YAFL - ECOLI - GREMLIN Contacts

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YAFL - Probable endopeptidase YafL

UniProt:	Q47151	Sequences: MSLPSIPSFVLSGLLLICLPFSSFASATTSHISFSYAARQRMQNRARLLKQYQTHLKKQASYIVEGNAESKRALRQHNREQIKQHPEWFPAPLKASDRRWQALAENNHFLSSDHLHNITEVAIHRLEQQLGKPYVWGGTRPDKGFDCSGLVFYAYNKILEAKLPRTANEMYHYRRATIVANNDLRRGDLLFFHIHSREIADHMGVYLGDGQFIESPRTGETIRISRLAEPFWQDHFLGARRILTEETIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13149
Length:	249 (211)
Sequences:	2914 (2603)
Seq/√Len:	179.2

ECOLI - YAFL MEPH MEPS NLPC
BACSU - CWLO LYTF YDDH LYTE YKFC CWLS PGDS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
207_L	224_I	3.705	1.00
129_Q	132_K	3.347	1.00
138_G	144_G	3.089	1.00
184_L	239_A	2.826	1.00
127_E	213_I	2.719	1.00
216_P	221_T	2.690	1.00
130_L	213_I	2.680	1.00
220_E	223_R	2.602	1.00
123_I	207_L	2.598	1.00
180_A	183_D	2.590	1.00
139_T	165_R	2.530	1.00
127_E	224_I	2.488	1.00
236_F	239_A	2.482	1.00
193_H	201_D	2.277	1.00
166_T	169_E	2.200	1.00
151_V	205_V	2.190	1.00
140_R	144_G	2.169	1.00
178_I	240_R	2.115	1.00
151_V	189_L	2.094	1.00
152_F	165_R	2.030	1.00
151_V	170_M	1.959	1.00
132_K	145_F	1.933	1.00
145_F	153_Y	1.912	1.00
217_R	220_E	1.895	1.00
125_R	153_Y	1.867	1.00
214_E	225_S	1.842	1.00
76_Q	80_E	1.819	1.00
164_P	175_R	1.797	1.00
125_R	157_K	1.784	1.00
132_K	140_R	1.782	1.00
167_A	171_Y	1.767	1.00
75_R	79_R	1.738	1.00
189_L	203_M	1.731	1.00
192_F	212_F	1.725	1.00
191_F	203_M	1.686	1.00
216_P	219_G	1.658	1.00
125_R	145_F	1.649	1.00
120_E	124_H	1.648	1.00
133_P	144_G	1.623	1.00
176_A	240_R	1.594	1.00
126_L	213_I	1.593	1.00
192_F	204_G	1.543	1.00
181_N	236_F	1.514	1.00
71_K	74_L	1.462	1.00
212_F	227_L	1.439	1.00
132_K	144_G	1.426	1.00
42_M	46_A	1.416	1.00
119_T	123_I	1.408	1.00
211_Q	224_I	1.404	1.00
31_H	35_S	1.399	1.00
216_P	223_R	1.398	1.00
153_Y	157_K	1.396	1.00
171_Y	200_A	1.386	1.00
45_R	49_L	1.373	1.00
151_V	163_L	1.359	1.00
150_L	154_A	1.355	1.00
171_Y	238_G	1.334	1.00
84_Q	88_W	1.330	1.00
125_R	128_Q	1.318	1.00
181_N	184_L	1.317	1.00
70_S	74_L	1.312	1.00
82_I	86_P	1.310	1.00
130_L	221_T	1.308	1.00
216_P	220_E	1.303	1.00
193_H	199_I	1.298	1.00
132_K	138_G	1.298	1.00
152_F	156_N	1.295	1.00
79_R	83_K	1.295	1.00
83_K	87_E	1.279	1.00
77_H	81_Q	1.267	1.00
74_L	78_N	1.254	1.00
192_F	236_F	1.251	1.00
125_R	129_Q	1.246	1.00
81_Q	85_H	1.244	1.00
217_R	221_T	1.228	1.00
193_H	235_H	1.201	1.00
60_A	63_I	1.191	1.00
77_H	80_E	1.188	1.00
86_P	90_P	1.178	1.00
218_T	221_T	1.171	1.00
63_I	67_N	1.167	1.00
164_P	169_E	1.156	1.00
86_P	89_F	1.153	1.00
71_K	75_R	1.144	1.00
130_L	224_I	1.133	1.00
83_K	86_P	1.130	1.00
168_N	200_A	1.114	1.00
139_T	152_F	1.112	1.00
204_G	212_F	1.111	1.00
49_L	53_Q	1.107	1.00
78_N	82_I	1.106	1.00
28_T	31_H	1.104	1.00
52_Y	56_L	1.098	1.00
27_A	30_S	1.097	1.00
192_F	201_D	1.096	1.00
126_L	205_V	1.091	1.00
123_I	213_I	1.090	1.00
179_V	183_D	1.087	1.00
72_R	76_Q	1.086	1.00
35_S	39_R	1.077	1.00
184_L	227_L	1.075	1.00
169_E	172_H	1.053	1.00
56_L	60_A	1.051	1.00
76_Q	79_R	1.048	1.00
98_R	101_Q	1.023	0.99
141_P	145_F	1.023	0.99
81_Q	84_Q	1.023	0.99
125_R	158_I	1.023	0.99
135_V	138_G	1.015	0.99
41_R	44_N	1.008	0.99
32_I	36_Y	1.007	0.99
181_N	228_A	1.003	0.99
124_H	127_E	0.999	0.99
84_Q	87_E	0.989	0.99
135_V	218_T	0.974	0.99
95_A	99_R	0.969	0.99
62_Y	65_E	0.969	0.99
123_I	127_E	0.969	0.99
211_Q	226_R	0.964	0.99
145_F	222_I	0.962	0.99
154_A	158_I	0.961	0.99
184_L	190_L	0.957	0.99
85_H	89_F	0.956	0.99
152_F	166_T	0.955	0.99
20_P	23_S	0.949	0.99
58_K	62_Y	0.949	0.99
89_F	92_P	0.944	0.99
125_R	154_A	0.941	0.99
171_Y	237_L	0.930	0.99
164_P	167_A	0.928	0.99
118_I	121_V	0.924	0.99
46_A	50_K	0.919	0.99
120_E	186_R	0.915	0.99
165_R	169_E	0.913	0.99
105_E	108_H	0.910	0.99
80_E	84_Q	0.909	0.99
135_V	144_G	0.903	0.99
156_N	162_K	0.897	0.99
127_E	207_L	0.895	0.99
167_A	200_A	0.892	0.99
105_E	109_F	0.890	0.99
69_E	73_A	0.878	0.98
168_N	171_Y	0.876	0.98
129_Q	140_R	0.875	0.98
75_R	78_N	0.875	0.98
34_F	37_A	0.874	0.98
90_P	94_K	0.869	0.98
68_A	72_R	0.864	0.98
171_Y	176_A	0.861	0.98
55_H	58_K	0.859	0.98
69_E	72_R	0.856	0.98
29_T	36_Y	0.855	0.98
122_A	158_I	0.855	0.98
214_E	223_R	0.854	0.98
73_A	76_Q	0.849	0.98
210_G	227_L	0.843	0.98
73_A	77_H	0.841	0.98
78_N	81_Q	0.839	0.98
40_Q	44_N	0.835	0.98
99_R	102_A	0.829	0.98
73_A	81_Q	0.826	0.98
186_R	207_L	0.823	0.98
152_F	170_M	0.822	0.98
129_Q	150_L	0.822	0.98
51_Q	55_H	0.822	0.98
25_A	28_T	0.818	0.97
165_R	168_N	0.811	0.97
129_Q	154_A	0.808	0.97
70_S	73_A	0.806	0.97
204_G	214_E	0.805	0.97
59_Q	63_I	0.802	0.97
96_S	99_R	0.797	0.97
140_R	145_F	0.796	0.97
53_Q	57_K	0.793	0.97
25_A	29_T	0.792	0.97
180_A	184_L	0.791	0.97
186_R	206_Y	0.789	0.97
88_W	92_P	0.788	0.97
171_Y	191_F	0.787	0.97
122_A	155_Y	0.782	0.97
153_Y	156_N	0.780	0.97
80_E	83_K	0.780	0.97
21_F	25_A	0.775	0.96
155_Y	163_L	0.762	0.96
82_I	85_H	0.762	0.96
127_E	130_L	0.755	0.96
30_S	34_F	0.752	0.96
190_L	204_G	0.751	0.96
18_C	21_F	0.750	0.96
190_L	239_A	0.749	0.96
18_C	22_S	0.734	0.95
60_A	64_V	0.733	0.95
181_N	190_L	0.731	0.95
92_P	96_S	0.729	0.95
22_S	25_A	0.728	0.95
19_L	22_S	0.723	0.95
53_Q	56_L	0.718	0.95
119_T	186_R	0.717	0.95
57_K	60_A	0.714	0.94
122_A	154_A	0.709	0.94
214_E	228_A	0.698	0.94
89_F	93_L	0.698	0.94
191_F	200_A	0.694	0.94
102_A	108_H	0.691	0.93
192_F	228_A	0.688	0.93
132_K	222_I	0.677	0.93
25_A	31_H	0.676	0.93
184_L	236_F	0.675	0.93
21_F	28_T	0.672	0.92
100_W	103_L	0.672	0.92
38_A	42_M	0.670	0.92
181_N	239_A	0.670	0.92
45_R	48_L	0.664	0.92
26_S	30_S	0.660	0.92
213_I	224_I	0.659	0.92
85_H	88_W	0.656	0.92
28_T	32_I	0.656	0.92
24_F	28_T	0.654	0.91
139_T	149_G	0.653	0.91
216_P	222_I	0.653	0.91
132_K	142_D	0.649	0.91
102_A	106_N	0.648	0.91
88_W	91_A	0.646	0.91
63_I	66_G	0.641	0.91
171_Y	239_A	0.640	0.91
31_H	42_M	0.639	0.90
72_R	75_R	0.633	0.90
54_T	58_K	0.623	0.89
220_E	225_S	0.620	0.89
101_Q	104_A	0.617	0.89
172_H	176_A	0.615	0.89
93_L	96_S	0.611	0.88
236_F	240_R	0.604	0.88
87_E	91_A	0.603	0.88
167_A	203_M	0.602	0.88
139_T	166_T	0.601	0.88
128_Q	132_K	0.596	0.87
139_T	145_F	0.592	0.87
106_N	109_F	0.590	0.87
93_L	97_D	0.589	0.87
128_Q	153_Y	0.589	0.87
21_F	24_F	0.588	0.86
129_Q	153_Y	0.586	0.86
99_R	103_L	0.585	0.86
200_A	237_L	0.584	0.86
71_K	81_Q	0.583	0.86
136_W	144_G	0.581	0.86
79_R	82_I	0.579	0.86
163_L	176_A	0.578	0.86
136_W	149_G	0.576	0.85
138_G	149_G	0.575	0.85
177_T	183_D	0.575	0.85
201_D	235_H	0.574	0.85
79_R	86_P	0.574	0.85
96_S	100_W	0.572	0.85
152_F	163_L	0.571	0.85
233_Q	236_F	0.570	0.85
121_V	124_H	0.569	0.85
98_R	102_A	0.568	0.85
23_S	26_S	0.566	0.84
57_K	61_S	0.564	0.84
121_V	158_I	0.562	0.84
21_F	26_S	0.561	0.84
201_D	212_F	0.558	0.84
141_P	153_Y	0.554	0.83
31_H	59_Q	0.552	0.83
129_Q	145_F	0.552	0.83
32_I	35_S	0.549	0.83
206_Y	210_G	0.546	0.82
70_S	77_H	0.546	0.82
71_K	77_H	0.542	0.82
62_Y	67_N	0.542	0.82
172_H	178_I	0.541	0.82
133_P	221_T	0.540	0.81
155_Y	161_A	0.539	0.81
62_Y	66_G	0.539	0.81
45_R	63_I	0.538	0.81
167_A	170_M	0.537	0.81
101_Q	106_N	0.536	0.81
81_Q	86_P	0.535	0.81
167_A	191_F	0.534	0.81
50_K	53_Q	0.533	0.81
135_V	139_T	0.532	0.81
59_Q	62_Y	0.532	0.81
90_P	93_L	0.531	0.80
50_K	54_T	0.528	0.80
154_A	157_K	0.526	0.80
123_I	186_R	0.526	0.80
155_Y	176_A	0.524	0.80
100_W	107_N	0.524	0.80
81_Q	87_E	0.523	0.79
206_Y	209_D	0.520	0.79
61_S	64_V	0.518	0.79
87_E	90_P	0.518	0.79
171_Y	236_F	0.517	0.79
105_E	111_S	0.517	0.79
151_V	203_M	0.517	0.79
48_L	51_Q	0.516	0.79
207_L	211_Q	0.513	0.78
201_D	214_E	0.512	0.78
172_H	175_R	0.512	0.78
27_A	39_R	0.511	0.78
45_R	59_Q	0.510	0.78
77_H	85_H	0.509	0.78
227_L	236_F	0.508	0.77
184_L	206_Y	0.507	0.77
139_T	156_N	0.507	0.77
104_A	107_N	0.506	0.77
44_N	47_R	0.505	0.77
129_Q	158_I	0.504	0.77
56_L	63_I	0.502	0.77
129_Q	144_G	0.502	0.77
206_Y	211_Q	0.501	0.76
212_F	234_D	0.501	0.76
24_F	27_A	0.501	0.76
18_C	25_A	0.500	0.76

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
4q4gX	1	0.5502	100	0.33	Contact Map
2k1gA	1	0.5181	100	0.421	Contact Map
4hpeA	1	0.7068	100	0.442	Contact Map
4xcmA	2	0.8273	100	0.443	Contact Map
4fdyA	1	0.9157	100	0.445	Contact Map
3h41A	1	0.8233	100	0.446	Contact Map
3npfA	2	0.9076	100	0.457	Contact Map
3pbiA	1	0.7108	100	0.462	Contact Map
4lj1A	1	0.4739	100	0.465	Contact Map
2hbwA	1	0.8153	100	0.475	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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