YWOC - BACSU - GREMLIN Contacts

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YWOC - Uncharacterized isochorismatase family protein YwoC

UniProt:	P94573	Sequences: MMNTLNIDFQKTALVIIDLQKGIVPIDQSGQVVPNAKKLVDEFRKHNGFISFVNVAFHDGADALKPQTDEPAQGGSGEMPADWAEFVPEIGVQDGDYTVTKRQWGAFFGTDLDLQLRRRGIDTIVLCGIATNIGVESTAREAFQLGYQQIFITDAMSTFSDEEHEATLRFIFPRIGKSRTTEEFLEQVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	189 (167)
Sequences:	10200 (7031)
Seq/√Len:	544.1

ECOLI - RUTB YECD PNCA YCAC
BACSU - YWOC YAAI YRDC YDDQ 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
113_D	117_R	3.207	1.00
123_T	148_Q	2.752	1.00
113_D	147_Y	2.657	1.00
43_F	48_G	2.577	1.00
105_G	141_E	2.570	1.00
54_N	100_T	2.550	1.00
12_T	123_T	2.324	1.00
113_D	145_L	2.236	1.00
19_L	36_A	2.165	1.00
36_A	127_C	2.165	1.00
123_T	150_I	2.142	1.00
126_L	139_A	2.134	1.00
161_D	165_E	2.129	1.00
39_L	152_I	2.047	1.00
11_K	122_D	2.026	1.00
171_I	176_G	1.952	1.00
22_G	83_W	1.882	1.00
21_K	82_D	1.850	1.00
111_D	115_Q	1.839	1.00
180_T	183_E	1.838	1.00
142_A	149_Q	1.817	1.00
13_A	121_I	1.812	1.00
136_E	140_R	1.780	1.00
35_N	155_A	1.770	1.00
42_E	46_H	1.767	1.00
99_V	115_Q	1.762	1.00
35_N	181_T	1.747	1.00
106_A	138_T	1.731	1.00
21_K	88_P	1.714	1.00
35_N	38_K	1.692	1.00
153_T	178_S	1.649	1.00
153_T	180_T	1.639	1.00
12_T	125_V	1.613	1.00
51_S	115_Q	1.611	1.00
131_T	164_H	1.591	1.00
24_V	87_V	1.586	1.00
97_Y	115_Q	1.528	1.00
53_V	106_A	1.525	1.00
49_F	119_R	1.476	1.00
125_V	152_I	1.452	1.00
16_I	40_V	1.418	1.00
124_I	142_A	1.412	1.00
44_R	96_D	1.411	1.00
38_K	182_E	1.399	1.00
82_D	85_E	1.395	1.00
154_D	181_T	1.390	1.00
16_I	127_C	1.390	1.00
43_F	125_V	1.378	1.00
158_T	164_H	1.352	1.00
131_T	156_M	1.349	1.00
136_E	170_F	1.349	1.00
115_Q	119_R	1.333	1.00
37_K	89_E	1.316	1.00
37_K	41_D	1.313	1.00
28_Q	31_Q	1.309	1.00
126_L	138_T	1.301	1.00
132_N	158_T	1.292	1.00
162_E	165_E	1.275	1.00
135_V	151_F	1.256	1.00
15_V	126_L	1.243	1.00
79_M	100_T	1.229	1.00
56_A	84_A	1.219	1.00
114_L	118_R	1.217	1.00
131_T	168_L	1.217	1.00
153_T	168_L	1.213	1.00
54_N	86_F	1.212	1.00
41_D	45_K	1.205	1.00
117_R	147_Y	1.190	1.00
16_I	19_L	1.177	1.00
136_E	167_T	1.172	1.00
14_L	43_F	1.172	1.00
32_V	36_A	1.164	1.00
16_I	36_A	1.150	1.00
151_F	156_M	1.150	1.00
17_I	134_G	1.147	1.00
165_E	169_R	1.144	1.00
141_E	145_L	1.141	1.00
155_A	181_T	1.118	1.00
56_A	100_T	1.111	1.00
34_P	89_E	1.091	1.00
54_N	98_T	1.075	1.00
125_V	150_I	1.058	1.00
56_A	79_M	1.047	1.00
139_A	151_F	1.037	1.00
40_V	44_R	1.024	1.00
39_L	155_A	1.021	1.00
124_I	149_Q	1.018	1.00
148_Q	177_K	0.980	1.00
111_D	114_L	0.977	1.00
13_A	51_S	0.976	1.00
12_T	48_G	0.974	1.00
21_K	85_E	0.971	1.00
156_M	164_H	0.962	1.00
107_F	142_A	0.960	1.00
86_F	98_T	0.960	1.00
35_N	154_D	0.952	1.00
150_I	177_K	0.945	1.00
58_H	79_M	0.931	1.00
137_S	140_R	0.927	1.00
40_V	52_F	0.910	1.00
139_A	171_I	0.910	1.00
162_E	166_A	0.909	1.00
160_S	163_E	0.905	1.00
21_K	25_P	0.901	1.00
131_T	158_T	0.892	1.00
115_Q	118_R	0.890	1.00
168_L	178_S	0.886	1.00
162_E	169_R	0.880	1.00
150_I	179_R	0.880	1.00
39_L	127_C	0.879	1.00
75_G	78_E	0.877	1.00
164_H	168_L	0.876	1.00
103_Q	146_G	0.867	1.00
42_E	45_K	0.862	1.00
116_L	147_Y	0.862	1.00
93_Q	96_D	0.859	1.00
52_F	86_F	0.855	1.00
179_R	183_E	0.855	1.00
85_E	91_G	0.846	1.00
41_D	93_Q	0.845	1.00
152_I	155_A	0.839	1.00
32_V	157_S	0.831	1.00
108_F	145_L	0.826	1.00
122_D	148_Q	0.822	1.00
19_L	129_I	0.822	1.00
37_K	92_V	0.821	1.00
15_V	112_L	0.817	1.00
52_F	95_G	0.814	1.00
18_D	101_K	0.804	1.00
38_K	41_D	0.803	1.00
52_F	92_V	0.800	1.00
40_V	50_I	0.793	1.00
11_K	123_T	0.792	1.00
17_I	126_L	0.791	1.00
49_F	121_I	0.789	1.00
152_I	179_R	0.787	1.00
127_C	155_A	0.786	1.00
106_A	112_L	0.778	1.00
51_S	119_R	0.772	1.00
38_K	42_E	0.769	1.00
81_A	84_A	0.761	1.00
78_E	81_A	0.760	1.00
126_L	135_V	0.760	1.00
97_Y	119_R	0.757	1.00
129_I	157_S	0.757	1.00
21_K	87_V	0.753	1.00
141_E	144_Q	0.750	1.00
92_V	96_D	0.750	1.00
169_R	172_F	0.748	1.00
33_V	37_K	0.747	1.00
38_K	181_T	0.739	1.00
31_Q	34_P	0.737	1.00
60_G	63_A	0.725	1.00
39_L	181_T	0.723	1.00
13_A	116_L	0.721	1.00
132_N	159_F	0.717	1.00
166_A	170_F	0.711	1.00
167_T	171_I	0.711	1.00
82_D	88_P	0.705	1.00
132_N	170_F	0.705	1.00
132_N	163_E	0.704	1.00
103_Q	109_G	0.704	1.00
44_R	93_Q	0.700	1.00
163_E	166_A	0.699	1.00
34_P	37_K	0.694	1.00
49_F	115_Q	0.689	1.00
25_P	30_G	0.686	1.00
92_V	98_T	0.677	1.00
14_L	39_L	0.675	1.00
44_R	95_G	0.672	1.00
156_M	168_L	0.670	1.00
23_I	134_G	0.667	1.00
88_P	91_G	0.660	1.00
36_A	155_A	0.660	1.00
16_I	52_F	0.658	1.00
14_L	127_C	0.653	1.00
169_R	173_P	0.653	1.00
32_V	129_I	0.652	1.00
51_S	97_Y	0.651	1.00
139_A	176_G	0.648	1.00
19_L	87_V	0.646	1.00
130_A	133_I	0.644	1.00
114_L	117_R	0.643	1.00
41_D	91_G	0.639	1.00
151_F	171_I	0.637	1.00
34_P	38_K	0.636	1.00
39_L	43_F	0.636	1.00
130_A	158_T	0.636	1.00
37_K	91_G	0.635	1.00
143_F	176_G	0.633	1.00
151_F	168_L	0.633	1.00
80_P	85_E	0.622	1.00
166_A	169_R	0.622	1.00
52_F	90_I	0.617	1.00
33_V	87_V	0.616	1.00
52_F	96_D	0.614	1.00
109_G	114_L	0.613	1.00
87_V	90_I	0.611	1.00
126_L	149_Q	0.609	1.00
59_D	75_G	0.601	1.00
139_A	149_Q	0.601	1.00
11_K	120_G	0.595	1.00
51_S	99_V	0.593	1.00
108_F	144_Q	0.591	1.00
54_N	84_A	0.589	1.00
163_E	169_R	0.587	1.00
149_Q	152_I	0.584	0.99
29_S	32_V	0.579	0.99
108_F	141_E	0.579	0.99
14_L	50_I	0.574	0.99
40_V	43_F	0.572	0.99
29_S	129_I	0.568	0.99
44_R	50_I	0.567	0.99
127_C	152_I	0.565	0.99
24_V	33_V	0.563	0.99
40_V	96_D	0.559	0.99
57_F	63_A	0.558	0.99
71_P	75_G	0.558	0.99
52_F	98_T	0.557	0.99
17_I	135_V	0.555	0.99
140_R	174_R	0.555	0.99
49_F	96_D	0.548	0.99
19_L	32_V	0.548	0.99
130_A	159_F	0.546	0.99
73_Q	76_S	0.546	0.99
33_V	89_E	0.543	0.99
14_L	40_V	0.542	0.99
33_V	90_I	0.542	0.99
153_T	164_H	0.541	0.99
92_V	95_G	0.539	0.99
168_L	172_F	0.538	0.99
135_V	156_M	0.535	0.99
19_L	90_I	0.534	0.99
22_G	77_G	0.533	0.99
105_G	144_Q	0.530	0.99
25_P	82_D	0.527	0.99
24_V	29_S	0.522	0.99
30_G	89_E	0.521	0.99
49_F	97_Y	0.519	0.99
54_N	85_E	0.518	0.99
103_Q	108_F	0.518	0.99
39_L	125_V	0.518	0.99
58_H	61_A	0.518	0.99
153_T	172_F	0.517	0.99
137_S	175_I	0.512	0.99
99_V	111_D	0.507	0.99
43_F	49_F	0.505	0.99
104_W	144_Q	0.505	0.99
31_Q	35_N	0.505	0.99
104_W	138_T	0.500	0.98

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
3kl2A	4	0.9894	100	0.149	Contact Map
3irvA	2	0.9788	100	0.16	Contact Map
2fq1A	2	0.9894	100	0.164	Contact Map
3hb7A	3	0.9418	100	0.166	Contact Map
3ot4A	4	0.9841	100	0.166	Contact Map
4l07A	4	1	100	0.169	Contact Map
1j2rA	4	0.9683	100	0.17	Contact Map
1nbaA	4	0.9947	100	0.17	Contact Map
3txyA	2	0.9788	100	0.173	Contact Map
3hu5A	3	0.9524	100	0.175	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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