAD OHRR YKOM YDGG YPOP YWOH YWHA YDCH YDGJ YHJH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_Q	91_K	2.992	1.00
122_E	132_K	2.915	1.00
81_C	89_R	2.602	1.00
46_D	91_K	2.588	1.00
48_S	87_A	2.550	1.00
77_S	91_K	2.540	1.00
125_Q	129_L	2.341	1.00
119_S	122_E	2.285	1.00
125_Q	128_T	2.167	1.00
80_T	88_K	2.115	1.00
41_H	100_I	2.033	1.00
48_S	51_Q	1.971	1.00
117_G	136_N	1.942	1.00
33_H	73_K	1.940	1.00
122_E	125_Q	1.850	1.00
118_I	129_L	1.808	1.00
41_H	92_L	1.806	1.00
81_C	87_A	1.742	1.00
95_K	99_L	1.626	1.00
74_G	95_K	1.600	1.00
71_E	78_R	1.577	1.00
8_D	131_A	1.551	1.00
99_L	102_E	1.511	1.00
49_Q	67_L	1.478	1.00
126_L	129_L	1.477	1.00
122_E	128_T	1.459	1.00
95_K	98_P	1.444	1.00
33_H	69_Q	1.431	1.00
36_T	66_T	1.428	1.00
67_L	90_I	1.421	1.00
43_L	55_A	1.417	1.00
68_D	72_E	1.399	1.00
39_N	55_A	1.398	1.00
30_T	33_H	1.366	1.00
8_D	134_E	1.364	1.00
23_R	106_V	1.348	1.00
41_H	97_E	1.338	1.00
27_L	102_E	1.312	1.00
8_D	127_I	1.291	1.00
129_L	132_K	1.268	1.00
27_L	106_V	1.229	1.00
122_E	129_L	1.204	1.00
51_Q	54_K	1.175	1.00
43_L	47_Q	1.167	1.00
49_Q	88_K	1.164	1.00
98_P	102_E	1.160	1.00
12_L	134_E	1.151	1.00
46_D	89_R	1.150	1.00
68_D	85_R	1.149	1.00
50_I	60_Q	1.147	1.00
128_T	132_K	1.144	1.00
59_E	62_S	1.138	1.00
78_R	88_K	1.137	1.00
75_L	99_L	1.135	1.00
127_I	131_A	1.114	1.00
50_I	54_K	1.113	1.00
36_T	63_L	1.113	1.00
11_R	134_E	1.105	1.00
58_I	62_S	1.105	1.00
106_V	109_K	1.084	1.00
21_D	25_K	1.083	1.00
123_L	127_I	1.061	1.00
23_R	109_K	1.057	1.00
49_Q	90_I	1.021	1.00
121_E	125_Q	1.012	1.00
111_R	114_I	1.008	1.00
26_P	106_V	0.983	1.00
10_A	13_V	0.978	1.00
64_V	68_D	0.978	1.00
23_R	113_E	0.977	1.00
68_D	71_E	0.964	1.00
12_L	130_I	0.962	1.00
73_K	99_L	0.951	1.00
49_Q	60_Q	0.948	1.00
46_D	79_Q	0.946	1.00
32_T	66_T	0.941	1.00
61_P	64_V	0.940	1.00
97_E	101_S	0.939	1.00
47_Q	55_A	0.931	1.00
49_Q	63_L	0.926	1.00
47_Q	51_Q	0.923	1.00
19_L	110_T	0.923	1.00
75_L	95_K	0.920	1.00
62_S	65_R	0.917	1.00
13_V	17_R	0.914	1.00
92_L	96_A	0.911	1.00
58_I	63_L	0.911	1.00
77_S	93_T	0.905	1.00
51_Q	55_A	0.903	1.00
59_E	65_R	0.889	1.00
40_I	76_I	0.884	1.00
94_E	97_E	0.880	1.00
107_I	111_R	0.873	1.00
94_E	98_P	0.873	1.00
15_I	134_E	0.863	1.00
80_T	85_R	0.861	1.00
73_K	95_K	0.861	1.00
120_A	124_E	0.847	1.00
79_Q	89_R	0.843	1.00
34_W	103_M	0.834	1.00
37_L	100_I	0.819	1.00
65_R	69_Q	0.817	1.00
125_Q	132_K	0.813	1.00
28_E	73_K	0.811	1.00
84_D	87_A	0.810	1.00
27_L	103_M	0.801	1.00
102_E	106_V	0.798	1.00
105_A	109_K	0.795	1.00
23_R	26_P	0.792	1.00
109_K	112_A	0.790	1.00
65_R	68_D	0.789	1.00
92_L	97_E	0.788	1.00
81_C	84_D	0.785	1.00
69_Q	72_E	0.780	1.00
10_A	14_R	0.778	1.00
115_L	123_L	0.777	1.00
41_H	104_E	0.773	1.00
67_L	76_I	0.765	1.00
21_D	31_Q	0.764	1.00
32_T	62_S	0.751	1.00
45_P	97_E	0.750	1.00
118_I	133_L	0.750	1.00
36_T	52_L	0.748	1.00
41_H	101_S	0.747	1.00
9_L	13_V	0.737	1.00
71_E	76_I	0.736	1.00
82_A	89_R	0.733	1.00
119_S	123_L	0.733	1.00
113_E	116_H	0.732	1.00
109_K	113_E	0.731	1.00
71_E	77_S	0.729	1.00
39_N	56_I	0.728	1.00
67_L	71_E	0.726	1.00
39_N	43_L	0.713	1.00
108_N	112_A	0.712	1.00
124_E	127_I	0.708	1.00
53_A	63_L	0.708	1.00
17_R	21_D	0.706	1.00
23_R	110_T	0.704	1.00
12_L	133_L	0.700	1.00
19_L	113_E	0.694	1.00
69_Q	73_K	0.694	1.00
131_A	135_H	0.690	1.00
53_A	60_Q	0.682	1.00
14_R	18_A	0.682	1.00
35_V	56_I	0.682	1.00
43_L	51_Q	0.681	1.00
39_N	47_Q	0.672	1.00
68_D	78_R	0.670	1.00
9_L	12_L	0.665	1.00
45_P	91_K	0.660	1.00
34_W	107_I	0.660	1.00
98_P	101_S	0.660	1.00
49_Q	64_V	0.659	1.00
105_A	108_N	0.650	1.00
132_K	136_N	0.647	1.00
40_I	92_L	0.646	1.00
124_E	128_T	0.643	1.00
20_I	23_R	0.641	1.00
39_N	52_L	0.636	1.00
121_E	124_E	0.635	1.00
38_H	42_Q	0.626	1.00
36_T	56_I	0.623	1.00
8_D	11_R	0.623	1.00
70_L	75_L	0.602	1.00
102_E	105_A	0.592	1.00
40_I	47_Q	0.585	1.00
63_L	67_L	0.584	1.00
110_T	113_E	0.582	1.00
50_I	53_A	0.574	1.00
101_S	104_E	0.574	1.00
38_H	100_I	0.570	1.00
34_W	100_I	0.568	1.00
38_H	104_E	0.568	1.00
20_I	107_I	0.564	1.00
104_E	108_N	0.556	1.00
119_S	132_K	0.553	1.00
31_Q	35_V	0.546	1.00
8_D	130_I	0.539	1.00
129_L	136_N	0.537	1.00
9_L	130_I	0.535	1.00
101_S	105_A	0.534	1.00
118_I	123_L	0.534	1.00
100_I	104_E	0.533	1.00
19_L	22_H	0.531	1.00
35_V	39_N	0.531	1.00
78_R	90_I	0.530	1.00
118_I	132_K	0.528	1.00
128_T	131_A	0.521	1.00
116_H	136_N	0.520	1.00
33_H	66_T	0.519	1.00
37_L	41_H	0.519	1.00
52_L	90_I	0.505	1.00
9_L	16_W	0.502	1.00
118_I	122_E	0.500	1.00

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
3deuA	2	0.9167	99.9	0.205	Contact Map
3cjnA	2	0.9653	99.9	0.235	Contact Map
3e6mA	2	0.9653	99.9	0.239	Contact Map
4rguA	4	0.9861	99.9	0.24	Contact Map
3u2rA	4	0.9028	99.9	0.241	Contact Map
3cdhA	4	0.9236	99.9	0.243	Contact Map
4yifA	2	0.9722	99.9	0.248	Contact Map
3boqA	2	0.9097	99.9	0.248	Contact Map
3oopA	2	0.9236	99.9	0.252	Contact Map
2fbkA	2	0.9167	99.9	0.254	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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