YDCA - BACSU - GREMLIN Contacts

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YDCA - Putative rhomboid protease YdcA

UniProt:	P96617	Sequences: MFIRTENFQTFIRLYPVVTFILALQAVLWLFFSLPAHSVVLWRDTVTGYNLGVANGEWWRLITPILLHAGFTHLLFNSMSIFLFAPALERMLGKARFLLVYAGSGIIGNIGTYVTEPLDYVHVGASGAIFGLFGVYLFMVLFRNELIGQEHSKMIITLLAFAVLMSFINSNINMMAHLFGLCGGFLLSFLCVQKKERRY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	199 (178)
Sequences:	6384 (4878)
Seq/√Len:	365.6

ECOLI - GLPG
BACSU - YDCA GLUP
HALSA - Q9HS82
SULSO - Q97ZW2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_I	105_G	5.934	1.00
104_S	131_G	5.412	1.00
107_I	183_G	4.002	1.00
57_E	60_R	3.595	1.00
64_P	109_N	3.523	1.00
105_G	128_A	3.321	1.00
69_A	123_V	3.205	1.00
112_T	173_N	3.042	1.00
26_A	74_L	2.711	1.00
71_F	75_L	2.702	1.00
18_V	97_F	2.656	1.00
111_G	179_F	2.532	1.00
134_G	181_L	2.448	1.00
22_L	78_S	2.439	1.00
25_Q	101_Y	2.421	1.00
112_T	122_H	2.416	1.00
122_H	173_N	2.069	1.00
22_L	82_F	2.053	1.00
25_Q	78_S	1.976	1.00
138_F	185_F	1.892	1.00
100_V	104_S	1.762	1.00
17_V	98_L	1.725	1.00
49_Y	52_G	1.715	1.00
79_M	83_L	1.714	1.00
100_V	135_V	1.676	1.00
17_V	94_K	1.658	1.00
41_L	45_T	1.656	1.00
156_I	160_A	1.641	1.00
76_F	80_S	1.628	1.00
101_Y	128_A	1.620	1.00
47_T	121_V	1.599	1.00
108_G	127_G	1.553	1.00
135_V	188_S	1.528	1.00
22_L	25_Q	1.495	1.00
62_I	106_I	1.422	1.00
64_P	122_H	1.421	1.00
138_F	188_S	1.399	1.00
21_I	25_Q	1.395	1.00
157_T	160_A	1.381	1.00
127_G	176_A	1.370	1.00
81_I	129_I	1.329	1.00
86_P	90_R	1.317	1.00
18_V	89_E	1.270	1.00
45_T	49_Y	1.257	1.00
164_L	168_I	1.219	1.00
92_L	100_V	1.214	1.00
99_L	103_G	1.210	1.00
43_R	47_T	1.210	1.00
183_G	187_L	1.196	1.00
175_M	179_F	1.184	1.00
108_G	179_F	1.177	1.00
81_I	85_A	1.164	1.00
16_P	94_K	1.162	1.00
65_I	128_A	1.153	1.00
48_G	53_V	1.151	1.00
75_L	79_M	1.141	1.00
104_S	183_G	1.139	1.00
19_T	23_A	1.126	1.00
53_V	56_G	1.118	1.00
29_W	74_L	1.114	1.00
59_W	63_T	1.098	1.00
22_L	26_A	1.091	1.00
61_L	113_Y	1.091	1.00
61_L	109_N	1.085	1.00
20_F	24_L	1.083	1.00
68_H	73_H	1.077	1.00
101_Y	125_A	1.062	1.00
173_N	176_A	1.060	1.00
80_S	129_I	1.059	1.00
41_L	44_D	1.034	1.00
115_T	175_M	1.033	1.00
166_S	174_M	1.021	1.00
40_V	44_D	1.019	1.00
29_W	32_F	1.013	1.00
78_S	81_I	1.000	1.00
77_N	126_S	0.999	1.00
16_P	19_T	0.998	1.00
70_G	123_V	0.993	1.00
150_E	153_K	0.986	1.00
137_L	155_I	0.983	1.00
65_I	106_I	0.983	1.00
30_L	34_L	0.975	1.00
46_V	49_Y	0.958	1.00
65_I	109_N	0.958	1.00
23_A	27_V	0.952	1.00
80_S	83_L	0.951	1.00
67_L	123_V	0.937	1.00
130_F	162_A	0.936	1.00
58_W	62_I	0.931	1.00
107_I	111_G	0.925	1.00
109_N	122_H	0.924	1.00
159_L	181_L	0.920	1.00
138_F	189_F	0.918	1.00
25_Q	66_L	0.913	1.00
136_Y	151_H	0.909	1.00
187_L	191_C	0.902	1.00
29_W	33_S	0.900	1.00
185_F	189_F	0.899	1.00
141_L	145_E	0.898	1.00
158_L	162_A	0.897	1.00
72_T	75_L	0.897	1.00
66_L	102_A	0.895	1.00
26_A	78_S	0.894	1.00
55_N	58_W	0.886	1.00
14_L	19_T	0.879	1.00
130_F	158_L	0.864	1.00
21_I	81_I	0.863	1.00
134_G	185_F	0.862	1.00
109_N	127_G	0.857	1.00
97_F	101_Y	0.851	1.00
48_G	109_N	0.849	1.00
21_I	101_Y	0.848	1.00
134_G	188_S	0.847	1.00
159_L	178_L	0.847	1.00
108_G	131_G	0.845	1.00
62_I	65_I	0.840	1.00
47_T	123_V	0.839	1.00
103_G	183_G	0.836	1.00
51_L	55_N	0.834	1.00
116_E	119_D	0.830	1.00
107_I	179_F	0.827	1.00
25_Q	32_F	0.823	1.00
189_F	192_V	0.823	1.00
91_M	140_V	0.817	1.00
77_N	177_H	0.813	1.00
28_L	32_F	0.809	1.00
111_G	115_T	0.807	1.00
27_V	31_F	0.806	1.00
65_I	101_Y	0.798	1.00
162_A	174_M	0.797	1.00
61_L	106_I	0.796	1.00
58_W	61_L	0.794	1.00
126_S	177_H	0.793	1.00
48_G	113_Y	0.790	1.00
102_A	106_I	0.789	1.00
28_L	67_L	0.789	1.00
88_L	92_L	0.787	1.00
62_I	66_L	0.785	1.00
98_L	102_A	0.785	1.00
16_P	20_F	0.783	1.00
111_G	175_M	0.782	1.00
106_I	110_I	0.779	1.00
85_A	89_E	0.778	1.00
41_L	47_T	0.776	1.00
185_F	188_S	0.771	1.00
88_L	135_V	0.771	1.00
89_E	94_K	0.761	1.00
100_V	188_S	0.757	1.00
103_G	187_L	0.756	1.00
21_I	98_L	0.753	1.00
25_Q	29_W	0.749	1.00
125_A	128_A	0.747	1.00
20_F	23_A	0.739	1.00
50_N	53_V	0.739	1.00
73_H	126_S	0.736	1.00
41_L	49_Y	0.735	1.00
92_L	139_M	0.732	1.00
72_T	76_F	0.731	1.00
54_A	113_Y	0.731	1.00
60_R	63_T	0.731	1.00
17_V	97_F	0.726	1.00
153_K	157_T	0.725	1.00
26_A	30_L	0.722	1.00
90_R	94_K	0.722	1.00
15_Y	19_T	0.719	1.00
45_T	48_G	0.712	0.99
103_G	107_I	0.700	0.99
42_W	46_V	0.697	0.99
87_A	90_R	0.696	0.99
73_H	177_H	0.692	0.99
157_T	161_F	0.689	0.99
17_V	20_F	0.684	0.99
42_W	48_G	0.684	0.99
95_A	99_L	0.680	0.99
19_T	22_L	0.678	0.99
106_I	109_N	0.678	0.99
45_T	52_G	0.678	0.99
89_E	93_G	0.673	0.99
47_T	51_L	0.667	0.99
141_L	149_Q	0.666	0.99
47_T	50_N	0.666	0.99
104_S	108_G	0.662	0.99
179_F	183_G	0.660	0.99
160_A	164_L	0.660	0.99
161_F	165_M	0.656	0.99
29_W	70_G	0.656	0.99
108_G	111_G	0.654	0.99
101_Y	132_L	0.641	0.99
162_A	165_M	0.640	0.99
49_Y	53_V	0.640	0.99
100_V	187_L	0.639	0.99
62_I	102_A	0.638	0.99
152_S	156_I	0.638	0.99
19_T	82_F	0.630	0.99
163_V	178_L	0.628	0.99
77_N	125_A	0.627	0.99
73_H	77_N	0.625	0.99
74_L	78_S	0.624	0.99
61_L	64_P	0.621	0.99
46_V	67_L	0.615	0.98
144_N	150_E	0.612	0.98
22_L	81_I	0.609	0.98
82_F	141_L	0.608	0.98
78_S	101_Y	0.606	0.98
53_V	113_Y	0.603	0.98
104_S	188_S	0.596	0.98
186_L	189_F	0.595	0.98
154_M	158_L	0.594	0.98
24_L	28_L	0.593	0.98
81_I	101_Y	0.591	0.98
44_D	47_T	0.588	0.98
52_G	56_G	0.586	0.98
142_F	152_S	0.585	0.98
154_M	157_T	0.585	0.98
105_G	108_G	0.581	0.98
25_Q	28_L	0.580	0.98
87_A	136_Y	0.579	0.98
33_S	36_A	0.575	0.98
92_L	97_F	0.575	0.98
64_P	127_G	0.575	0.98
178_L	182_C	0.574	0.98
112_T	116_E	0.573	0.98
36_A	39_V	0.571	0.98
103_G	108_G	0.568	0.97
26_A	29_W	0.563	0.97
157_T	164_L	0.562	0.97
80_S	84_F	0.562	0.97
26_A	71_F	0.561	0.97
32_F	67_L	0.560	0.97
56_G	60_R	0.560	0.97
112_T	175_M	0.554	0.97
147_I	150_E	0.553	0.97
186_L	190_L	0.552	0.97
84_F	132_L	0.550	0.97
93_G	96_R	0.548	0.97
101_Y	105_G	0.547	0.97
36_A	41_L	0.547	0.97
76_F	83_L	0.546	0.97
154_M	162_A	0.545	0.97
96_R	99_L	0.545	0.97
46_V	53_V	0.544	0.97
162_A	166_S	0.544	0.97
122_H	175_M	0.542	0.97
154_M	165_M	0.541	0.97
35_P	38_S	0.540	0.97
147_I	152_S	0.540	0.97
139_M	188_S	0.540	0.97
127_G	177_H	0.534	0.96
32_F	45_T	0.532	0.96
102_A	105_G	0.532	0.96
54_A	58_W	0.530	0.96
72_T	79_M	0.529	0.96
107_I	131_G	0.529	0.96
100_V	191_C	0.524	0.96
135_V	139_M	0.524	0.96
80_S	133_F	0.522	0.96
92_L	135_V	0.520	0.96
53_V	58_W	0.519	0.96
84_F	136_Y	0.519	0.96
122_H	176_A	0.519	0.96
86_P	94_K	0.518	0.96
50_N	113_Y	0.509	0.95
41_L	52_G	0.509	0.95
99_L	187_L	0.508	0.95
68_H	77_N	0.503	0.95
29_W	71_F	0.500	0.95
38_S	41_L	0.500	0.95

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
2nr9A	2	0.9347	100	0.262	Contact Map
4njnA	4	0.8995	100	0.269	Contact Map
2xovA	1	0.8945	100	0.301	Contact Map
3giaA	1	0.9196	33.1	0.927	Contact Map
3l1lA	2	0.9246	19.9	0.934	Contact Map
4tphA	2	0.8492	14.7	0.938	Contact Map
4pypA	1	0.8693	13.8	0.939	Contact Map
2wswA	3	0.9598	12.1	0.941	Contact Map
2kluA	1	0.1508	11.1	0.941	Contact Map
1pw4A	1	0.8995	8.4	0.945	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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