YTMA - BACSU - GREMLIN Contacts

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YTMA - Uncharacterized peptidase YtmA

UniProt:	O34493	Sequences: MIVEKRRFPSPSQHVRLYTICYLSNGLRVKGLLAEPAEPGQYDGFLYLRGGIKSVGMVRPGRIIQFASQGFVVFAPFYRGNQGGEGNEDFAGEDREDAFSAFRLLQQHPNVKKDRIHIFGFSRGGIMGMLTAIEMGGQAASFVSWGGVSDMILTYEERQDLRRMMKRVIGGTPKKVPEEYQWRTPFDQVNKIQAPVLLIHGEKDQNVSIQHSYLLEEKLKQLHKPVETWYYSTFTHYFPPKENRRIVRQLTQWMKNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	257 (224)
Sequences:	40360 (29293)
Seq/√Len:	1957.2

ECOLI - FRSA PTRB DLHH YJFP YFHR AES YCJY YGHX PLDB YIEL
BACSU - YTMA YUXL CAH YTAP YITV YQKD PLBAC EST YBAC
HALSA - Q9HN07 Q9HS46 Q9HPY2 Q9HP29
SULSO - Q97VD6 Q97YB2 Q7LX61 Q97VT8 Q97VW1 Q97VU2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_R	97_D	4.192	1.00
117_H	141_S	4.095	1.00
132_A	142_F	3.363	1.00
48_L	98_A	2.872	1.00
216_E	226_V	2.780	1.00
213_Y	230_Y	2.559	1.00
202_E	232_S	2.498	1.00
229_W	249_Q	2.378	1.00
21_C	28_R	2.332	1.00
144_S	147_G	2.308	1.00
102_F	139_A	2.216	1.00
104_L	108_H	2.046	1.00
42_Y	72_V	2.027	1.00
69_Q	251_T	2.021	1.00
45_F	119_F	1.974	1.00
231_Y	249_Q	1.954	1.00
44_G	111_V	1.931	1.00
209_I	230_Y	1.892	1.00
227_E	249_Q	1.891	1.00
44_G	72_V	1.888	1.00
202_E	230_Y	1.851	1.00
65_Q	69_Q	1.843	1.00
216_E	228_T	1.837	1.00
112_K	115_R	1.821	1.00
23_L	28_R	1.794	1.00
209_I	213_Y	1.781	1.00
196_V	219_L	1.780	1.00
219_L	224_K	1.760	1.00
143_V	250_L	1.724	1.00
74_F	105_L	1.710	1.00
129_M	144_S	1.696	1.00
35_E	72_V	1.692	1.00
31_G	74_F	1.690	1.00
53_K	126_I	1.677	1.00
142_F	196_V	1.675	1.00
36_P	72_V	1.668	1.00
128_G	142_F	1.668	1.00
198_L	216_E	1.637	1.00
200_H	212_S	1.622	1.00
121_F	146_G	1.597	1.00
213_Y	228_T	1.559	1.00
118_I	128_G	1.503	1.00
98_A	131_T	1.500	1.00
99_F	135_M	1.487	1.00
33_L	72_V	1.478	1.00
33_L	74_F	1.471	1.00
216_E	220_K	1.470	1.00
45_F	71_F	1.466	1.00
89_D	93_E	1.454	1.00
47_Y	119_F	1.439	1.00
72_V	111_V	1.433	1.00
76_P	101_A	1.419	1.00
44_G	105_L	1.414	1.00
197_L	229_W	1.410	1.00
106_Q	138_Q	1.401	1.00
99_F	134_E	1.400	1.00
188_Q	191_K	1.397	1.00
36_P	42_Y	1.388	1.00
46_L	101_A	1.387	1.00
145_W	250_L	1.367	1.00
248_R	252_Q	1.365	1.00
119_F	143_V	1.354	1.00
44_G	74_F	1.342	1.00
202_E	233_T	1.339	1.00
200_H	209_I	1.334	1.00
20_I	31_G	1.321	1.00
129_M	215_L	1.304	1.00
217_E	221_Q	1.303	1.00
99_F	103_R	1.289	1.00
245_R	249_Q	1.289	1.00
220_K	226_V	1.280	1.00
50_G	122_S	1.259	1.00
22_Y	101_A	1.257	1.00
231_Y	234_F	1.257	1.00
46_L	102_F	1.250	1.00
249_Q	252_Q	1.245	1.00
203_K	233_T	1.243	1.00
63_I	75_A	1.240	1.00
198_L	212_S	1.237	1.00
96_E	134_E	1.236	1.00
43_D	115_R	1.235	1.00
48_L	76_P	1.229	1.00
210_Q	213_Y	1.216	1.00
58_V	77_F	1.216	1.00
91_A	94_D	1.203	1.00
218_K	222_L	1.200	1.00
213_Y	217_E	1.198	1.00
198_L	215_L	1.192	1.00
144_S	198_L	1.186	1.00
103_R	135_M	1.183	1.00
103_R	107_Q	1.181	1.00
95_R	130_L	1.179	1.00
115_R	140_A	1.178	1.00
176_V	179_E	1.172	1.00
184_T	187_D	1.168	1.00
121_F	145_W	1.162	1.00
103_R	138_Q	1.158	1.00
214_L	217_E	1.146	1.00
135_M	138_Q	1.144	1.00
59_R	121_F	1.141	1.00
64_I	68_S	1.133	1.00
104_L	107_Q	1.130	1.00
100_S	103_R	1.124	1.00
118_I	131_T	1.117	1.00
202_E	209_I	1.117	1.00
142_F	215_L	1.114	1.00
200_H	230_Y	1.092	1.00
99_F	131_T	1.086	1.00
199_I	229_W	1.086	1.00
34_A	75_A	1.085	1.00
146_G	237_Y	1.069	1.00
74_F	101_A	1.068	1.00
48_L	128_G	1.065	1.00
200_H	228_T	1.064	1.00
63_I	67_A	1.062	1.00
231_Y	245_R	1.049	1.00
78_Y	123_R	1.039	1.00
199_I	231_Y	1.025	1.00
31_G	101_A	1.021	1.00
178_E	182_W	1.020	1.00
47_Y	63_I	1.012	1.00
24_S	27_L	1.011	1.00
89_D	92_G	0.998	1.00
218_K	221_Q	0.997	1.00
163_R	167_R	0.989	1.00
142_F	194_A	0.987	1.00
178_E	181_Q	0.987	1.00
177_P	181_Q	0.986	1.00
60_P	64_I	0.985	1.00
51_G	123_R	0.973	1.00
41_Q	112_K	0.971	1.00
199_I	246_I	0.965	1.00
92_G	96_E	0.964	1.00
43_D	71_F	0.962	1.00
65_Q	68_S	0.959	1.00
32_L	58_V	0.954	1.00
22_Y	31_G	0.951	1.00
189_V	192_I	0.949	1.00
102_F	106_Q	0.948	1.00
146_G	238_F	0.944	1.00
118_I	142_F	0.936	1.00
122_S	236_H	0.930	1.00
39_P	42_Y	0.929	1.00
146_G	204_D	0.923	1.00
98_A	127_M	0.920	1.00
195_P	225_P	0.920	1.00
119_F	145_W	0.916	1.00
246_I	250_L	0.912	1.00
19_T	30_K	0.908	1.00
129_M	149_S	0.907	1.00
166_K	170_G	0.891	1.00
214_L	218_K	0.885	1.00
93_E	96_E	0.881	1.00
102_F	116_I	0.880	1.00
180_Y	183_R	0.876	1.00
21_C	30_K	0.875	1.00
151_M	184_T	0.874	1.00
245_R	248_R	0.872	1.00
219_L	226_V	0.867	1.00
30_K	77_F	0.856	1.00
179_E	182_W	0.850	1.00
53_K	148_V	0.850	1.00
67_A	73_V	0.849	1.00
47_Y	73_V	0.845	1.00
177_P	180_Y	0.840	1.00
133_I	215_L	0.836	1.00
181_Q	187_D	0.834	1.00
44_G	116_I	0.830	1.00
231_Y	238_F	0.828	1.00
49_R	78_Y	0.828	1.00
19_T	32_L	0.827	1.00
126_I	130_L	0.825	1.00
48_L	118_I	0.819	1.00
45_F	117_H	0.811	1.00
149_S	215_L	0.809	1.00
133_I	188_Q	0.806	1.00
130_L	134_E	0.805	1.00
176_V	180_Y	0.797	1.00
157_E	210_Q	0.796	1.00
132_A	194_A	0.793	1.00
125_G	147_G	0.788	1.00
31_G	104_L	0.788	1.00
47_Y	75_A	0.787	1.00
46_L	74_F	0.784	1.00
43_D	112_K	0.770	1.00
240_P	243_N	0.768	1.00
48_L	78_Y	0.768	1.00
106_Q	140_A	0.768	1.00
130_L	133_I	0.766	1.00
128_G	144_S	0.764	1.00
69_Q	248_R	0.764	1.00
150_D	214_L	0.761	1.00
165_M	168_V	0.760	1.00
114_D	140_A	0.760	1.00
146_G	239_P	0.758	1.00
42_Y	70_G	0.758	1.00
201_G	238_F	0.757	1.00
129_M	147_G	0.752	1.00
20_I	33_L	0.750	1.00
34_A	73_V	0.745	1.00
134_E	182_W	0.744	1.00
89_D	94_D	0.738	1.00
112_K	140_A	0.736	1.00
129_M	142_F	0.734	1.00
165_M	169_I	0.729	1.00
38_E	42_Y	0.728	1.00
190_N	218_K	0.723	1.00
102_F	131_T	0.722	1.00
32_L	60_P	0.720	1.00
150_D	153_L	0.720	1.00
118_I	139_A	0.718	1.00
25_N	79_R	0.718	1.00
217_E	220_K	0.718	1.00
174_K	178_E	0.717	1.00
41_Q	110_N	0.716	1.00
150_D	184_T	0.715	1.00
164_M	168_V	0.711	1.00
145_W	199_I	0.710	1.00
96_E	100_S	0.702	1.00
24_S	100_S	0.701	1.00
47_Y	121_F	0.699	1.00
125_G	144_S	0.697	1.00
45_F	66_F	0.695	1.00
212_S	216_E	0.691	1.00
167_R	170_G	0.688	1.00
94_D	127_M	0.687	1.00
144_S	149_S	0.686	1.00
71_F	117_H	0.683	1.00
129_M	196_V	0.682	1.00
90_F	94_D	0.681	1.00
143_V	197_L	0.677	1.00
162_R	165_M	0.677	1.00
210_Q	214_L	0.676	1.00
163_R	166_K	0.673	1.00
146_G	201_G	0.666	1.00
175_K	178_E	0.665	1.00
132_A	196_V	0.664	1.00
34_A	67_A	0.662	1.00
20_I	104_L	0.661	1.00
106_Q	113_K	0.658	1.00
117_H	143_V	0.658	1.00
141_S	197_L	0.658	1.00
117_H	140_A	0.655	1.00
145_W	246_I	0.654	1.00
148_V	151_M	0.653	1.00
152_I	187_D	0.652	1.00
24_S	29_V	0.652	1.00
35_E	42_Y	0.650	1.00
46_L	105_L	0.644	1.00
136_G	139_A	0.640	1.00
125_G	149_S	0.640	1.00
24_S	28_R	0.639	1.00
66_F	73_V	0.629	1.00
174_K	177_P	0.628	1.00
186_F	189_V	0.628	1.00
32_L	55_V	0.627	1.00
101_A	104_L	0.625	1.00
53_K	123_R	0.623	1.00
193_Q	196_V	0.617	1.00
76_P	98_A	0.615	1.00
141_S	195_P	0.614	1.00
241_K	244_R	0.614	1.00
126_I	148_V	0.613	1.00
65_Q	251_T	0.612	1.00
106_Q	116_I	0.611	1.00
47_Y	59_R	0.608	1.00
198_L	219_L	0.607	1.00
81_N	94_D	0.603	1.00
31_G	76_P	0.603	1.00
121_F	237_Y	0.602	1.00
229_W	245_R	0.598	1.00
51_G	78_Y	0.598	1.00
102_F	135_M	0.596	1.00
49_R	80_G	0.596	1.00
196_V	215_L	0.595	1.00
162_R	166_K	0.592	1.00
63_I	73_V	0.591	1.00
247_V	250_L	0.589	1.00
190_N	222_L	0.586	1.00
90_F	93_E	0.585	1.00
153_L	214_L	0.583	1.00
65_Q	247_V	0.582	1.00
240_P	244_R	0.581	1.00
51_G	56_G	0.579	1.00
59_R	62_R	0.578	1.00
189_V	222_L	0.578	1.00
113_K	116_I	0.577	1.00
143_V	199_I	0.573	1.00
197_L	227_E	0.573	1.00
150_D	211_H	0.570	1.00
184_T	188_Q	0.569	1.00
147_G	207_V	0.569	1.00
66_F	119_F	0.563	1.00
106_Q	109_P	0.561	1.00
99_F	102_F	0.561	1.00
187_D	190_N	0.561	1.00
55_V	83_G	0.561	1.00
164_M	167_R	0.557	1.00
234_F	243_N	0.556	1.00
78_Y	81_N	0.556	1.00
133_I	193_Q	0.554	1.00
93_E	97_D	0.553	1.00
130_L	188_Q	0.552	1.00
200_H	207_V	0.552	1.00
99_F	139_A	0.552	1.00
123_R	127_M	0.551	1.00
204_D	207_V	0.546	1.00
198_L	226_V	0.546	1.00
34_A	63_I	0.543	1.00
209_I	228_T	0.542	1.00
133_I	192_I	0.541	1.00
48_L	131_T	0.537	1.00
29_V	76_P	0.535	1.00
162_R	170_G	0.533	1.00
22_Y	100_S	0.532	1.00
92_G	134_E	0.531	1.00
25_N	96_E	0.530	1.00
165_M	170_G	0.530	1.00
53_K	57_M	0.530	1.00
212_S	228_T	0.528	1.00
193_Q	224_K	0.524	1.00
197_L	249_Q	0.523	1.00
105_L	111_V	0.522	1.00
133_I	136_G	0.521	1.00
66_F	250_L	0.517	1.00
152_I	181_Q	0.517	1.00
166_K	169_I	0.513	1.00
153_L	211_H	0.512	1.00
162_R	168_V	0.510	1.00
221_Q	226_V	0.509	1.00
95_R	127_M	0.509	1.00
103_R	106_Q	0.504	1.00
151_M	165_M	0.502	1.00
137_G	193_Q	0.502	1.00
150_D	186_F	0.501	1.00
116_I	139_A	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
2z3zA	2	0.9455	100	0.319	Contact Map
4q1vA	2	0.9728	100	0.321	Contact Map
1xfdA	2	0.9728	100	0.325	Contact Map
4wjlA	2	0.9728	100	0.326	Contact Map
4hxfB	4	0.9922	100	0.326	Contact Map
4bp8A	1	0.9961	100	0.331	Contact Map
2ecfA	2	0.9728	100	0.333	Contact Map
1z68A	2	0.9767	100	0.336	Contact Map
2xdwA	2	0.9961	100	0.339	Contact Map
1yr2A	1	0.9611	100	0.34	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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