SPSA - BACSU - GREMLIN Contacts

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SPSA - Spore coat polysaccharide biosynthesis protein SpsA

UniProt:	P39621	Sequences: MPKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	256 (208)
Sequences:	39373 (33773)
Seq/√Len:	2341.7

ECOLI - YIBD WCAA WCAE ARNC WBBL GTRB PGAC YAIP
BACSU - SPSA CGED GGAA EPSE EPSJ EPSH GGAB YFNE TUAG YWDF YKOT YKCC CSBB YDAM TAGF
HALSA - Q9HQP4 Q9HQP8 Q9HQP3 Q9HNK3 Q9HSC8 Q9HQQ6 Q9HR08 Q9HSB1
SULSO - Q7LXF7 Q97TZ0 Q97X05 Q97TY0 Q7LXG6 Q7LXY2 Q97YG5 Q97WK7 Q97W52 Q97YM4 Q97YN4 Q97UK7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
166_Y	170_E	3.061	1.00
13_K	98_D	3.014	1.00
14_S	44_E	2.568	1.00
193_R	197_R	2.356	1.00
109_K	209_E	2.342	1.00
63_S	83_Q	2.334	1.00
38_D	62_Q	2.239	1.00
5_S	90_G	2.223	1.00
83_Q	87_M	2.218	1.00
103_M	213_L	2.194	1.00
92_Y	114_L	2.097	1.00
10_S	45_T	2.081	1.00
46_L	62_Q	2.072	1.00
28_T	108_L	2.051	1.00
33_E	59_R	2.041	1.00
37_M	84_A	1.939	1.00
18_A	22_S	1.928	1.00
8_M	34_L	1.925	1.00
46_L	50_R	1.917	1.00
63_S	75_T	1.900	1.00
75_T	79_A	1.889	1.00
7_I	84_A	1.876	1.00
120_K	205_Y	1.851	1.00
121_A	202_Y	1.820	1.00
19_K	215_Y	1.808	1.00
86_E	178_S	1.777	1.00
18_A	52_F	1.750	1.00
168_V	202_Y	1.724	1.00
12_N	42_N	1.716	1.00
44_E	47_N	1.713	1.00
81_I	97_T	1.694	1.00
61_Y	87_M	1.679	1.00
113_E	207_L	1.677	1.00
5_S	33_E	1.676	1.00
19_K	101_I	1.655	1.00
102_Y	106_R	1.652	1.00
94_T	163_M	1.645	1.00
113_E	205_Y	1.644	1.00
14_S	48_V	1.638	1.00
4_V	111_V	1.636	1.00
128_K	213_L	1.631	1.00
77_Y	81_I	1.606	1.00
29_F	111_V	1.593	1.00
105_D	109_K	1.580	1.00
110_M	163_M	1.577	1.00
50_R	62_Q	1.575	1.00
121_A	165_R	1.552	1.00
38_D	41_S	1.539	1.00
106_R	110_M	1.537	1.00
59_R	87_M	1.519	1.00
172_V	177_G	1.516	1.00
8_M	20_S	1.496	1.00
83_Q	86_E	1.485	1.00
101_I	213_L	1.479	1.00
36_I	49_I	1.476	1.00
92_Y	163_M	1.443	1.00
3_K	91_E	1.437	1.00
18_A	48_V	1.430	1.00
22_S	26_S	1.419	1.00
63_S	79_A	1.407	1.00
96_A	102_Y	1.403	1.00
22_S	52_F	1.403	1.00
10_S	36_I	1.401	1.00
18_A	51_P	1.396	1.00
122_V	204_F	1.395	1.00
114_L	163_M	1.384	1.00
33_E	90_G	1.383	1.00
94_T	106_R	1.382	1.00
11_Y	74_K	1.371	1.00
46_L	60_F	1.360	1.00
94_T	107_L	1.349	1.00
109_K	112_R	1.345	1.00
61_Y	83_Q	1.342	1.00
78_A	190_G	1.329	1.00
29_F	32_F	1.320	1.00
108_L	112_R	1.302	1.00
167_S	171_K	1.297	1.00
4_V	107_L	1.279	1.00
81_I	95_Y	1.255	1.00
93_I	166_Y	1.246	1.00
5_S	88_A	1.240	1.00
85_I	169_L	1.227	1.00
162_V	195_F	1.226	1.00
23_S	102_Y	1.224	1.00
171_K	202_Y	1.219	1.00
10_S	13_K	1.216	1.00
50_R	53_L	1.167	1.00
21_I	34_L	1.159	1.00
3_K	31_D	1.157	1.00
12_N	41_S	1.153	1.00
10_S	98_D	1.148	1.00
48_V	52_F	1.147	1.00
114_L	123_I	1.144	1.00
63_S	80_L	1.128	1.00
91_E	165_R	1.127	1.00
13_K	16_Y	1.122	1.00
110_M	125_S	1.121	1.00
77_Y	190_G	1.117	1.00
85_I	95_Y	1.110	1.00
130_Y	213_L	1.109	1.00
101_I	215_Y	1.102	1.00
39_D	74_K	1.101	1.00
88_A	166_Y	1.100	1.00
126_A	206_P	1.098	1.00
168_V	198_V	1.095	1.00
113_E	116_T	1.061	1.00
167_S	170_E	1.056	1.00
111_V	115_D	1.055	1.00
20_S	96_A	1.055	1.00
25_L	55_D	1.054	1.00
112_R	116_T	1.052	1.00
33_E	89_E	1.044	1.00
105_D	108_L	1.036	1.00
4_V	163_M	1.034	1.00
37_M	80_L	1.032	1.00
26_S	104_P	1.022	1.00
38_D	46_L	1.019	1.00
77_Y	221_I	0.992	1.00
5_S	35_F	0.988	1.00
94_T	102_Y	0.976	1.00
165_R	168_V	0.973	1.00
128_K	210_E	0.960	1.00
119_E	203_P	0.959	1.00
51_P	54_N	0.956	1.00
34_L	58_V	0.951	1.00
101_I	130_Y	0.947	1.00
48_V	51_P	0.941	1.00
22_S	25_L	0.940	1.00
47_N	50_R	0.940	1.00
9_T	80_L	0.936	1.00
109_K	207_L	0.934	1.00
39_D	63_S	0.932	1.00
3_K	89_E	0.930	1.00
23_S	101_I	0.922	1.00
110_M	123_I	0.920	1.00
28_T	105_D	0.916	1.00
127_S	160_C	0.915	1.00
121_A	203_P	0.915	1.00
169_L	194_F	0.914	1.00
3_K	90_G	0.911	1.00
59_R	89_E	0.910	1.00
49_I	60_F	0.907	1.00
25_L	52_F	0.902	1.00
113_E	123_I	0.902	1.00
103_M	128_K	0.899	1.00
24_I	96_A	0.897	1.00
122_V	198_V	0.897	1.00
171_K	200_H	0.893	1.00
106_R	211_L	0.891	1.00
106_R	125_S	0.891	1.00
85_I	93_I	0.888	1.00
110_M	114_L	0.853	1.00
25_L	57_R	0.849	1.00
6_V	24_I	0.849	1.00
81_I	190_G	0.845	1.00
172_V	178_S	0.843	1.00
92_Y	111_V	0.838	1.00
75_T	80_L	0.835	1.00
109_K	113_E	0.826	1.00
44_E	48_V	0.820	1.00
79_A	83_Q	0.819	1.00
78_A	82_N	0.816	1.00
10_S	17_V	0.801	1.00
25_L	58_V	0.801	1.00
39_D	80_L	0.799	1.00
24_I	34_L	0.788	1.00
77_Y	159_H	0.788	1.00
217_T	220_S	0.788	1.00
21_I	52_F	0.786	1.00
6_V	94_T	0.781	1.00
16_Y	215_Y	0.768	1.00
3_K	115_D	0.765	1.00
10_S	49_I	0.754	1.00
47_N	51_P	0.754	1.00
77_Y	97_T	0.748	1.00
39_D	76_R	0.747	1.00
63_S	73_E	0.744	1.00
136_R	139_V	0.743	1.00
20_S	23_S	0.741	1.00
53_L	60_F	0.739	1.00
37_M	83_Q	0.733	1.00
39_D	75_T	0.733	1.00
121_A	168_V	0.732	1.00
21_I	36_I	0.729	1.00
29_F	108_L	0.728	1.00
186_F	189_I	0.724	1.00
13_K	217_T	0.723	1.00
32_F	107_L	0.719	1.00
79_A	184_P	0.717	1.00
19_K	22_S	0.710	1.00
130_Y	215_Y	0.709	1.00
125_S	211_L	0.708	1.00
24_I	102_Y	0.708	1.00
159_H	162_V	0.707	1.00
129_T	216_I	0.700	1.00
184_P	187_Y	0.699	1.00
82_N	178_S	0.699	1.00
220_S	223_F	0.697	1.00
168_V	172_V	0.694	1.00
6_V	107_L	0.692	1.00
77_Y	80_L	0.688	1.00
28_T	104_P	0.682	1.00
40_N	63_S	0.681	1.00
164_H	195_F	0.676	1.00
124_Y	206_P	0.676	1.00
172_V	198_V	0.670	1.00
53_L	58_V	0.666	1.00
9_T	98_D	0.664	1.00
160_C	212_D	0.663	1.00
22_S	54_N	0.662	1.00
172_V	200_H	0.662	1.00
95_Y	179_Y	0.660	1.00
85_I	88_A	0.660	1.00
52_F	55_D	0.660	1.00
35_F	84_A	0.658	1.00
14_S	18_A	0.658	1.00
80_L	83_Q	0.658	1.00
113_E	120_K	0.658	1.00
103_M	211_L	0.657	1.00
4_V	94_T	0.654	1.00
8_M	24_I	0.652	1.00
194_F	198_V	0.649	1.00
126_A	208_D	0.649	1.00
103_M	106_R	0.644	1.00
168_V	171_K	0.639	1.00
159_H	179_Y	0.637	1.00
29_F	107_L	0.629	1.00
88_A	93_I	0.628	1.00
111_V	163_M	0.628	1.00
35_F	87_M	0.628	1.00
171_K	201_F	0.628	1.00
114_L	120_K	0.624	1.00
17_V	98_D	0.624	1.00
21_I	25_L	0.618	1.00
63_S	74_K	0.618	1.00
50_R	60_F	0.615	1.00
59_R	62_Q	0.615	1.00
91_E	167_S	0.612	1.00
46_L	49_I	0.610	1.00
11_Y	39_D	0.609	1.00
79_A	185_A	0.607	1.00
17_V	48_V	0.604	1.00
164_H	194_F	0.604	1.00
125_S	161_S	0.603	1.00
75_T	83_Q	0.602	1.00
16_Y	217_T	0.601	1.00
20_S	99_D	0.599	1.00
82_N	86_E	0.598	1.00
49_I	53_L	0.596	1.00
112_R	115_D	0.593	1.00
55_D	58_V	0.592	1.00
225_L	229_E	0.589	1.00
178_S	194_F	0.588	1.00
106_R	161_S	0.584	1.00
20_S	24_I	0.584	1.00
94_T	161_S	0.582	1.00
9_T	81_I	0.580	1.00
207_L	210_E	0.580	1.00
164_H	169_L	0.575	1.00
37_M	63_S	0.575	1.00
40_N	74_K	0.573	1.00
74_K	80_L	0.572	1.00
14_S	47_N	0.572	1.00
189_I	192_A	0.571	1.00
100_N	214_N	0.571	1.00
85_I	178_S	0.570	1.00
151_W	155_C	0.570	1.00
9_T	39_D	0.568	1.00
6_V	32_F	0.568	1.00
3_K	32_F	0.562	1.00
114_L	165_R	0.559	1.00
97_T	190_G	0.556	1.00
124_Y	157_I	0.555	1.00
192_A	196_W	0.553	1.00
92_Y	165_R	0.552	1.00
152_N	155_C	0.551	1.00
109_K	211_L	0.551	1.00
14_S	17_V	0.550	1.00
169_L	178_S	0.549	1.00
27_Q	108_L	0.544	1.00
151_W	154_P	0.544	1.00
18_A	54_N	0.542	1.00
35_F	88_A	0.541	1.00
25_L	54_N	0.541	1.00
17_V	49_I	0.540	1.00
35_F	59_R	0.540	1.00
157_I	195_F	0.539	1.00
226_F	229_E	0.539	1.00
28_T	32_F	0.538	1.00
8_M	21_I	0.536	1.00
170_E	178_S	0.535	1.00
102_Y	107_L	0.532	1.00
143_V	147_A	0.532	1.00
149_V	152_N	0.530	1.00
9_T	77_Y	0.525	1.00
5_S	89_E	0.524	1.00
10_S	38_D	0.521	1.00
113_E	118_P	0.519	1.00
118_P	205_Y	0.517	1.00
142_T	145_P	0.516	1.00
145_P	149_V	0.513	1.00
100_N	160_C	0.510	1.00
216_I	223_F	0.509	1.00
7_I	37_M	0.508	1.00
3_K	29_F	0.508	1.00
210_E	213_L	0.507	1.00
160_C	214_N	0.505	1.00
199_N	204_F	0.504	1.00
144_R	147_A	0.503	1.00
121_A	167_S	0.502	1.00
121_A	124_Y	0.501	1.00
96_A	100_N	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
1qg8A	1	0.9102	100	0.215	Contact Map
3bcvA	2	0.6914	100	0.297	Contact Map
3l7iA	4	0	100	0.303	Contact Map
2z86A	2	0.918	100	0.309	Contact Map
2d7iA	1	0.9336	100	0.326	Contact Map
5ajoA	1	0.9258	100	0.343	Contact Map
1xhbA	1	0.9023	100	0.344	Contact Map
4fixA	3	0.9219	100	0.386	Contact Map
3ckjA	2	0.8984	100	0.412	Contact Map
4p02A	1	0.9102	100	0.415	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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