YdjM - PFAM28P - GREMLIN Contacts

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YdjM - LexA-binding, inner membrane-associated putative hydrolase

PFAM:	PF04307	Sequences: MDSLTHALLGAALGRAVLGRKTGRRSARALLAGALGALLPDLDVVLSLLGDPLGYLSGLLSRLFGHRGFTHSLLFALLLALLLALLLRRLGRRRRRLGLLFFLGYLSHLLLDALTSYGVQLLWPFSDRRFALDLIFIPVDPLFTLPRRRRWAWLALVLLVLYLGLGLVAKQRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	173 (154)
Sequences:	23566 (18089)
Seq/√Len:	1457.6
META:	0.862

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_L	111_L	3.848	1.00
113_A	121_L	3.596	1.00
80_A	102_F	2.686	1.00
7_A	38_L	2.492	1.00
107_S	111_L	2.203	1.00
7_A	34_A	2.096	1.00
155_A	159_L	2.031	1.00
150_R	153_W	2.004	1.00
154_L	160_V	2.001	1.00
51_D	54_G	1.998	1.00
95_R	99_L	1.985	1.00
152_A	155_A	1.971	1.00
76_A	105_Y	1.920	1.00
155_A	162_Y	1.886	1.00
52_P	55_Y	1.774	1.00
149_R	153_W	1.764	1.00
120_Q	123_W	1.760	1.00
150_R	154_L	1.756	1.00
69_F	123_W	1.734	1.00
109_L	121_L	1.729	1.00
28_R	32_A	1.728	1.00
29_A	33_G	1.714	1.00
154_L	157_V	1.703	1.00
153_W	157_V	1.690	1.00
3_S	38_L	1.681	1.00
9_L	107_S	1.649	1.00
96_R	99_L	1.624	1.00
85_L	89_R	1.624	1.00
151_W	155_A	1.605	1.00
32_A	36_G	1.595	1.00
84_A	88_R	1.587	1.00
154_L	158_L	1.586	1.00
160_V	164_G	1.579	1.00
156_L	160_V	1.562	1.00
110_L	114_L	1.560	1.00
105_Y	109_L	1.544	1.00
155_A	160_V	1.497	1.00
72_S	123_W	1.493	1.00
155_A	158_L	1.485	1.00
96_R	100_L	1.437	1.00
148_R	151_W	1.436	1.00
39_L	42_L	1.431	1.00
123_W	127_D	1.389	1.00
54_G	57_S	1.388	1.00
122_L	130_F	1.385	1.00
75_F	105_Y	1.359	1.00
157_V	161_L	1.358	1.00
147_R	150_R	1.350	1.00
109_L	119_V	1.349	1.00
37_A	107_S	1.328	1.00
158_L	162_Y	1.322	1.00
8_L	12_A	1.315	1.00
50_G	54_G	1.296	1.00
95_R	98_G	1.294	1.00
45_V	48_L	1.253	1.00
148_R	152_A	1.251	1.00
11_A	15_R	1.238	1.00
29_A	32_A	1.234	1.00
33_G	36_G	1.216	1.00
44_V	47_S	1.216	1.00
76_A	109_L	1.194	1.00
9_L	12_A	1.186	1.00
31_L	34_A	1.180	1.00
149_R	152_A	1.172	1.00
47_S	50_G	1.165	1.00
36_G	101_F	1.165	1.00
40_P	105_Y	1.157	1.00
10_G	37_A	1.153	1.00
106_L	109_L	1.148	1.00
156_L	162_Y	1.142	1.00
154_L	159_L	1.138	1.00
72_S	75_F	1.122	1.00
113_A	119_V	1.115	1.00
76_A	106_L	1.114	1.00
36_G	104_G	1.106	1.00
28_R	31_L	1.102	1.00
120_Q	129_R	1.101	1.00
81_L	85_L	1.098	1.00
151_W	154_L	1.088	1.00
156_L	159_L	1.042	1.00
51_D	55_Y	1.041	1.00
46_L	51_D	1.040	1.00
134_L	137_I	1.040	1.00
90_L	93_R	1.038	1.00
13_L	107_S	1.036	1.00
80_A	84_A	1.031	1.00
77_L	80_A	1.025	1.00
30_L	33_G	1.022	1.00
76_A	102_F	1.006	1.00
115_T	118_G	1.003	1.00
139_V	142_L	1.000	1.00
68_G	72_S	0.997	1.00
33_G	37_A	0.991	1.00
91_G	94_R	0.990	1.00
31_L	35_L	0.961	1.00
48_L	52_P	0.960	1.00
147_R	151_W	0.959	1.00
153_W	159_L	0.945	1.00
150_R	155_A	0.941	1.00
133_D	137_I	0.928	1.00
159_L	162_Y	0.927	1.00
159_L	163_L	0.921	1.00
143_F	146_P	0.920	1.00
55_Y	58_G	0.903	1.00
2_D	5_T	0.901	1.00
15_R	19_G	0.891	1.00
85_L	88_R	0.889	1.00
43_D	66_H	0.877	1.00
74_L	77_L	0.871	1.00
10_G	107_S	0.869	1.00
131_A	134_L	0.863	1.00
157_V	162_Y	0.859	1.00
9_L	13_L	0.857	1.00
46_L	50_G	0.854	1.00
49_L	53_L	0.843	1.00
46_L	49_L	0.833	1.00
47_S	51_D	0.826	1.00
97_L	100_L	0.822	1.00
30_L	34_A	0.820	1.00
132_L	136_F	0.816	1.00
139_V	144_T	0.815	1.00
126_S	130_F	0.807	1.00
36_G	79_L	0.791	1.00
18_L	22_T	0.789	1.00
84_A	98_G	0.788	1.00
10_G	14_G	0.787	1.00
77_L	102_F	0.785	1.00
32_A	87_L	0.785	1.00
87_L	91_G	0.784	1.00
113_A	132_L	0.784	1.00
157_V	160_V	0.776	1.00
79_L	105_Y	0.775	1.00
130_F	133_D	0.775	1.00
81_L	98_G	0.771	1.00
142_L	145_L	0.766	1.00
47_S	55_Y	0.765	1.00
45_V	49_L	0.747	1.00
80_A	83_L	0.737	1.00
42_L	70_T	0.736	1.00
129_R	133_D	0.725	1.00
136_F	141_P	0.720	1.00
131_A	137_I	0.719	1.00
153_W	156_L	0.718	1.00
14_G	18_L	0.717	1.00
162_Y	165_L	0.711	1.00
101_F	104_G	0.710	1.00
98_G	102_F	0.706	1.00
20_R	23_G	0.703	1.00
74_L	123_W	0.699	1.00
45_V	50_G	0.699	1.00
44_V	48_L	0.690	1.00
75_F	79_L	0.690	1.00
151_W	156_L	0.681	1.00
151_W	162_Y	0.677	1.00
76_A	80_A	0.674	1.00
137_I	140_D	0.673	1.00
4_L	7_A	0.671	1.00
6_H	37_A	0.669	1.00
54_G	58_G	0.668	1.00
14_G	30_L	0.658	1.00
153_W	160_V	0.657	1.00
7_A	11_A	0.654	1.00
50_G	55_Y	0.653	1.00
78_L	81_L	0.642	1.00
3_S	7_A	0.641	1.00
5_T	8_L	0.637	1.00
140_D	143_F	0.635	1.00
100_L	104_G	0.633	1.00
131_A	136_F	0.633	1.00
120_Q	126_S	0.628	1.00
153_W	161_L	0.619	1.00
76_A	79_L	0.615	1.00
152_A	159_L	0.614	1.00
148_R	154_L	0.613	1.00
39_L	105_Y	0.611	1.00
155_A	161_L	0.609	1.00
154_L	162_Y	0.601	1.00
46_L	55_Y	0.596	1.00
147_R	154_L	0.594	1.00
136_F	139_V	0.587	1.00
19_G	23_G	0.583	1.00
29_A	100_L	0.581	1.00
122_L	126_S	0.577	1.00
10_G	33_G	0.576	1.00
48_L	53_L	0.574	1.00
139_V	143_F	0.574	1.00
149_R	154_L	0.574	1.00
75_F	78_L	0.573	1.00
132_L	137_I	0.573	1.00
13_L	17_V	0.571	1.00
44_V	50_G	0.571	1.00
12_A	15_R	0.568	1.00
48_L	55_Y	0.565	1.00
68_G	120_Q	0.562	1.00
148_R	153_W	0.561	1.00
161_L	165_L	0.560	1.00
102_F	106_L	0.560	1.00
111_L	115_T	0.552	1.00
142_L	146_P	0.552	1.00
32_A	101_F	0.550	1.00
135_I	141_P	0.549	1.00
135_I	140_D	0.549	1.00
90_L	94_R	0.546	1.00
40_P	108_H	0.546	1.00
35_L	38_L	0.545	1.00
11_A	14_G	0.543	1.00
161_L	164_G	0.541	1.00
86_L	90_L	0.540	1.00
149_R	155_A	0.537	1.00
8_L	11_A	0.534	1.00
15_R	30_L	0.534	1.00
52_P	57_S	0.532	1.00
36_G	105_Y	0.529	1.00
53_L	57_S	0.529	1.00
32_A	35_L	0.524	1.00
69_F	72_S	0.522	1.00
106_L	110_L	0.521	1.00
77_L	81_L	0.520	1.00
33_G	104_G	0.518	1.00
156_L	163_L	0.512	1.00
147_R	152_A	0.511	1.00
88_R	91_G	0.511	1.00
15_R	18_L	0.510	1.00
88_R	94_R	0.507	1.00
152_A	156_L	0.505	1.00
99_L	102_F	0.504	1.00
137_I	141_P	0.504	1.00
79_L	83_L	0.504	1.00
50_G	58_G	0.503	1.00
98_G	101_F	0.500	1.00
131_A	135_I	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
4d5sA	2	0.3584	8.9	0.911	Contact Map
4p6vB	1	0.3179	1.9	0.936	Contact Map
4d5tA	1	0.3642	1.6	0.939	Contact Map
2mfrA	1	0.2543	1.6	0.939	Contact Map
2k1kA	2	0.2197	1.2	0.943	Contact Map
4b19A	1	0.1734	1.1	0.944	Contact Map
2l6wA	2	0.2023	1.1	0.944	Contact Map
2mofA	1	0.2023	0.9	0.947	Contact Map
3j61A	1	0.3006	0.9	0.948	Contact Map
2jvxA	1	0.1618	0.8	0.95	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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