XERD - ECOLI - GREMLIN Contacts

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XERD - Tyrosine recombinase XerD

UniProt:	P0A8P8	Sequences: MKQDLARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSARLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERLLQAPLIDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQQHHPRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11071
Length:	298 (269)
Sequences:	37778 (30311)
Seq/√Len:	1848.1

ECOLI - XERD XERC INTQ INTR INTF INTD INTB INTZ INTA INTS INTE FIMB FIME
BACSU - XERD XERC INT YOPP YOMM YOEC
HALSA - Q9HR66 Q9HQV5 O54590 Q9HSI7 O52010
SULSO - Q980D9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
251_A	268_L	5.057	1.00
157_M	193_L	3.223	1.00
51_Q	54_D	3.184	1.00
177_R	269_G	3.080	1.00
146_G	250_F	2.785	1.00
242_S	245_V	2.746	1.00
142_L	243_P	2.729	1.00
149_V	244_H	2.699	1.00
250_F	267_L	2.591	1.00
45_L	54_D	2.573	1.00
62_R	75_L	2.496	1.00
156_T	217_Q	2.226	1.00
156_T	208_V	2.202	1.00
142_L	152_L	2.190	1.00
168_R	178_L	2.178	1.00
270_H	276_T	2.155	1.00
165_G	186_V	2.067	1.00
248_H	281_H	2.050	1.00
32_D	74_R	2.048	1.00
137_A	192_Y	2.028	1.00
156_T	207_D	2.001	1.00
114_S	117_Q	1.969	1.00
144_A	182_G	1.933	1.00
260_D	263_V	1.907	1.00
166_V	178_L	1.892	1.00
255_L	264_V	1.879	1.00
59_L	76_L	1.860	1.00
186_V	190_E	1.849	1.00
262_R	265_Q	1.820	1.00
151_E	177_R	1.794	1.00
161_S	164_Q	1.781	1.00
32_D	78_A	1.758	1.00
35_M	75_L	1.747	1.00
30_R	34_S	1.739	1.00
180_P	267_L	1.727	1.00
85_Y	89_E	1.723	1.00
268_L	276_T	1.681	1.00
12_L	30_R	1.673	1.00
175_K	271_S	1.650	1.00
135_D	226_R	1.645	1.00
254_L	259_A	1.622	1.00
274_S	277_Q	1.598	1.00
55_L	97_S	1.578	1.00
147_L	152_L	1.575	1.00
256_N	286_R	1.530	1.00
115_E	253_H	1.526	1.00
250_F	254_L	1.512	1.00
255_L	280_T	1.500	1.00
82_L	86_L	1.495	1.00
25_T	29_Y	1.494	1.00
143_Y	253_H	1.487	1.00
8_I	33_L	1.481	1.00
181_L	186_V	1.471	1.00
138_M	223_F	1.466	1.00
162_L	190_E	1.437	1.00
8_I	82_L	1.435	1.00
136_K	140_E	1.433	1.00
50_A	83_F	1.430	1.00
156_T	159_D	1.419	1.00
46_T	49_T	1.414	1.00
140_E	188_W	1.412	1.00
157_M	209_L	1.402	1.00
149_V	220_R	1.401	1.00
70_T	74_R	1.400	1.00
149_V	153_V	1.395	1.00
265_Q	273_L	1.382	1.00
113_L	249_A	1.371	1.00
254_L	264_V	1.367	1.00
125_P	230_Y	1.363	1.00
252_T	281_H	1.361	1.00
275_T	278_I	1.357	1.00
144_A	185_A	1.345	1.00
161_S	166_V	1.337	1.00
24_N	27_N	1.327	1.00
262_R	266_M	1.319	1.00
118_V	143_Y	1.311	1.00
23_E	27_N	1.304	1.00
117_Q	120_R	1.282	1.00
137_A	191_T	1.281	1.00
122_L	140_E	1.263	1.00
150_S	154_G	1.255	1.00
58_L	75_L	1.252	1.00
63_L	72_S	1.244	1.00
73_A	103_P	1.240	1.00
113_L	241_L	1.238	1.00
208_V	217_Q	1.238	1.00
138_M	152_L	1.216	1.00
137_A	188_W	1.212	1.00
118_V	253_H	1.211	1.00
265_Q	276_T	1.210	1.00
36_M	39_W	1.207	1.00
58_L	62_R	1.202	1.00
220_R	224_W	1.200	1.00
27_N	31_R	1.199	1.00
148_R	244_H	1.188	1.00
147_L	169_V	1.187	1.00
158_S	207_D	1.186	1.00
143_Y	246_L	1.180	1.00
249_A	253_H	1.177	1.00
149_V	224_W	1.175	1.00
11_F	81_R	1.174	1.00
84_Q	98_A	1.170	1.00
59_L	63_L	1.166	1.00
16_W	26_L	1.166	1.00
39_W	61_E	1.165	1.00
71_S	75_L	1.164	1.00
256_N	283_A	1.154	1.00
119_E	123_Q	1.147	1.00
251_A	264_V	1.147	1.00
221_Q	224_W	1.137	1.00
76_L	80_R	1.125	1.00
87_Y	92_R	1.125	1.00
170_I	176_E	1.120	1.00
231_A	241_L	1.115	1.00
165_G	183_E	1.115	1.00
124_A	233_L	1.112	1.00
226_R	229_H	1.108	1.00
112_D	249_A	1.104	1.00
227_I	231_A	1.102	1.00
12_L	26_L	1.099	1.00
155_L	167_V	1.098	1.00
272_D	277_Q	1.096	1.00
115_E	257_H	1.095	1.00
124_A	234_A	1.095	1.00
168_R	176_E	1.093	1.00
67_Y	75_L	1.087	1.00
68_K	71_S	1.080	1.00
138_M	210_F	1.072	1.00
143_Y	249_A	1.071	1.00
219_T	222_T	1.070	1.00
272_D	275_T	1.069	1.00
56_Q	60_A	1.067	1.00
250_F	268_L	1.061	1.00
113_L	121_L	1.060	1.00
224_W	228_K	1.059	1.00
26_L	30_R	1.051	1.00
158_S	206_I	1.048	1.00
251_A	280_T	1.044	1.00
120_R	124_A	1.043	1.00
222_T	225_H	1.035	1.00
28_A	31_R	1.032	1.00
32_D	75_L	1.028	1.00
90_K	94_D	1.025	1.00
182_G	185_A	1.017	1.00
183_E	187_Y	1.015	1.00
39_W	57_A	1.005	1.00
29_Y	78_A	1.004	1.00
252_T	280_T	1.004	1.00
28_A	32_D	1.003	1.00
45_L	49_T	0.996	1.00
21_L	26_L	0.981	1.00
144_A	184_E	0.979	1.00
192_Y	196_G	0.974	1.00
141_V	210_F	0.965	1.00
286_R	289_Q	0.964	1.00
83_F	92_R	0.962	1.00
136_K	188_W	0.960	1.00
141_V	167_V	0.959	1.00
212_S	216_Q	0.956	1.00
115_E	119_E	0.954	1.00
52_S	56_Q	0.948	1.00
228_K	240_K	0.947	1.00
125_P	139_L	0.947	1.00
253_H	256_N	0.946	1.00
140_E	184_E	0.945	1.00
113_L	117_Q	0.940	1.00
153_V	220_R	0.937	1.00
84_Q	95_D	0.936	1.00
86_L	91_F	0.936	1.00
10_Q	14_A	0.934	1.00
170_I	174_N	0.929	1.00
56_Q	89_E	0.928	1.00
15_L	21_L	0.924	1.00
63_L	69_A	0.921	1.00
31_R	35_M	0.920	1.00
208_V	211_P	0.918	1.00
157_M	196_G	0.914	1.00
115_E	256_N	0.911	1.00
39_W	58_L	0.905	1.00
161_S	168_R	0.892	1.00
22_A	25_T	0.892	1.00
24_N	28_A	0.891	1.00
133_L	191_T	0.886	1.00
28_A	74_R	0.881	1.00
88_R	101_A	0.879	1.00
259_A	263_V	0.875	1.00
67_Y	71_S	0.874	1.00
62_R	67_Y	0.873	1.00
133_L	195_H	0.871	1.00
251_A	255_L	0.868	1.00
184_E	187_Y	0.864	1.00
10_Q	91_F	0.858	1.00
83_F	96_P	0.858	1.00
162_L	186_V	0.857	1.00
74_R	77_S	0.857	1.00
248_H	278_I	0.857	1.00
9_E	13_D	0.857	1.00
112_D	281_H	0.856	1.00
12_L	16_W	0.855	1.00
263_V	290_L	0.854	1.00
141_V	185_A	0.846	1.00
80_R	84_Q	0.846	1.00
137_A	210_F	0.844	1.00
36_M	41_H	0.844	1.00
266_M	287_L	0.842	1.00
21_L	29_Y	0.840	1.00
67_Y	72_S	0.838	1.00
34_S	38_E	0.835	1.00
111_K	245_V	0.835	1.00
52_S	88_R	0.834	1.00
261_L	277_Q	0.834	1.00
159_D	170_I	0.830	1.00
224_W	243_P	0.827	1.00
88_R	99_H	0.820	1.00
23_E	26_L	0.819	1.00
36_M	83_F	0.818	1.00
285_E	289_Q	0.817	1.00
133_L	137_A	0.814	1.00
155_L	160_I	0.813	1.00
229_H	233_L	0.808	1.00
129_Q	132_E	0.805	1.00
230_Y	233_L	0.805	1.00
62_R	72_S	0.802	1.00
265_Q	277_Q	0.802	1.00
149_V	223_F	0.798	1.00
54_D	57_A	0.797	1.00
33_L	38_E	0.795	1.00
153_V	223_F	0.794	1.00
145_T	179_V	0.789	1.00
11_F	15_L	0.786	1.00
228_K	232_V	0.782	1.00
87_Y	95_D	0.782	1.00
57_A	61_E	0.778	1.00
251_A	276_T	0.771	1.00
256_N	285_E	0.767	1.00
146_G	268_L	0.766	1.00
191_T	195_H	0.766	1.00
95_D	98_A	0.766	1.00
181_L	185_A	0.764	1.00
61_E	65_G	0.763	1.00
185_A	188_W	0.761	1.00
125_P	136_K	0.760	1.00
149_V	243_P	0.749	1.00
124_A	230_Y	0.748	1.00
133_L	136_K	0.743	1.00
135_D	230_Y	0.740	1.00
225_H	229_H	0.739	1.00
141_V	152_L	0.735	1.00
261_L	273_L	0.734	1.00
31_R	34_S	0.734	1.00
86_L	92_R	0.732	1.00
227_I	246_L	0.731	1.00
83_F	97_S	0.730	1.00
9_E	30_R	0.729	1.00
148_R	170_I	0.722	1.00
82_L	85_Y	0.721	1.00
8_I	12_L	0.720	1.00
37_V	41_H	0.717	1.00
121_L	231_A	0.716	1.00
221_Q	228_K	0.715	1.00
255_L	283_A	0.711	1.00
222_T	226_R	0.709	1.00
52_S	90_K	0.709	1.00
226_R	230_Y	0.704	1.00
190_E	194_E	0.704	1.00
121_L	139_L	0.703	1.00
58_L	61_E	0.699	1.00
196_G	211_P	0.698	1.00
15_L	19_K	0.696	1.00
113_L	245_V	0.695	1.00
190_E	193_L	0.694	1.00
267_L	287_L	0.692	1.00
87_Y	94_D	0.690	1.00
56_Q	59_L	0.690	1.00
141_V	147_L	0.687	1.00
35_M	65_G	0.687	1.00
155_L	209_L	0.685	1.00
263_V	267_L	0.685	1.00
87_Y	98_A	0.684	1.00
273_L	277_Q	0.683	1.00
60_A	63_L	0.682	1.00
228_K	231_A	0.680	1.00
70_T	73_A	0.680	1.00
36_M	79_V	0.680	1.00
193_L	196_G	0.680	1.00
76_L	97_S	0.678	1.00
251_A	270_H	0.678	1.00
39_W	42_H	0.674	1.00
142_L	149_V	0.674	1.00
161_S	165_G	0.673	1.00
53_D	57_A	0.672	1.00
16_W	30_R	0.671	1.00
33_L	82_L	0.669	1.00
227_I	243_P	0.669	1.00
244_H	248_H	0.669	1.00
273_L	276_T	0.666	1.00
53_D	89_E	0.665	1.00
187_Y	191_T	0.659	1.00
55_L	79_V	0.657	1.00
241_L	245_V	0.655	1.00
223_F	243_P	0.654	1.00
97_S	100_L	0.654	1.00
73_A	77_S	0.652	1.00
38_E	42_H	0.651	1.00
35_M	58_L	0.650	1.00
90_K	99_H	0.649	1.00
139_L	246_L	0.649	1.00
15_L	29_Y	0.648	1.00
272_D	276_T	0.646	1.00
187_Y	190_E	0.644	1.00
137_A	141_V	0.644	1.00
118_V	122_L	0.643	1.00
59_L	72_S	0.642	1.00
13_D	16_W	0.640	1.00
83_F	87_Y	0.639	1.00
137_A	185_A	0.639	1.00
40_L	61_E	0.636	1.00
112_D	252_T	0.633	1.00
9_E	38_E	0.631	1.00
140_E	185_A	0.631	1.00
284_T	287_L	0.630	1.00
120_R	123_Q	0.629	1.00
147_L	151_E	0.629	1.00
61_E	64_E	0.628	1.00
116_A	120_R	0.622	1.00
134_R	192_Y	0.622	1.00
84_Q	87_Y	0.619	1.00
255_L	260_D	0.618	1.00
36_M	58_L	0.617	1.00
145_T	182_G	0.616	1.00
259_A	290_L	0.616	1.00
262_R	277_Q	0.615	1.00
50_A	55_L	0.615	1.00
69_A	73_A	0.610	1.00
122_L	136_K	0.609	1.00
283_A	286_R	0.607	1.00
189_L	209_L	0.606	1.00
140_E	144_A	0.605	1.00
171_G	177_R	0.602	1.00
110_P	242_S	0.600	1.00
259_A	264_V	0.600	1.00
154_G	217_Q	0.599	1.00
36_M	40_L	0.596	1.00
80_R	102_S	0.595	1.00
264_V	280_T	0.595	1.00
147_L	167_V	0.592	1.00
38_E	41_H	0.590	1.00
41_H	58_L	0.589	1.00
188_W	191_T	0.588	1.00
245_V	248_H	0.588	1.00
115_E	249_A	0.587	1.00
118_V	249_A	0.586	1.00
265_Q	275_T	0.584	1.00
285_E	288_R	0.583	1.00
47_L	86_L	0.583	1.00
255_L	262_R	0.582	1.00
192_Y	195_H	0.581	1.00
10_Q	85_Y	0.579	1.00
255_L	261_L	0.578	1.00
80_R	97_S	0.578	1.00
14_A	85_Y	0.577	1.00
10_Q	13_D	0.577	1.00
58_L	79_V	0.575	1.00
116_A	119_E	0.573	1.00
85_Y	91_F	0.571	1.00
15_L	81_R	0.569	1.00
79_V	97_S	0.564	1.00
33_L	78_A	0.564	1.00
261_L	276_T	0.562	1.00
139_L	227_I	0.558	1.00
147_L	155_L	0.554	1.00
137_A	189_L	0.554	1.00
160_I	189_L	0.553	1.00
87_Y	90_K	0.542	1.00
265_Q	268_L	0.542	1.00
271_S	275_T	0.541	1.00
81_R	84_Q	0.537	1.00
253_H	257_H	0.537	1.00
151_E	269_G	0.536	1.00
141_V	189_L	0.535	1.00
10_Q	89_E	0.534	1.00
142_L	246_L	0.534	1.00
33_L	37_V	0.526	1.00
162_L	209_L	0.525	1.00
113_L	118_V	0.525	1.00
110_P	248_H	0.524	1.00
73_A	105_L	0.523	1.00
157_M	189_L	0.522	1.00
255_L	282_V	0.521	1.00
134_R	137_A	0.519	1.00
76_L	100_L	0.518	1.00
73_A	102_S	0.518	1.00
107_Q	278_I	0.516	1.00
230_Y	234_A	0.516	1.00
134_R	226_R	0.513	1.00
47_L	83_F	0.513	1.00
160_I	209_L	0.508	1.00
12_L	15_L	0.507	1.00
261_L	265_Q	0.506	1.00
87_Y	99_H	0.505	1.00
151_E	169_V	0.503	1.00
80_R	98_A	0.502	1.00
162_L	181_L	0.501	1.00
156_T	206_I	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
1a0pA	1	0.9094	100	0.127	Contact Map
1z1bA	3	0.9329	100	0.198	Contact Map
2a3vA	3	0.943	100	0.202	Contact Map
1z19A	3	0.9396	100	0.203	Contact Map
1xo0A	3	0.9631	100	0.218	Contact Map
4a8eA	2	0.8792	100	0.231	Contact Map
3nkhA	2	0.6409	100	0.397	Contact Map
1ae9A	4	0.5671	100	0.462	Contact Map
1aihA	2	0.5537	99.9	0.514	Contact Map
4e0gA	2	0.896	99.9	0.536	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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