AgrB - PFAM28P - GREMLIN Contacts

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

AgrB - Accessory gene regulator B

PFAM:	PF04647	Sequences: SEKIANYLIKNLNIIDEEDREIYEYGLEILLSTLLKIIIILLIGLLLGILLETLIFLLSFIPLRSFAGGYHAKTYLRCLIISILIFILILLLSKYIPINLSLLLIIILIILLIISLIIILLLAPVDTPNKPLSSKEKRKKLKILSIILLIILLIISLLLKNNIISNAIALGILLVAILQIITL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	183 (173)
Sequences:	3915 (3513)
Seq/√Len:	267.1
META:	0.746

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_I	79_L	5.793	1.00
74_T	77_R	5.425	1.00
73_K	77_R	3.616	1.00
49_I	52_E	3.364	1.00
44_G	53_T	3.024	1.00
72_A	81_I	2.790	1.00
67_A	179_Q	2.473	1.00
139_K	143_I	2.451	1.00
6_N	20_R	2.449	1.00
49_I	94_K	2.420	1.00
16_D	19_D	2.355	1.00
32_S	75_Y	2.290	1.00
126_D	131_P	2.233	1.00
24_E	28_E	2.233	1.00
9_I	20_R	2.188	1.00
20_R	24_E	2.014	1.00
49_I	90_L	2.011	1.00
19_D	22_I	1.982	1.00
167_A	171_G	1.959	1.00
117_I	121_L	1.856	1.00
59_S	168_I	1.811	1.00
171_G	175_V	1.705	1.00
40_I	53_T	1.664	1.00
141_L	144_L	1.621	1.00
5_A	9_I	1.611	1.00
28_E	75_Y	1.611	1.00
67_A	145_S	1.602	1.00
141_L	145_S	1.594	1.00
5_A	24_E	1.570	1.00
56_F	89_I	1.556	1.00
72_A	77_R	1.537	1.00
118_I	122_L	1.506	1.00
33_T	36_K	1.504	1.00
7_Y	11_N	1.468	1.00
122_L	125_V	1.467	1.00
21_E	24_E	1.453	1.00
18_E	22_I	1.423	1.00
79_L	83_I	1.396	1.00
165_S	168_I	1.379	1.00
144_L	151_I	1.367	1.00
28_E	32_S	1.362	1.00
59_S	62_P	1.342	1.00
5_A	20_R	1.320	1.00
75_Y	79_L	1.319	1.00
43_I	83_I	1.291	1.00
67_A	123_A	1.281	1.00
91_L	94_K	1.276	1.00
176_A	179_Q	1.273	1.00
147_I	151_I	1.270	1.00
148_L	152_L	1.249	1.00
127_T	132_L	1.248	1.00
17_E	20_R	1.235	1.00
4_I	27_L	1.234	1.00
140_K	144_L	1.232	1.00
41_L	54_L	1.226	1.00
23_Y	27_L	1.224	1.00
4_I	31_L	1.211	1.00
58_L	62_P	1.193	1.00
126_D	132_L	1.189	1.00
32_S	36_K	1.184	1.00
36_K	82_S	1.180	1.00
56_F	90_L	1.171	1.00
107_I	111_L	1.162	1.00
26_G	29_I	1.132	1.00
136_E	140_K	1.123	1.00
140_K	145_S	1.121	1.00
53_T	86_F	1.120	1.00
56_F	60_F	1.108	1.00
137_K	141_L	1.089	1.00
119_I	149_L	1.081	1.00
45_L	50_L	1.067	1.00
41_L	50_L	1.062	1.00
130_K	140_K	1.060	1.00
135_K	139_K	1.057	1.00
112_L	116_L	1.052	1.00
40_I	86_F	1.047	1.00
60_F	178_L	1.030	1.00
112_L	153_L	1.024	1.00
127_T	130_K	1.020	1.00
66_F	144_L	1.014	1.00
137_K	140_K	1.014	1.00
59_S	171_G	1.003	1.00
82_S	86_F	1.000	1.00
48_G	51_L	0.998	1.00
5_A	27_L	0.993	1.00
85_I	178_L	0.993	1.00
33_T	75_Y	0.985	1.00
127_T	131_P	0.982	1.00
37_I	57_L	0.979	1.00
15_I	23_Y	0.978	1.00
36_K	75_Y	0.972	1.00
126_D	130_K	0.968	1.00
36_K	79_L	0.962	1.00
160_K	163_I	0.960	1.00
115_S	176_A	0.943	1.00
106_I	110_I	0.941	1.00
6_N	10_K	0.938	1.00
152_L	156_S	0.935	1.00
92_L	95_Y	0.929	1.00
5_A	23_Y	0.926	1.00
75_Y	127_T	0.915	1.00
41_L	44_G	0.911	1.00
139_K	142_K	0.910	1.00
63_L	67_A	0.902	1.00
50_L	53_T	0.898	1.00
56_F	171_G	0.888	1.00
144_L	148_L	0.887	1.00
164_I	168_I	0.886	1.00
145_S	151_I	0.882	1.00
145_S	152_L	0.881	1.00
68_G	130_K	0.876	1.00
124_P	131_P	0.875	1.00
63_L	123_A	0.870	1.00
138_R	141_L	0.866	1.00
53_T	90_L	0.863	1.00
67_A	175_V	0.853	1.00
29_I	65_S	0.847	1.00
76_L	80_I	0.839	0.99
71_H	78_C	0.826	0.99
67_A	119_I	0.817	0.99
44_G	86_F	0.810	0.99
26_G	30_L	0.810	0.99
23_Y	26_G	0.802	0.99
40_I	82_S	0.800	0.99
83_I	87_I	0.799	0.99
8_L	23_Y	0.798	0.99
62_P	65_S	0.794	0.99
120_L	145_S	0.792	0.99
73_K	128_P	0.788	0.99
39_I	83_I	0.782	0.99
31_L	35_L	0.780	0.99
23_Y	56_F	0.768	0.99
49_I	53_T	0.768	0.99
51_L	55_I	0.766	0.99
126_D	137_K	0.758	0.99
7_Y	10_K	0.754	0.99
70_Y	73_K	0.753	0.99
33_T	37_I	0.753	0.99
36_K	83_I	0.750	0.99
9_I	15_I	0.750	0.99
56_F	86_F	0.749	0.99
60_F	75_Y	0.749	0.99
130_K	136_E	0.745	0.99
8_L	27_L	0.740	0.99
87_I	90_L	0.740	0.99
148_L	151_I	0.738	0.99
79_L	82_S	0.737	0.99
41_L	57_L	0.730	0.99
126_D	138_R	0.729	0.99
115_S	149_L	0.729	0.99
9_I	14_I	0.726	0.99
115_S	169_A	0.726	0.99
70_Y	74_T	0.723	0.98
166_N	169_A	0.723	0.98
80_I	84_L	0.722	0.98
29_I	82_S	0.722	0.98
23_Y	60_F	0.721	0.98
112_L	115_S	0.721	0.98
125_V	179_Q	0.719	0.98
133_S	136_E	0.715	0.98
11_N	14_I	0.709	0.98
85_I	174_L	0.706	0.98
37_I	41_L	0.704	0.98
88_L	92_L	0.704	0.98
142_K	145_S	0.699	0.98
20_R	23_Y	0.699	0.98
36_K	40_I	0.694	0.98
29_I	33_T	0.690	0.98
42_L	46_L	0.690	0.98
52_E	163_I	0.689	0.98
28_E	31_L	0.689	0.98
94_K	97_P	0.687	0.98
146_I	149_L	0.685	0.98
60_F	86_F	0.684	0.98
32_S	79_L	0.681	0.98
77_R	81_I	0.679	0.98
172_I	175_V	0.679	0.98
167_A	175_V	0.675	0.98
47_L	50_L	0.674	0.98
29_I	83_I	0.674	0.98
66_F	140_K	0.669	0.97
91_L	95_Y	0.665	0.97
25_Y	129_N	0.662	0.97
60_F	130_K	0.660	0.97
133_S	137_K	0.659	0.97
44_G	50_L	0.658	0.97
125_V	129_N	0.657	0.97
60_F	64_R	0.651	0.97
144_L	147_I	0.643	0.97
163_I	166_N	0.639	0.97
67_A	124_P	0.638	0.97
35_L	75_Y	0.638	0.97
109_I	113_I	0.635	0.97
115_S	172_I	0.633	0.97
33_T	40_I	0.631	0.96
32_S	82_S	0.629	0.96
30_L	34_L	0.627	0.96
10_K	13_N	0.623	0.96
72_A	75_Y	0.619	0.96
153_L	157_L	0.618	0.96
108_L	166_N	0.616	0.96
54_L	58_L	0.614	0.96
5_A	8_L	0.613	0.96
22_I	26_G	0.611	0.96
152_L	155_I	0.609	0.96
25_Y	67_A	0.609	0.96
3_K	10_K	0.605	0.96
63_L	172_I	0.603	0.95
34_L	38_I	0.600	0.95
156_S	159_L	0.600	0.95
167_A	170_L	0.599	0.95
40_I	44_G	0.598	0.95
168_I	172_I	0.598	0.95
112_L	169_A	0.597	0.95
149_L	152_L	0.593	0.95
166_N	170_L	0.590	0.95
172_I	176_A	0.589	0.95
8_L	14_I	0.588	0.95
70_Y	81_I	0.586	0.95
60_F	82_S	0.585	0.95
145_S	149_L	0.581	0.94
14_I	23_Y	0.577	0.94
18_E	21_E	0.577	0.94
112_L	172_I	0.575	0.94
29_I	86_F	0.573	0.94
3_K	6_N	0.567	0.94
175_V	179_Q	0.567	0.94
60_F	125_V	0.564	0.94
57_L	61_I	0.564	0.94
4_I	7_Y	0.561	0.93
108_L	165_S	0.558	0.93
132_L	136_E	0.557	0.93
62_P	152_L	0.557	0.93
95_Y	98_I	0.552	0.93
64_R	82_S	0.551	0.93
143_I	147_I	0.551	0.93
5_A	15_I	0.547	0.92
134_S	150_I	0.545	0.92
176_A	180_I	0.545	0.92
26_G	72_A	0.545	0.92
90_L	125_V	0.545	0.92
38_I	42_L	0.540	0.92
108_L	112_L	0.538	0.92
14_I	19_D	0.535	0.92
3_K	7_Y	0.529	0.91
111_L	173_L	0.527	0.91
150_I	154_I	0.527	0.91
151_I	155_I	0.527	0.91
61_I	100_L	0.523	0.91
164_I	167_A	0.522	0.91
115_S	180_I	0.522	0.91
25_Y	29_I	0.517	0.90
94_K	98_I	0.516	0.90
59_S	175_V	0.513	0.90
33_T	82_S	0.512	0.90
49_I	93_S	0.511	0.90
5_A	64_R	0.511	0.90
52_E	56_F	0.503	0.89
6_N	88_L	0.500	0.89
138_R	142_K	0.500	0.89

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
2xq2A	2	0.9617	8.5	0.927	Contact Map
2cfqA	1	0.6776	3	0.941	Contact Map
2k1eA	3	0.5628	1.8	0.948	Contact Map
1ji8A	1	0.3388	1.7	0.949	Contact Map
2okrC	1	0.1311	1.7	0.949	Contact Map
2dj6A	3	0.2131	1.6	0.949	Contact Map
4q2eA	2	0.224	1.6	0.949	Contact Map
4aq5B	1	0.3388	1.6	0.949	Contact Map
4wfeA	2	0.6339	1.5	0.95	Contact Map
2i9nA	1	0.0601	1.5	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.

Page generated in 0.0064 seconds.