YRAK - BACSU - GREMLIN Contacts

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YRAK - Uncharacterized hydrolase YraK

UniProt:	O07937	Sequences: MTINNGTLQVPGANIHYQVRGSGPIILLVHGGGGDADKFHHVANHLANWYTVVTYDRRGHSRSNLANQIEGYRVETHSDDAHRLLAKITNKPAYVFGSSSGAVIGLDLCIRHPEQVHVMIPHEPILLQLLHGNELKQAEQFMEDLKKNHRSEVIKLMSRLETDEQSKAVLTKRLLGNSTYFTEYEIQGILSYTLDFEALKTVFTSSPMKILPAGGSASRELFPYRCANALAEQLETEWVEFPGNHTGYTMYHKEFSERLHDMLEKEKKHTC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	271 (252)
Sequences:	61135 (50567)
Seq/√Len:	3185.4

ECOLI - MHPC YBFF RUTD PLDB BIOH MENH YCJY YFHR
BACSU - YRAK YDJP YCGS YFHM YBDG YISY NAP RSBQ YUGF YBFK MENH YVAM YCLE YBAC YQJL PLBAC EST YQKD
HALSA - Q9HPT9 Q9HHP4 Q9HRJ0
SULSO - PIP Q97WG0 Q7LXY9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_V	51_T	4.910	1.00
94_Y	118_V	4.295	1.00
58_R	80_D	3.672	1.00
42_V	256_S	3.192	1.00
82_H	108_L	2.910	1.00
251_Y	254_E	2.794	1.00
216_S	242_P	2.765	1.00
211_L	262_M	2.692	1.00
239_V	258_R	2.679	1.00
92_P	117_H	2.620	1.00
94_Y	117_H	2.593	1.00
123_E	218_S	2.584	1.00
122_H	255_F	2.429	1.00
241_F	258_R	2.413	1.00
14_N	64_N	2.258	1.00
18_Q	36_A	2.215	1.00
82_H	115_Q	2.117	1.00
108_L	112_H	2.086	1.00
216_S	240_E	2.081	1.00
85_L	93_A	2.070	1.00
82_H	112_H	2.027	1.00
82_H	86_A	2.022	1.00
95_V	105_G	1.980	1.00
49_W	260_H	1.964	1.00
86_A	115_Q	1.950	1.00
102_A	124_P	1.944	1.00
16_H	62_R	1.923	1.00
230_L	236_T	1.922	1.00
17_Y	84_L	1.920	1.00
45_H	256_S	1.892	1.00
25_I	53_V	1.837	1.00
94_Y	263_L	1.818	1.00
19_V	53_V	1.794	1.00
107_D	111_R	1.792	1.00
109_C	119_M	1.767	1.00
24_P	94_Y	1.759	1.00
20_R	54_T	1.741	1.00
79_D	111_R	1.725	1.00
25_I	51_T	1.721	1.00
94_Y	120_I	1.719	1.00
25_I	90_N	1.718	1.00
223_P	240_E	1.710	1.00
16_H	36_A	1.694	1.00
24_P	117_H	1.690	1.00
30_H	60_H	1.671	1.00
211_L	239_V	1.612	1.00
50_Y	94_Y	1.607	1.00
30_H	57_R	1.599	1.00
258_R	261_D	1.597	1.00
105_G	119_M	1.583	1.00
75_E	111_R	1.554	1.00
34_G	38_K	1.531	1.00
228_N	232_E	1.527	1.00
11_P	83_R	1.522	1.00
57_R	104_I	1.520	1.00
55_Y	81_A	1.506	1.00
78_S	107_D	1.504	1.00
29_V	57_R	1.490	1.00
29_V	81_A	1.474	1.00
257_E	261_D	1.463	1.00
81_A	108_L	1.454	1.00
112_H	115_Q	1.428	1.00
108_L	116_V	1.426	1.00
210_I	233_Q	1.391	1.00
16_H	56_D	1.378	1.00
45_H	260_H	1.372	1.00
90_N	93_A	1.368	1.00
36_A	56_D	1.353	1.00
107_D	110_I	1.332	1.00
73_R	76_T	1.326	1.00
53_V	84_L	1.318	1.00
86_A	112_H	1.316	1.00
29_V	105_G	1.314	1.00
28_L	96_F	1.313	1.00
45_H	48_N	1.307	1.00
98_S	248_Y	1.304	1.00
120_I	259_L	1.303	1.00
254_E	258_R	1.290	1.00
108_L	115_Q	1.274	1.00
243_G	251_Y	1.273	1.00
106_L	121_P	1.269	1.00
20_R	43_A	1.252	1.00
43_A	54_T	1.242	1.00
33_G	60_H	1.241	1.00
15_I	80_D	1.241	1.00
227_A	231_A	1.228	1.00
254_E	257_E	1.226	1.00
121_P	124_P	1.223	1.00
13_A	58_R	1.206	1.00
96_F	122_H	1.200	1.00
84_L	88_I	1.175	1.00
163_D	166_S	1.170	1.00
36_A	62_R	1.166	1.00
214_G	226_C	1.163	1.00
99_S	245_H	1.158	1.00
28_L	52_V	1.158	1.00
120_I	211_L	1.137	1.00
26_I	50_Y	1.126	1.00
202_V	205_S	1.121	1.00
38_K	248_Y	1.116	1.00
23_G	51_T	1.115	1.00
27_L	85_L	1.098	1.00
214_G	238_W	1.098	1.00
33_G	99_S	1.097	1.00
45_H	253_K	1.096	1.00
213_A	241_F	1.087	1.00
223_P	227_A	1.085	1.00
93_A	116_V	1.067	1.00
237_E	258_R	1.050	1.00
36_A	54_T	1.050	1.00
214_G	240_E	1.049	1.00
49_W	264_E	1.047	1.00
186_I	189_I	1.043	1.00
255_F	259_L	1.032	1.00
24_P	50_Y	1.032	1.00
233_Q	236_T	1.031	1.00
211_L	237_E	1.029	1.00
31_G	99_S	1.027	1.00
96_F	259_L	1.025	1.00
118_V	209_K	1.024	1.00
17_Y	88_I	1.010	1.00
173_R	176_G	1.008	1.00
55_Y	84_L	1.004	1.00
182_T	185_E	1.003	1.00
185_E	188_G	1.001	1.00
214_G	223_P	1.000	1.00
24_P	92_P	0.999	1.00
50_Y	263_L	0.996	1.00
260_H	264_E	0.990	1.00
82_H	111_R	0.987	1.00
228_N	231_A	0.980	1.00
253_K	257_E	0.979	1.00
75_E	107_D	0.977	1.00
154_I	158_S	0.968	1.00
29_V	95_V	0.967	1.00
230_L	238_W	0.965	1.00
78_S	104_I	0.965	1.00
244_N	250_M	0.962	1.00
20_R	47_A	0.961	1.00
98_S	246_T	0.957	1.00
213_A	258_R	0.956	1.00
44_N	47_A	0.952	1.00
204_T	232_E	0.947	1.00
239_V	261_D	0.945	1.00
146_K	149_H	0.942	1.00
56_D	61_S	0.933	1.00
21_G	51_T	0.930	1.00
85_L	108_L	0.930	1.00
203_F	206_S	0.930	1.00
241_F	254_E	0.929	1.00
122_H	248_Y	0.927	1.00
97_G	105_G	0.925	1.00
93_A	115_Q	0.921	1.00
47_A	52_V	0.916	1.00
50_Y	264_E	0.913	1.00
15_I	63_S	0.912	1.00
41_H	44_N	0.911	1.00
13_A	64_N	0.911	1.00
227_A	240_E	0.906	1.00
27_L	93_A	0.898	1.00
227_A	238_W	0.894	1.00
40_H	54_T	0.892	1.00
155_K	158_S	0.884	1.00
53_V	88_I	0.878	1.00
122_H	247_G	0.870	1.00
227_A	230_L	0.868	1.00
28_L	39_F	0.862	1.00
173_R	177_N	0.859	1.00
26_I	52_V	0.857	1.00
163_D	167_K	0.854	1.00
76_T	79_D	0.851	1.00
239_V	254_E	0.844	1.00
119_M	210_I	0.843	1.00
25_I	93_A	0.838	1.00
71_G	76_T	0.828	1.00
83_R	87_K	0.826	1.00
109_C	116_V	0.822	1.00
29_V	55_Y	0.820	1.00
26_I	96_F	0.819	1.00
154_I	157_M	0.819	1.00
118_V	262_M	0.817	1.00
170_L	173_R	0.815	1.00
24_P	118_V	0.813	1.00
57_R	100_S	0.810	1.00
83_R	86_A	0.808	1.00
174_L	177_N	0.803	1.00
184_Y	188_G	0.798	1.00
183_E	187_Q	0.798	1.00
212_P	236_T	0.795	1.00
97_G	102_A	0.795	1.00
144_D	148_N	0.793	1.00
27_L	81_A	0.792	1.00
25_I	50_Y	0.790	1.00
79_D	82_H	0.785	1.00
241_F	251_Y	0.785	1.00
82_H	85_L	0.782	1.00
78_S	111_R	0.775	1.00
178_S	185_E	0.772	1.00
85_L	90_N	0.766	1.00
181_F	184_Y	0.766	1.00
37_D	40_H	0.766	1.00
157_M	160_L	0.766	1.00
180_Y	185_E	0.764	1.00
77_H	100_S	0.762	1.00
195_D	198_A	0.761	1.00
43_A	52_V	0.759	1.00
110_I	202_V	0.756	1.00
170_L	174_L	0.750	1.00
44_N	48_N	0.746	1.00
95_V	116_V	0.745	1.00
139_E	143_E	0.744	1.00
215_G	247_G	0.743	1.00
162_T	167_K	0.742	1.00
79_D	83_R	0.740	1.00
123_E	247_G	0.731	1.00
18_Q	40_H	0.729	1.00
36_A	55_Y	0.728	1.00
164_E	167_K	0.727	1.00
225_R	228_N	0.724	1.00
141_F	145_L	0.723	1.00
179_T	183_E	0.722	1.00
95_V	108_L	0.721	1.00
162_T	166_S	0.720	1.00
184_Y	187_Q	0.714	1.00
185_E	189_I	0.713	1.00
180_Y	184_Y	0.712	1.00
171_T	174_L	0.710	1.00
164_E	168_A	0.709	1.00
182_T	186_I	0.709	1.00
30_H	55_Y	0.707	1.00
190_L	193_T	0.704	1.00
256_S	260_H	0.701	1.00
22_S	51_T	0.700	1.00
50_Y	260_H	0.700	1.00
143_E	147_K	0.700	1.00
78_S	108_L	0.699	1.00
171_T	175_L	0.699	1.00
107_D	202_V	0.696	1.00
224_Y	227_A	0.695	1.00
166_S	169_V	0.694	1.00
33_G	100_S	0.694	1.00
40_H	44_N	0.687	1.00
43_A	47_A	0.685	1.00
26_I	94_Y	0.684	1.00
181_F	185_E	0.683	1.00
27_L	95_V	0.683	1.00
178_S	182_T	0.681	1.00
120_I	262_M	0.680	1.00
91_K	115_Q	0.679	1.00
179_T	182_T	0.678	1.00
42_V	45_H	0.678	1.00
180_Y	183_E	0.677	1.00
172_K	176_G	0.677	1.00
140_Q	143_E	0.674	1.00
178_S	181_F	0.673	1.00
32_G	100_S	0.672	1.00
168_A	171_T	0.672	1.00
123_E	215_G	0.671	1.00
39_F	43_A	0.670	1.00
116_V	208_M	0.664	1.00
98_S	123_E	0.662	1.00
109_C	208_M	0.662	1.00
20_R	44_N	0.660	1.00
162_T	165_Q	0.660	1.00
153_V	160_L	0.660	1.00
213_A	255_F	0.659	1.00
96_F	120_I	0.658	1.00
26_I	263_L	0.657	1.00
216_S	223_P	0.657	1.00
48_N	260_H	0.657	1.00
97_G	101_G	0.655	1.00
147_K	151_S	0.651	1.00
146_K	150_R	0.650	1.00
118_V	263_L	0.648	1.00
58_R	77_H	0.646	1.00
53_V	90_N	0.645	1.00
123_E	214_G	0.645	1.00
39_F	42_V	0.639	1.00
57_R	77_H	0.638	1.00
120_I	263_L	0.637	1.00
56_D	62_R	0.636	1.00
106_L	126_L	0.633	1.00
89_T	92_P	0.632	1.00
153_V	157_M	0.631	1.00
103_V	125_I	0.630	1.00
42_V	255_F	0.630	1.00
257_E	260_H	0.630	1.00
75_E	79_D	0.629	1.00
98_S	122_H	0.628	1.00
156_L	159_R	0.627	1.00
179_T	185_E	0.625	1.00
139_E	142_M	0.625	1.00
226_C	238_W	0.624	1.00
206_S	210_I	0.624	1.00
252_H	256_S	0.623	1.00
143_E	146_K	0.620	1.00
11_P	76_T	0.618	1.00
172_K	175_L	0.617	1.00
51_T	90_N	0.614	1.00
110_I	205_S	0.613	1.00
152_E	156_L	0.608	1.00
165_Q	168_A	0.607	1.00
145_L	149_H	0.605	1.00
134_E	138_A	0.602	1.00
16_H	63_S	0.601	1.00
237_E	261_D	0.600	1.00
142_M	146_K	0.599	1.00
169_V	173_R	0.598	1.00
168_A	172_K	0.597	1.00
152_E	155_K	0.596	1.00
15_I	58_R	0.594	1.00
49_W	52_V	0.594	1.00
156_L	160_L	0.592	1.00
93_A	117_H	0.591	1.00
99_S	246_T	0.585	1.00
142_M	145_L	0.584	1.00
26_I	46_L	0.581	1.00
11_P	79_D	0.575	1.00
19_V	88_I	0.574	1.00
230_L	234_L	0.573	1.00
167_K	171_T	0.573	1.00
28_L	54_T	0.568	1.00
171_T	177_N	0.566	1.00
134_E	137_Q	0.562	1.00
57_R	60_H	0.562	1.00
28_L	46_L	0.561	1.00
154_I	160_L	0.561	1.00
74_V	107_D	0.560	1.00
121_P	212_P	0.559	1.00
188_G	191_S	0.557	1.00
259_L	263_L	0.555	1.00
217_A	243_G	0.552	1.00
153_V	156_L	0.550	1.00
196_F	199_L	0.550	1.00
78_S	82_H	0.549	1.00
18_Q	37_D	0.545	1.00
218_S	245_H	0.543	1.00
229_A	233_Q	0.543	1.00
46_L	259_L	0.543	1.00
93_A	108_L	0.543	1.00
149_H	152_E	0.542	1.00
77_H	104_I	0.541	1.00
57_R	81_A	0.540	1.00
140_Q	144_D	0.540	1.00
109_C	206_S	0.538	1.00
191_S	194_L	0.538	1.00
247_G	255_F	0.534	1.00
84_L	87_K	0.533	1.00
38_K	98_S	0.533	1.00
198_A	201_T	0.531	1.00
141_F	149_H	0.529	1.00
178_S	184_Y	0.528	1.00
207_P	234_L	0.527	1.00
42_V	46_L	0.527	1.00
144_D	147_K	0.524	1.00
213_A	239_V	0.523	1.00
18_Q	54_T	0.522	1.00
224_Y	228_N	0.521	1.00
31_G	98_S	0.521	1.00
187_Q	191_S	0.520	1.00
144_D	149_H	0.520	1.00
68_Q	71_G	0.520	1.00
102_A	121_P	0.519	1.00
34_G	246_T	0.518	1.00
118_V	211_L	0.517	1.00
122_H	213_A	0.514	1.00
111_R	202_V	0.513	1.00
155_K	160_L	0.513	1.00
120_I	213_A	0.512	1.00
155_K	159_R	0.510	1.00
197_E	200_K	0.508	1.00
226_C	230_L	0.507	1.00
212_P	238_W	0.506	1.00
85_L	115_Q	0.504	1.00
248_Y	255_F	0.504	1.00
147_K	150_R	0.500	1.00
106_L	124_P	0.500	1.00
30_H	39_F	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
4inzA	1	0.9668	100	0.174	Contact Map
1ehyA	1	0.9299	100	0.186	Contact Map
3oosA	1	0.9594	100	0.189	Contact Map
3om8A	4	0.952	100	0.19	Contact Map
2xuaA	2	0.9225	100	0.2	Contact Map
2pujA	4	0.9779	100	0.207	Contact Map
3r40A	2	0.9483	100	0.213	Contact Map
2wueA	4	0.9742	100	0.22	Contact Map
4opmA	2	0.9852	100	0.221	Contact Map
1iupA	2	0.952	100	0.225	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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