YDDQ - BACSU - GREMLIN Contacts

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YDDQ - Uncharacterized isochorismatase family protein YddQ

UniProt:	P96654	Sequences: MTTALLVIDIQNDYFPNGKMALTNPEKAAQNAAKLLSHFRNTGAPVFHVQHITEGNIAHFFHPNTEGVEIHESVRPLEKETVIVKHMPNSFFNTDLNGKLQEEGVKELVVCGMMSHMCIDATVRSAVEHGYVCQVVEDACATTTLQIEDKIVPAEHVHYAFMAALNGVYATVKTTEAFLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	180 (163)
Sequences:	10567 (7358)
Seq/√Len:	576.3

ECOLI - RUTB YECD PNCA YCAC
BACSU - YDDQ YRDC YAAI YWOC PNCA
HALSA - Q9HMH5 Q9HQL7
SULSO - Q97VZ5 Q97YW7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_N	101_Q	3.400	1.00
107_E	132_V	2.778	1.00
50_Q	84_V	2.763	1.00
39_F	44_A	2.715	1.00
97_N	131_Y	2.700	1.00
89_N	125_S	2.596	1.00
32_A	111_C	2.429	1.00
3_T	107_E	2.418	1.00
97_N	129_H	2.394	1.00
10_I	32_A	2.270	1.00
107_E	134_Q	2.269	1.00
35_L	136_V	2.257	1.00
110_V	123_V	2.135	1.00
145_L	149_D	2.112	1.00
31_N	139_A	1.962	1.00
95_D	99_K	1.950	1.00
13_D	67_G	1.919	1.00
126_A	133_C	1.910	1.00
120_D	124_R	1.907	1.00
83_I	99_K	1.856	1.00
12_N	66_E	1.850	1.00
90_S	122_T	1.832	1.00
155_E	160_A	1.824	1.00
4_A	105_V	1.818	1.00
31_N	34_K	1.803	1.00
38_H	42_T	1.796	1.00
47_F	99_K	1.726	1.00
12_N	72_E	1.707	1.00
31_N	165_L	1.620	1.00
15_F	71_H	1.615	1.00
3_T	109_V	1.594	1.00
40_R	80_E	1.569	1.00
49_V	90_S	1.517	1.00
24_N	27_K	1.515	1.00
45_P	103_E	1.507	1.00
137_E	164_A	1.506	1.00
81_T	99_K	1.498	1.00
39_F	109_V	1.492	1.00
109_V	136_V	1.480	1.00
7_V	36_L	1.477	1.00
137_E	162_M	1.460	1.00
115_S	148_E	1.448	1.00
66_E	69_E	1.435	1.00
108_L	126_A	1.408	1.00
33_A	37_S	1.396	1.00
33_A	73_S	1.390	1.00
7_V	111_C	1.375	1.00
52_I	68_V	1.373	1.00
115_S	140_C	1.372	1.00
119_I	135_V	1.365	1.00
138_D	165_L	1.345	1.00
116_H	142_T	1.340	1.00
110_V	122_T	1.321	1.00
99_K	103_E	1.305	1.00
146_Q	149_D	1.283	1.00
34_K	166_N	1.273	1.00
125_S	129_H	1.268	1.00
52_I	84_V	1.266	1.00
120_D	154_A	1.260	1.00
28_A	32_A	1.248	1.00
98_G	102_E	1.244	1.00
6_L	110_V	1.244	1.00
8_I	118_C	1.236	1.00
135_V	140_C	1.232	1.00
115_S	152_V	1.225	1.00
63_P	84_V	1.225	1.00
37_S	41_N	1.208	1.00
142_T	148_E	1.205	1.00
7_V	10_I	1.202	1.00
50_Q	70_I	1.200	1.00
101_Q	131_Y	1.178	1.00
5_L	39_F	1.176	1.00
30_Q	73_S	1.176	1.00
35_L	139_A	1.105	1.00
7_V	32_A	1.104	1.00
12_N	69_E	1.097	1.00
3_T	44_A	1.084	1.00
50_Q	82_V	1.078	1.00
149_D	153_P	1.076	1.00
109_V	134_Q	1.049	1.00
137_E	152_V	1.045	1.00
36_L	48_H	1.044	1.00
31_N	138_D	1.041	1.00
36_L	40_R	1.020	1.00
121_A	124_R	1.012	1.00
139_A	165_L	1.004	1.00
120_D	151_I	0.984	1.00
123_V	135_V	0.977	1.00
99_K	102_E	0.976	1.00
52_I	63_P	0.974	1.00
77_L	80_E	0.973	1.00
70_I	82_V	0.959	1.00
108_L	133_C	0.952	1.00
115_S	142_T	0.949	1.00
4_A	47_F	0.943	1.00
100_L	131_Y	0.929	1.00
91_F	126_A	0.910	1.00
28_A	141_A	0.905	1.00
95_D	98_G	0.900	1.00
34_K	38_H	0.888	1.00
54_E	63_P	0.885	1.00
132_V	161_F	0.877	1.00
59_H	62_H	0.875	1.00
87_M	93_N	0.864	1.00
35_L	111_C	0.862	1.00
9_D	85_K	0.858	1.00
153_P	156_H	0.857	1.00
10_I	113_M	0.847	1.00
6_L	96_L	0.844	1.00
136_V	139_A	0.841	1.00
38_H	41_N	0.836	1.00
45_P	105_V	0.833	1.00
90_S	96_L	0.830	1.00
69_E	75_R	0.824	1.00
150_K	154_A	0.821	1.00
48_H	76_P	0.818	1.00
148_E	152_V	0.812	1.00
48_H	70_I	0.811	1.00
134_Q	161_F	0.801	1.00
34_K	37_S	0.797	1.00
29_A	33_A	0.795	1.00
33_A	76_P	0.791	1.00
144_T	147_I	0.786	1.00
106_K	132_V	0.785	1.00
87_M	130_G	0.784	1.00
111_C	139_A	0.781	1.00
47_F	103_E	0.778	1.00
76_P	80_E	0.778	1.00
151_I	155_E	0.772	1.00
134_Q	163_A	0.770	1.00
62_H	65_T	0.764	1.00
146_Q	153_P	0.764	1.00
30_Q	33_A	0.760	1.00
123_V	155_E	0.760	1.00
36_L	46_V	0.760	1.00
125_S	128_E	0.755	1.00
92_F	129_H	0.750	1.00
76_P	82_V	0.748	1.00
113_M	141_A	0.729	1.00
48_H	79_K	0.725	1.00
140_C	148_E	0.722	1.00
8_I	110_V	0.721	1.00
30_Q	34_K	0.720	1.00
81_T	103_E	0.720	1.00
45_P	99_K	0.711	1.00
12_N	71_H	0.710	1.00
4_A	100_L	0.709	1.00
123_V	133_C	0.706	1.00
27_K	30_Q	0.699	1.00
116_H	154_A	0.698	1.00
29_A	71_H	0.691	1.00
33_A	75_R	0.689	1.00
110_V	133_C	0.689	1.00
136_V	163_A	0.688	1.00
66_E	72_E	0.688	1.00
65_T	68_V	0.682	1.00
110_V	119_I	0.682	1.00
32_A	139_A	0.682	1.00
153_P	157_V	0.680	1.00
5_L	111_C	0.680	1.00
10_I	71_H	0.670	1.00
40_R	77_L	0.670	1.00
28_A	113_M	0.668	1.00
14_Y	118_C	0.666	1.00
37_S	77_L	0.664	1.00
147_I	150_K	0.661	1.00
150_K	153_P	0.661	1.00
47_F	81_T	0.657	1.00
5_L	35_L	0.655	1.00
57_I	60_F	0.654	1.00
98_G	101_Q	0.651	1.00
72_E	75_R	0.649	1.00
152_V	162_M	0.643	1.00
37_S	75_R	0.640	1.00
17_N	21_A	0.638	1.00
40_R	79_K	0.635	1.00
114_M	142_T	0.631	1.00
114_M	143_T	0.629	1.00
127_V	160_A	0.627	1.00
7_V	48_H	0.624	1.00
29_A	74_V	0.622	1.00
86_H	93_N	0.620	1.00
34_K	165_L	0.616	1.00
15_F	29_A	0.614	1.00
48_H	82_V	0.613	1.00
23_T	27_K	0.612	1.00
146_Q	150_K	0.607	1.00
154_A	157_V	0.607	1.00
29_A	73_S	0.605	1.00
48_H	80_E	0.604	1.00
47_F	83_I	0.599	1.00
5_L	36_L	0.596	1.00
114_M	117_M	0.596	1.00
23_T	141_A	0.596	1.00
18_G	21_A	0.595	1.00
116_H	143_T	0.594	1.00
71_H	74_V	0.594	1.00
50_Q	68_V	0.593	1.00
123_V	160_A	0.591	1.00
36_L	39_F	0.587	1.00
35_L	109_V	0.586	1.00
25_P	113_M	0.586	1.00
92_F	125_S	0.581	1.00
140_C	152_V	0.574	1.00
133_C	136_V	0.571	1.00
45_P	80_E	0.568	0.99
87_M	92_F	0.566	0.99
40_R	46_V	0.565	0.99
92_F	128_E	0.564	0.99
48_H	74_V	0.563	0.99
161_F	164_A	0.561	0.99
89_N	128_E	0.558	0.99
88_P	122_T	0.555	0.99
24_N	141_A	0.554	0.99
54_E	86_H	0.553	0.99
88_P	127_V	0.551	0.99
119_I	140_C	0.551	0.99
36_L	80_E	0.549	0.99
13_D	18_G	0.547	0.99
39_F	45_P	0.543	0.99
15_F	25_P	0.543	0.99
55_G	59_H	0.538	0.99
8_I	119_I	0.537	0.99
61_F	67_G	0.535	0.99
50_Q	69_E	0.530	0.99
5_L	46_V	0.529	0.99
135_V	155_E	0.527	0.99
27_K	31_N	0.525	0.99
45_P	81_T	0.523	0.99
10_I	28_A	0.522	0.99
152_V	155_E	0.520	0.99
51_H	61_F	0.520	0.99
116_H	147_I	0.519	0.99
64_N	69_E	0.518	0.99
117_M	143_T	0.517	0.99
11_Q	50_Q	0.514	0.99
88_P	128_E	0.507	0.99
26_E	73_S	0.507	0.99
23_T	26_E	0.507	0.99
76_P	79_K	0.506	0.99
135_V	152_V	0.506	0.99
35_L	39_F	0.505	0.99
152_V	156_H	0.505	0.99
147_I	153_P	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
3lqyA	2	0.9333	100	0.154	Contact Map
1nbaA	4	0.9944	100	0.155	Contact Map
3irvA	2	0.9778	100	0.156	Contact Map
3ot4A	4	0.9611	100	0.158	Contact Map
3hb7A	3	0.9611	100	0.158	Contact Map
2fq1A	2	1	100	0.16	Contact Map
3hu5A	3	0.9667	100	0.164	Contact Map
4l07A	4	0.9833	100	0.164	Contact Map
3eefA	4	0.9222	100	0.168	Contact Map
3o94A	4	0.95	100	0.171	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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