CsiV - PFAM28P - GREMLIN Contacts

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CsiV - Peptidoglycan-binding protein, CsiV

PFAM:	PF10972	Sequences: LALLLLLLLLLASSAAAAERWYQVEVIVFERLDDASAGSEQWPDDLPLPDPENAIDLLSPYLAPDITALEEGLPECDAAEDGFYLLPESELQLNDIARRLRRSGGYRPLLHTAWRQPGLDREQAPPIRIQAGENLGDQFPEDGSEITDQPEPTLPIPVWELDGTIKLYLSRYLHLDTDLWLREPSPNEDPEAADDLPANSEAEPPSDLTSYRLKQSRRMRSGELHYFDHPLFGVLVQITPY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	241 (221)
Sequences:	1821 (1577)
Seq/√Len:	106.1
META:	0.812

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
175_L	236_V	4.720	1.00
30_E	107_R	4.414	1.00
171_R	174_H	4.273	1.00
97_A	108_P	4.272	1.00
128_R	162_D	3.976	1.00
91_L	113_A	3.946	1.00
100_L	108_P	3.457	1.00
23_Q	115_R	3.362	1.00
28_V	234_V	3.311	1.00
177_T	234_V	2.921	1.00
224_L	235_L	2.710	1.00
26_V	165_I	2.542	1.00
167_L	175_L	2.492	1.00
166_K	176_D	2.418	1.00
27_I	97_A	2.378	1.00
32_L	107_R	2.360	1.00
25_E	111_H	2.303	1.00
99_R	102_R	2.295	1.00
217_R	225_H	2.217	1.00
124_A	166_K	2.098	1.00
177_T	227_F	2.092	1.00
168_Y	176_D	2.091	1.00
130_Q	162_D	1.965	1.00
172_Y	218_R	1.929	1.00
219_M	227_F	1.917	1.00
132_G	160_E	1.876	1.00
222_G	240_P	1.808	1.00
178_D	212_R	1.773	1.00
221_S	240_P	1.713	1.00
178_D	214_K	1.701	1.00
96_I	235_L	1.685	1.00
118_G	169_L	1.663	1.00
100_L	106_Y	1.648	1.00
83_F	86_L	1.636	1.00
10_L	13_S	1.610	1.00
211_Y	231_L	1.605	1.00
170_S	174_H	1.600	1.00
14_S	17_A	1.576	1.00
169_L	221_S	1.563	1.00
17_A	20_R	1.556	1.00
126_P	166_K	1.554	1.00
217_R	220_R	1.545	1.00
21_W	82_G	1.533	1.00
86_L	113_A	1.517	1.00
83_F	117_P	1.476	1.00
131_A	160_E	1.471	1.00
24_V	238_I	1.457	1.00
25_E	113_A	1.425	1.00
27_I	93_L	1.404	1.00
29_F	233_G	1.380	1.00
103_S	106_Y	1.376	1.00
213_L	232_F	1.350	1.00
132_G	135_L	1.328	0.99
183_E	231_L	1.322	0.99
42_W	231_L	1.321	0.99
220_R	225_H	1.310	0.99
91_L	94_N	1.288	0.99
217_R	221_S	1.286	0.99
199_N	202_A	1.277	0.99
24_V	167_L	1.263	0.99
15_A	19_E	1.248	0.99
5_L	8_L	1.246	0.99
15_A	18_A	1.243	0.99
4_L	7_L	1.235	0.99
4_L	11_L	1.234	0.99
30_E	160_E	1.217	0.99
172_Y	221_S	1.217	0.99
167_L	238_I	1.209	0.99
181_L	232_F	1.206	0.99
48_L	51_P	1.201	0.99
86_L	111_H	1.191	0.99
98_R	102_R	1.182	0.99
227_F	236_V	1.170	0.99
219_M	225_H	1.165	0.99
22_Y	169_L	1.154	0.98
9_L	13_S	1.143	0.98
182_R	210_S	1.142	0.98
196_L	199_N	1.140	0.98
196_L	200_S	1.118	0.98
51_P	54_A	1.115	0.98
23_Q	92_Q	1.112	0.98
128_R	180_W	1.109	0.98
23_Q	239_T	1.108	0.98
202_A	205_P	1.094	0.98
197_P	200_S	1.093	0.98
91_L	111_H	1.093	0.98
180_W	210_S	1.093	0.98
21_W	117_P	1.077	0.98
173_L	218_R	1.071	0.97
172_Y	217_R	1.058	0.97
120_D	123_Q	1.043	0.97
171_R	218_R	1.035	0.97
73_L	76_C	1.027	0.97
25_E	91_L	1.025	0.97
21_W	180_W	1.021	0.97
97_A	111_H	1.018	0.97
51_P	58_L	1.010	0.96
220_R	223_E	1.004	0.96
96_I	99_R	0.995	0.96
23_Q	113_A	0.992	0.96
32_L	103_S	0.992	0.96
173_L	221_S	0.991	0.96
23_Q	111_H	0.991	0.96
42_W	229_H	0.987	0.96
118_G	125_P	0.980	0.96
177_T	213_L	0.977	0.96
198_A	204_P	0.972	0.95
51_P	57_L	0.971	0.95
224_L	237_Q	0.964	0.95
21_W	115_R	0.959	0.95
29_F	226_Y	0.959	0.95
229_H	232_F	0.957	0.95
197_P	201_E	0.954	0.95
95_D	99_R	0.946	0.95
55_I	58_L	0.945	0.95
104_G	115_R	0.943	0.95
56_D	59_S	0.937	0.94
77_D	80_E	0.932	0.94
33_D	37_A	0.930	0.94
6_L	9_L	0.930	0.94
163_G	179_L	0.928	0.94
227_F	234_V	0.927	0.94
169_L	219_M	0.920	0.94
176_D	216_S	0.918	0.94
106_Y	213_L	0.917	0.94
135_L	139_F	0.916	0.94
53_N	56_D	0.915	0.94
50_D	55_I	0.913	0.94
46_L	50_D	0.905	0.93
221_S	225_H	0.895	0.93
93_L	97_A	0.892	0.93
165_I	175_L	0.890	0.93
25_E	93_L	0.890	0.93
96_I	224_L	0.878	0.92
6_L	10_L	0.876	0.92
30_E	109_L	0.875	0.92
218_R	225_H	0.874	0.92
22_Y	238_I	0.873	0.92
121_R	168_Y	0.866	0.92
174_H	216_S	0.865	0.92
25_E	92_Q	0.860	0.92
164_T	178_D	0.852	0.91
162_D	182_R	0.851	0.91
198_A	202_A	0.847	0.91
109_L	161_L	0.840	0.91
120_D	222_G	0.837	0.90
29_F	106_Y	0.835	0.90
6_L	12_A	0.832	0.90
226_Y	233_G	0.822	0.90
101_R	108_P	0.821	0.90
129_I	161_L	0.814	0.89
126_P	164_T	0.813	0.89
9_L	12_A	0.812	0.89
74_P	78_A	0.809	0.89
69_L	73_L	0.807	0.89
194_D	197_P	0.806	0.89
7_L	10_L	0.805	0.89
24_V	116_Q	0.803	0.89
91_L	112_T	0.801	0.88
96_I	100_L	0.800	0.88
174_H	218_R	0.797	0.88
69_L	72_G	0.795	0.88
108_P	227_F	0.794	0.88
31_R	216_S	0.793	0.88
24_V	118_G	0.792	0.88
68_A	75_E	0.791	0.88
204_P	207_D	0.785	0.87
82_G	117_P	0.779	0.87
215_Q	227_F	0.776	0.87
93_L	113_A	0.774	0.87
67_T	71_E	0.774	0.87
92_Q	237_Q	0.771	0.86
5_L	11_L	0.768	0.86
200_S	204_P	0.767	0.86
196_L	203_E	0.766	0.86
5_L	9_L	0.763	0.86
164_T	179_L	0.761	0.86
130_Q	159_W	0.759	0.86
88_E	98_R	0.758	0.86
195_D	198_A	0.755	0.85
66_I	72_G	0.754	0.85
62_L	65_D	0.753	0.85
217_R	223_E	0.753	0.85
26_V	112_T	0.750	0.85
31_R	106_Y	0.749	0.85
198_A	201_E	0.749	0.85
40_E	230_P	0.744	0.84
200_S	203_E	0.743	0.84
27_I	62_L	0.740	0.84
199_N	204_P	0.740	0.84
228_D	233_G	0.737	0.84
195_D	201_E	0.733	0.84
123_Q	234_V	0.733	0.84
121_R	124_A	0.731	0.83
225_H	229_H	0.728	0.83
14_S	19_E	0.726	0.83
193_A	196_L	0.726	0.83
206_S	209_T	0.723	0.83
193_A	199_N	0.723	0.83
13_S	17_A	0.719	0.82
161_L	181_L	0.718	0.82
13_S	18_A	0.718	0.82
49_P	54_A	0.712	0.82
131_A	135_L	0.711	0.82
68_A	71_E	0.706	0.81
162_D	180_W	0.705	0.81
108_P	112_T	0.703	0.81
118_G	173_L	0.701	0.81
223_E	230_P	0.699	0.81
87_P	90_E	0.698	0.80
96_I	232_F	0.697	0.80
4_L	22_Y	0.695	0.80
42_W	220_R	0.693	0.80
190_P	194_D	0.681	0.79
172_Y	220_R	0.680	0.79
31_R	35_A	0.680	0.79
50_D	57_L	0.677	0.78
222_G	238_I	0.673	0.78
93_L	174_H	0.667	0.77
203_E	206_S	0.667	0.77
193_A	203_E	0.658	0.76
220_R	240_P	0.655	0.76
12_A	20_R	0.654	0.76
66_I	69_L	0.652	0.76
124_A	127_I	0.652	0.76
76_C	79_A	0.648	0.75
175_L	234_V	0.648	0.75
36_S	39_S	0.645	0.75
7_L	13_S	0.639	0.74
219_M	223_E	0.639	0.74
170_S	173_L	0.639	0.74
16_A	19_E	0.638	0.74
121_R	170_S	0.635	0.74
169_L	238_I	0.634	0.74
69_L	76_C	0.632	0.74
21_W	83_F	0.627	0.73
68_A	73_L	0.627	0.73
65_D	72_G	0.627	0.73
63_A	69_L	0.625	0.73
201_E	205_P	0.625	0.73
103_S	113_A	0.622	0.72
15_A	20_R	0.621	0.72
30_E	231_L	0.620	0.72
190_P	193_A	0.620	0.72
22_Y	235_L	0.619	0.72
164_T	216_S	0.614	0.71
200_S	205_P	0.613	0.71
85_L	110_L	0.609	0.71
211_Y	216_S	0.608	0.71
195_D	205_P	0.608	0.71
219_M	238_I	0.607	0.71
28_V	183_E	0.605	0.70
169_L	172_Y	0.599	0.70
64_P	234_V	0.597	0.69
7_L	12_A	0.597	0.69
69_L	75_E	0.596	0.69
81_D	127_I	0.594	0.69
66_I	71_E	0.592	0.69
74_P	79_A	0.589	0.68
199_N	203_E	0.589	0.68
201_E	204_P	0.589	0.68
215_Q	232_F	0.588	0.68
21_W	162_D	0.588	0.68
65_D	74_P	0.588	0.68
171_R	219_M	0.582	0.67
54_A	59_S	0.580	0.67
168_Y	219_M	0.580	0.67
26_V	236_V	0.579	0.67
8_L	13_S	0.577	0.67
97_A	112_T	0.577	0.67
194_D	205_P	0.575	0.66
103_S	116_Q	0.575	0.66
92_Q	111_H	0.574	0.66
27_I	235_L	0.574	0.66
4_L	12_A	0.573	0.66
119_L	226_Y	0.570	0.66
97_A	101_R	0.570	0.66
165_I	237_Q	0.568	0.65
169_L	216_S	0.566	0.65
14_S	18_A	0.564	0.65
180_W	212_R	0.564	0.65
194_D	201_E	0.563	0.65
96_I	116_Q	0.562	0.65
38_G	167_L	0.560	0.64
197_P	204_P	0.560	0.64
218_R	224_L	0.560	0.64
19_E	61_Y	0.558	0.64
225_H	235_L	0.558	0.64
70_E	78_A	0.554	0.64
51_P	55_I	0.551	0.63
72_G	75_E	0.549	0.63
192_A	209_T	0.549	0.63
93_L	106_Y	0.548	0.63
168_Y	216_S	0.547	0.63
169_L	173_L	0.543	0.62
68_A	80_E	0.542	0.62
68_A	72_G	0.541	0.62
112_T	232_F	0.540	0.62
202_A	207_D	0.540	0.62
198_A	207_D	0.536	0.61
22_Y	118_G	0.534	0.61
67_T	70_E	0.534	0.61
108_P	173_L	0.533	0.61
195_D	199_N	0.530	0.60
113_A	239_T	0.530	0.60
192_A	198_A	0.529	0.60
43_P	178_D	0.529	0.60
70_E	75_E	0.528	0.60
169_L	218_R	0.527	0.60
74_P	80_E	0.524	0.59
8_L	12_A	0.524	0.59
7_L	11_L	0.523	0.59
171_R	227_F	0.522	0.59
129_I	238_I	0.521	0.59
127_I	227_F	0.518	0.58
25_E	161_L	0.518	0.58
129_I	163_G	0.515	0.58
160_E	181_L	0.513	0.58
167_L	173_L	0.512	0.58
98_R	101_R	0.511	0.57
28_V	179_L	0.511	0.57
225_H	230_P	0.510	0.57
193_A	201_E	0.509	0.57
30_E	183_E	0.507	0.57
15_A	189_D	0.506	0.57
227_F	232_F	0.506	0.57
199_N	205_P	0.505	0.57
161_L	175_L	0.504	0.56
118_G	221_S	0.504	0.56
94_N	101_R	0.504	0.56
159_W	162_D	0.502	0.56
94_N	98_R	0.500	0.56

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
3n5bB	3	0.0788	66	0.925	Contact Map
2vdaB	1	0.0747	2.1	0.965	Contact Map
2d1gA	2	0.1992	2	0.966	Contact Map
4um9B	2	0	1.6	0.968	Contact Map
2mmjA	1	0.0456	1.6	0.968	Contact Map
4g3bA	3	0.0954	1.5	0.968	Contact Map
4dgfA	1	0.2988	1.4	0.969	Contact Map
4whiA	1	0.361	1.3	0.969	Contact Map
1sg5A	1	0.3444	1.3	0.969	Contact Map
1th8B	1	0.2863	1.2	0.97	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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