SPSD - BACSU - GREMLIN Contacts

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SPSD - Spore coat polysaccharide biosynthesis protein SpsD

UniProt:	P39624	Sequences: MYTVKENVSKEAIEEFLQSRKLTLDVPYQFSLGLFENSRLQGVLLYEDSLWESKVLQKKVMNVKLLAANSTGQLKRLFEAFYTVRQMDETDFIFVRVPAEDIGAAHVIQQQPSSYFVGSLLKLAMPPSFYDKTPPFFELGPPEPGDTEAICELARDSFTKSRYFQDPHLSRDAANEIFQEWTRNNLNGRAAVNIVAKHNGEVIGYLQGLSRDDECILDLMAVKPGFEGKRIAFHLLANLIEQPETQKHRTVTAGTQLHNVRAIRLYERMGFTAEQSYYYYHIWPGKEAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	289 (227)
Sequences:	249 (200)
Seq/√Len:	13.3

ECOLI - WECD
BACSU - SPSD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_S	221_A	4.756	1.00
51_W	162_R	3.682	0.99
232_A	266_Y	3.585	0.99
180_E	184_N	3.014	0.97
202_V	264_R	3.013	0.97
65_L	95_V	2.932	0.96
118_G	280_Y	2.925	0.96
140_G	197_K	2.733	0.95
220_M	262_A	2.543	0.92
262_A	266_Y	2.487	0.91
51_W	55_V	2.464	0.91
158_F	174_A	2.435	0.90
204_G	231_I	2.379	0.89
59_K	91_D	2.328	0.88
182_T	207_Q	2.237	0.86
181_W	219_L	2.197	0.85
233_F	268_R	2.188	0.84
232_A	262_A	2.137	0.83
121_L	233_F	2.004	0.79
150_I	186_L	1.999	0.79
118_G	281_H	1.923	0.76
56_L	178_F	1.916	0.75
96_R	279_Y	1.906	0.75
161_S	232_A	1.903	0.75
161_S	266_Y	1.890	0.74
195_V	198_H	1.843	0.72
178_F	181_W	1.833	0.72
140_G	264_R	1.821	0.71
161_S	262_A	1.815	0.71
53_S	59_K	1.807	0.71
53_S	235_L	1.798	0.70
217_L	253_A	1.763	0.69
150_I	182_T	1.746	0.68
113_S	282_I	1.724	0.67
94_F	279_Y	1.717	0.67
105_A	280_Y	1.708	0.66
166_D	281_H	1.698	0.66
55_V	162_R	1.679	0.65
53_S	58_K	1.673	0.65
207_Q	240_I	1.669	0.65
128_S	132_K	1.666	0.64
86_Q	213_D	1.656	0.64
235_L	255_T	1.649	0.64
218_D	262_A	1.634	0.63
224_P	227_E	1.575	0.60
61_M	90_T	1.561	0.59
221_A	238_N	1.550	0.59
94_F	162_R	1.506	0.56
62_N	222_V	1.481	0.55
219_L	256_Q	1.467	0.54
207_Q	218_D	1.450	0.53
205_Y	219_L	1.441	0.53
170_S	173_A	1.433	0.52
96_R	120_L	1.425	0.52
58_K	249_R	1.424	0.52
154_A	221_A	1.404	0.51
55_V	163_Y	1.402	0.51
53_S	60_V	1.394	0.50
177_I	255_T	1.393	0.50
162_R	266_Y	1.382	0.50
49_S	262_A	1.380	0.50
253_A	256_Q	1.378	0.50
198_H	201_E	1.373	0.49
232_A	265_L	1.360	0.49
123_L	263_I	1.347	0.48
125_M	240_I	1.340	0.48
219_L	255_T	1.329	0.47
120_L	158_F	1.311	0.46
120_L	177_I	1.311	0.46
55_V	266_Y	1.284	0.45
48_D	192_V	1.261	0.43
85_R	264_R	1.243	0.42
167_P	239_L	1.227	0.42
157_S	231_I	1.226	0.42
218_D	254_G	1.220	0.41
120_L	279_Y	1.211	0.41
184_N	187_N	1.206	0.41
115_Y	264_R	1.201	0.40
119_S	281_H	1.194	0.40
131_D	172_D	1.192	0.40
122_K	254_G	1.191	0.40
139_L	272_T	1.172	0.39
203_I	211_R	1.166	0.39
190_A	281_H	1.158	0.38
47_E	146_D	1.153	0.38
44_L	95_V	1.144	0.37
55_V	262_A	1.142	0.37
98_P	103_G	1.139	0.37
177_I	262_A	1.132	0.37
256_Q	266_Y	1.130	0.37
63_V	90_T	1.126	0.37
51_W	163_Y	1.126	0.37
132_K	245_T	1.125	0.37
60_V	158_F	1.125	0.37
233_F	269_M	1.122	0.36
185_N	190_A	1.116	0.36
161_S	217_L	1.115	0.36
59_K	222_V	1.114	0.36
94_F	165_Q	1.114	0.36
89_E	144_P	1.113	0.36
90_T	231_I	1.111	0.36
57_Q	144_P	1.103	0.35
55_V	177_I	1.097	0.35
154_A	205_Y	1.077	0.34
221_A	282_I	1.065	0.34
168_H	281_H	1.065	0.34
85_R	247_K	1.060	0.33
161_S	256_Q	1.055	0.33
49_S	255_T	1.054	0.33
55_V	169_L	1.050	0.33
177_I	256_Q	1.044	0.33
118_G	168_H	1.039	0.32
91_D	127_P	1.035	0.32
169_L	173_A	1.033	0.32
162_R	177_I	1.018	0.31
206_L	262_A	1.016	0.31
263_I	273_A	1.014	0.31
95_V	280_Y	1.014	0.31
225_G	229_K	1.005	0.31
99_A	229_K	0.999	0.31
101_D	104_A	0.996	0.30
217_L	266_Y	0.991	0.30
154_A	161_S	0.981	0.30
93_I	240_I	0.973	0.29
256_Q	262_A	0.970	0.29
162_R	232_A	0.970	0.29
229_K	258_H	0.969	0.29
253_A	262_A	0.959	0.29
139_L	197_K	0.957	0.29
210_S	246_Q	0.956	0.29
133_T	212_D	0.955	0.29
161_S	253_A	0.955	0.29
158_F	177_I	0.954	0.29
255_T	262_A	0.948	0.28
49_S	177_I	0.948	0.28
55_V	279_Y	0.941	0.28
139_L	264_R	0.940	0.28
157_S	213_D	0.939	0.28
54_K	102_I	0.937	0.28
103_G	110_Q	0.932	0.28
49_S	55_V	0.928	0.28
150_I	268_R	0.927	0.27
60_V	282_I	0.913	0.27
82_Y	251_V	0.912	0.27
151_C	183_R	0.903	0.26
182_T	193_N	0.890	0.26
57_Q	160_K	0.883	0.26
217_L	256_Q	0.882	0.26
50_L	199_N	0.871	0.25
132_K	172_D	0.870	0.25
185_N	209_L	0.867	0.25
120_L	254_G	0.865	0.25
49_S	256_Q	0.863	0.25
62_N	182_T	0.858	0.25
98_P	101_D	0.857	0.25
61_M	149_A	0.856	0.25
55_V	256_Q	0.853	0.24
172_D	202_V	0.852	0.24
52_E	207_Q	0.852	0.24
83_T	248_H	0.851	0.24
63_V	162_R	0.851	0.24
123_L	267_E	0.846	0.24
254_G	262_A	0.845	0.24
85_R	115_Y	0.836	0.24
217_L	251_V	0.831	0.24
196_A	234_H	0.829	0.24
121_L	223_K	0.823	0.23
217_L	220_M	0.819	0.23
161_S	218_D	0.819	0.23
203_I	226_F	0.818	0.23
130_Y	139_L	0.817	0.23
153_L	157_S	0.815	0.23
59_K	83_T	0.811	0.23
70_S	280_Y	0.804	0.23
144_P	152_E	0.799	0.22
120_L	163_Y	0.798	0.22
202_V	261_R	0.798	0.22
52_E	151_C	0.796	0.22
166_D	279_Y	0.777	0.22
206_L	217_L	0.777	0.22
101_D	149_A	0.771	0.21
220_M	242_Q	0.769	0.21
142_P	158_F	0.769	0.21
62_N	117_V	0.765	0.21
177_I	186_L	0.763	0.21
162_R	279_Y	0.762	0.21
139_L	145_G	0.756	0.21
149_A	195_V	0.753	0.21
49_S	216_I	0.750	0.21
91_D	211_R	0.747	0.21
150_I	267_E	0.740	0.20
134_P	260_V	0.739	0.20
204_G	260_V	0.735	0.20
92_F	265_L	0.734	0.20
241_E	246_Q	0.733	0.20
51_W	232_A	0.726	0.20
133_T	141_P	0.721	0.20
249_R	275_Q	0.719	0.20
120_L	262_A	0.718	0.20
94_F	158_F	0.717	0.20
169_L	254_G	0.714	0.19
56_L	185_N	0.707	0.19
191_A	218_D	0.706	0.19
161_S	281_H	0.705	0.19
153_L	223_K	0.704	0.19
168_H	279_Y	0.700	0.19
55_V	255_T	0.697	0.19
54_K	193_N	0.696	0.19
142_P	167_P	0.692	0.19
63_V	152_E	0.690	0.19
57_Q	86_Q	0.688	0.19
234_H	247_K	0.688	0.19
232_A	235_L	0.679	0.18
68_A	156_D	0.676	0.18
167_P	256_Q	0.673	0.18
131_D	274_E	0.673	0.18
162_R	166_D	0.672	0.18
51_W	266_Y	0.672	0.18
115_Y	121_L	0.663	0.18
140_G	234_H	0.663	0.18
110_Q	197_K	0.663	0.18
156_D	196_A	0.662	0.18
59_K	124_A	0.660	0.18
204_G	264_R	0.658	0.18
254_G	279_Y	0.658	0.18
204_G	266_Y	0.658	0.18
96_R	113_S	0.657	0.18
211_R	267_E	0.657	0.18
69_N	225_G	0.657	0.18
236_L	256_Q	0.657	0.18
158_F	181_W	0.657	0.18
186_L	190_A	0.656	0.18
152_E	199_N	0.653	0.18
49_S	163_Y	0.651	0.17
182_T	238_N	0.650	0.17
193_N	207_Q	0.646	0.17
204_G	262_A	0.644	0.17
64_K	109_Q	0.643	0.17
194_I	216_I	0.640	0.17
151_C	246_Q	0.638	0.17
258_H	280_Y	0.638	0.17
176_E	262_A	0.637	0.17
192_V	208_G	0.636	0.17
117_V	263_I	0.634	0.17
174_A	177_I	0.629	0.17
56_L	163_Y	0.628	0.17
264_R	272_T	0.627	0.17
118_G	169_L	0.627	0.17
205_Y	230_R	0.627	0.17
112_P	282_I	0.626	0.17
173_A	176_E	0.621	0.17
141_P	241_E	0.621	0.17
153_L	158_F	0.621	0.17
119_S	279_Y	0.617	0.16
191_A	255_T	0.615	0.16
57_Q	184_N	0.613	0.16
177_I	254_G	0.612	0.16
197_K	204_G	0.612	0.16
201_E	268_R	0.610	0.16
194_I	198_H	0.610	0.16
260_V	268_R	0.609	0.16
217_L	262_A	0.605	0.16
176_E	194_I	0.602	0.16
177_I	190_A	0.602	0.16
110_Q	198_H	0.599	0.16
127_P	193_N	0.599	0.16
111_Q	125_M	0.598	0.16
203_I	233_F	0.598	0.16
94_F	281_H	0.597	0.16
254_G	281_H	0.595	0.16
113_S	142_P	0.594	0.16
114_S	248_H	0.588	0.16
44_L	65_L	0.586	0.16
59_K	231_I	0.586	0.16
67_A	247_K	0.585	0.16
94_F	174_A	0.583	0.15
105_A	136_F	0.582	0.15
68_A	196_A	0.578	0.15
206_L	255_T	0.577	0.15
234_H	280_Y	0.575	0.15
117_V	212_D	0.574	0.15
88_D	144_P	0.573	0.15
91_D	156_D	0.573	0.15
160_K	269_M	0.572	0.15
131_D	149_A	0.572	0.15
133_T	143_E	0.571	0.15
209_L	243_P	0.569	0.15
163_Y	209_L	0.566	0.15
148_E	249_R	0.560	0.15
84_V	247_K	0.559	0.15
271_F	281_H	0.557	0.15
167_P	255_T	0.554	0.15
206_L	256_Q	0.554	0.15
98_P	104_A	0.551	0.15
64_K	225_G	0.550	0.15
120_L	232_A	0.549	0.15
60_V	114_S	0.545	0.14
176_E	189_R	0.544	0.14
118_G	171_R	0.543	0.14
92_F	254_G	0.542	0.14
56_L	175_N	0.541	0.14
60_V	92_F	0.539	0.14
139_L	207_Q	0.538	0.14
119_S	209_L	0.538	0.14
120_L	218_D	0.537	0.14
99_A	276_S	0.535	0.14
101_D	171_R	0.530	0.14
123_L	266_Y	0.529	0.14
141_P	193_N	0.529	0.14
97_V	278_Y	0.528	0.14
58_K	231_I	0.527	0.14
238_N	270_G	0.526	0.14
181_W	205_Y	0.526	0.14
236_L	255_T	0.524	0.14
46_Y	102_I	0.522	0.14
178_F	218_D	0.522	0.14
200_G	209_L	0.519	0.14
202_V	233_F	0.518	0.14
195_V	245_T	0.518	0.14
124_A	143_E	0.517	0.14
242_Q	271_F	0.516	0.14
105_A	109_Q	0.515	0.14
252_T	274_E	0.515	0.14
55_V	117_V	0.514	0.14
82_Y	154_A	0.513	0.14
150_I	276_S	0.512	0.14
196_A	217_L	0.512	0.14
178_F	219_L	0.511	0.14
59_K	84_V	0.511	0.14
233_F	260_V	0.510	0.14
197_K	247_K	0.509	0.14
96_R	165_Q	0.507	0.13
162_R	263_I	0.507	0.13
93_I	179_Q	0.507	0.13
56_L	259_N	0.506	0.13
108_I	182_T	0.505	0.13
109_Q	260_V	0.505	0.13
188_G	191_A	0.504	0.13
122_K	235_L	0.504	0.13
50_L	152_E	0.500	0.13

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
2ft0A	2	0.7578	100	0.648	Contact Map
3tt2A	1	0.9308	99.9	0.718	Contact Map
1p0hA	1	0.8997	99.8	0.74	Contact Map
2wpxA	1	0.91	99.8	0.742	Contact Map
1ufhA	3	0.5087	99.8	0.756	Contact Map
1s3zA	2	0.481	99.8	0.757	Contact Map
1vkcA	2	0.4913	99.8	0.759	Contact Map
3frmA	3	0.8512	99.8	0.759	Contact Map
1on0A	4	0.5156	99.8	0.761	Contact Map
3owcA	1	0.5294	99.8	0.761	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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