XERD - BACSU - GREMLIN Contacts

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XERD - Tyrosine recombinase XerD

UniProt:	P46352	Sequences: MKDQIKDFIHYVMVERGLSQNTIVSYERDLKSYSLYLTETLHVTDWNHVTRIHIIQYLKHLKDSGKSGKTSARHLASIRSFHQFLLREKVTDKDPSVHIETQKTERALPKVLALNEVERLLDTPKLTSPFGYRDKAMLELLYATGIRVSEMIELKTADVHLSMGFIRCFGKGRKERIVPIGEAAASAIEEYMTKARGKLLKNNVSDALFLNHHGKQISRQGFWKNLKKIALEAGIKKELTPHTLRHSFATHLLENGADLRAVQEMLGHADISTTQIYTHVTKTRLKDVYKQFHPRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	296 (268)
Sequences:	37774 (30299)
Seq/√Len:	1850.8

ECOLI - XERD XERC INTR INTF INTQ INTZ INTD INTB INTA INTS INTE FIMB FIME
BACSU - XERD XERC YOMM INT YOPP YOEC
HALSA - Q9HR66 Q9HQV5 O54590 O52010 Q9HSI7
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
249_A	266_L	5.098	1.00
50_T	53_H	3.248	1.00
156_T	192_M	3.247	1.00
176_R	267_G	3.203	1.00
240_T	243_T	2.775	1.00
141_L	241_P	2.772	1.00
145_G	248_F	2.771	1.00
148_V	242_H	2.711	1.00
248_F	265_M	2.595	1.00
61_L	74_H	2.551	1.00
44_T	53_H	2.475	1.00
155_K	216_Q	2.230	1.00
155_K	207_A	2.229	1.00
141_L	151_M	2.182	1.00
268_H	274_T	2.166	1.00
167_R	177_I	2.149	1.00
164_G	185_A	2.117	1.00
246_H	279_H	2.112	1.00
136_A	191_Y	2.063	1.00
113_A	116_E	2.044	1.00
155_K	206_D	2.009	1.00
29_D	73_R	1.938	1.00
258_D	261_A	1.933	1.00
58_L	75_L	1.926	1.00
253_L	262_V	1.918	1.00
143_A	181_G	1.918	1.00
150_E	176_R	1.914	1.00
185_A	189_E	1.913	1.00
260_R	263_Q	1.866	1.00
84_F	88_E	1.814	1.00
165_F	177_I	1.789	1.00
27_E	31_K	1.781	1.00
160_H	163_M	1.747	1.00
32_S	74_H	1.737	1.00
174_K	269_A	1.717	1.00
29_D	77_S	1.708	1.00
134_D	225_N	1.668	1.00
252_L	257_A	1.667	1.00
179_P	265_M	1.664	1.00
54_I	96_S	1.650	1.00
266_L	274_T	1.640	1.00
254_E	284_R	1.629	1.00
272_S	275_Q	1.616	1.00
146_I	151_M	1.611	1.00
9_I	27_E	1.601	1.00
114_L	251_H	1.589	1.00
45_D	48_H	1.513	1.00
81_F	85_L	1.511	1.00
248_F	252_L	1.510	1.00
135_K	139_E	1.497	1.00
142_Y	251_H	1.484	1.00
253_L	278_T	1.475	1.00
180_I	185_A	1.474	1.00
139_E	187_A	1.468	1.00
49_V	82_H	1.462	1.00
156_T	208_L	1.454	1.00
69_K	73_R	1.452	1.00
137_M	222_F	1.446	1.00
148_V	152_I	1.435	1.00
161_L	189_E	1.433	1.00
155_K	158_D	1.417	1.00
148_V	219_R	1.416	1.00
252_L	262_V	1.414	1.00
250_T	279_H	1.408	1.00
263_Q	271_I	1.403	1.00
112_L	247_S	1.381	1.00
160_H	165_F	1.380	1.00
21_N	24_V	1.376	1.00
22_T	26_Y	1.371	1.00
273_T	276_I	1.364	1.00
57_Y	74_H	1.352	1.00
117_V	142_Y	1.342	1.00
116_E	119_R	1.338	1.00
143_A	184_A	1.334	1.00
125_K	135_K	1.324	1.00
20_Q	24_V	1.319	1.00
260_R	264_E	1.318	1.00
124_P	229_I	1.313	1.00
207_A	216_Q	1.293	1.00
57_Y	61_L	1.290	1.00
136_A	190_E	1.285	1.00
149_S	153_E	1.262	1.00
157_A	206_D	1.251	1.00
219_R	223_W	1.245	1.00
62_K	71_S	1.242	1.00
117_V	251_H	1.240	1.00
121_L	139_E	1.238	1.00
112_L	239_L	1.228	1.00
8_F	80_S	1.226	1.00
58_L	62_K	1.222	1.00
137_M	151_M	1.216	1.00
249_A	262_V	1.207	1.00
247_S	251_H	1.193	1.00
263_Q	274_T	1.192	1.00
24_V	28_R	1.191	1.00
147_R	242_H	1.190	1.00
75_L	79_R	1.189	1.00
142_Y	244_L	1.180	1.00
72_A	102_Q	1.172	1.00
118_E	122_D	1.172	1.00
70_T	74_H	1.172	1.00
136_A	187_A	1.167	1.00
220_Q	223_W	1.162	1.00
148_V	223_W	1.162	1.00
254_E	281_T	1.153	1.00
19_S	169_F	1.150	1.00
9_I	23_I	1.150	1.00
13_M	23_I	1.142	1.00
83_Q	97_V	1.137	1.00
137_M	209_F	1.127	1.00
225_N	228_K	1.119	1.00
164_G	182_E	1.119	1.00
230_A	239_L	1.116	1.00
55_I	59_K	1.113	1.00
218_S	221_G	1.112	1.00
157_A	205_S	1.099	1.00
86_L	91_T	1.096	1.00
111_V	247_S	1.089	1.00
169_F	175_E	1.089	1.00
226_L	230_A	1.088	1.00
270_D	275_Q	1.087	1.00
221_G	224_K	1.085	1.00
223_W	227_K	1.078	1.00
270_D	273_T	1.077	1.00
23_I	27_E	1.077	1.00
67_S	70_T	1.075	1.00
248_F	266_L	1.067	1.00
119_R	123_T	1.065	1.00
182_E	186_S	1.063	1.00
123_T	232_E	1.060	1.00
154_L	166_I	1.058	1.00
112_L	120_L	1.056	1.00
142_Y	247_S	1.050	1.00
40_T	60_H	1.044	1.00
66_K	74_H	1.044	1.00
123_T	233_A	1.043	1.00
89_K	93_K	1.032	1.00
250_T	278_T	1.027	1.00
29_D	74_H	1.027	1.00
114_L	255_N	1.023	1.00
181_G	184_A	1.023	1.00
25_S	28_R	1.019	1.00
249_A	278_T	1.016	1.00
25_S	29_D	1.015	1.00
146_I	168_C	1.011	1.00
167_R	175_E	1.009	1.00
82_H	91_T	0.998	1.00
135_K	187_A	0.996	1.00
143_A	183_A	0.985	1.00
284_R	287_D	0.984	1.00
140_L	209_F	0.984	1.00
156_T	195_A	0.978	1.00
28_R	32_S	0.972	1.00
139_E	183_A	0.965	1.00
21_N	25_S	0.965	1.00
51_R	55_I	0.961	1.00
227_K	238_E	0.959	1.00
251_H	254_E	0.955	1.00
124_P	138_L	0.952	1.00
18_L	23_I	0.948	1.00
191_Y	195_A	0.948	1.00
114_L	118_E	0.945	1.00
55_I	88_E	0.941	1.00
60_H	64_S	0.940	1.00
152_I	219_R	0.940	1.00
85_L	90_V	0.939	1.00
62_K	68_G	0.928	1.00
207_A	210_L	0.927	1.00
61_L	66_K	0.909	1.00
261_A	288_V	0.908	1.00
12_V	18_L	0.903	1.00
249_A	253_L	0.896	1.00
114_L	254_E	0.895	1.00
112_L	116_E	0.895	1.00
264_E	285_L	0.889	1.00
26_Y	77_S	0.888	1.00
132_Y	190_E	0.887	1.00
79_R	83_Q	0.886	1.00
183_A	186_S	0.883	1.00
246_H	276_I	0.882	1.00
169_F	173_R	0.880	1.00
170_G	176_R	0.880	1.00
44_T	48_H	0.879	1.00
6_K	10_H	0.877	1.00
228_K	232_E	0.875	1.00
19_S	22_T	0.875	1.00
257_A	261_A	0.873	1.00
83_Q	94_D	0.873	1.00
132_Y	194_K	0.872	1.00
73_R	76_A	0.869	1.00
82_H	95_P	0.868	1.00
51_R	87_R	0.867	1.00
18_L	26_Y	0.863	1.00
7_D	11_Y	0.863	1.00
223_W	241_P	0.860	1.00
111_V	279_H	0.856	1.00
87_R	100_E	0.856	1.00
140_L	166_I	0.854	1.00
259_L	275_Q	0.853	1.00
227_K	231_L	0.851	1.00
263_Q	275_Q	0.850	1.00
160_H	167_R	0.849	1.00
148_V	222_F	0.847	1.00
161_L	185_A	0.846	1.00
9_I	13_M	0.845	1.00
110_K	243_T	0.843	1.00
66_K	70_T	0.841	1.00
7_D	90_V	0.838	1.00
229_I	232_E	0.838	1.00
25_S	73_R	0.837	1.00
8_F	12_V	0.837	1.00
86_L	94_D	0.836	1.00
56_Q	60_H	0.832	1.00
154_L	159_V	0.828	1.00
61_L	71_S	0.826	1.00
140_L	184_A	0.825	1.00
283_T	287_D	0.820	1.00
20_Q	23_I	0.820	1.00
53_H	56_Q	0.811	1.00
87_R	98_H	0.808	1.00
144_T	178_V	0.807	1.00
82_H	96_S	0.802	1.00
152_I	222_F	0.796	1.00
136_A	209_F	0.789	1.00
33_Y	82_H	0.788	1.00
132_Y	136_A	0.779	1.00
254_E	283_T	0.777	1.00
94_D	97_V	0.776	1.00
184_A	187_A	0.772	1.00
224_K	228_K	0.771	1.00
211_N	215_K	0.768	1.00
140_L	151_M	0.767	1.00
190_E	194_K	0.766	1.00
145_G	266_L	0.765	1.00
148_V	241_P	0.764	1.00
59_K	62_K	0.756	1.00
132_Y	135_K	0.754	1.00
120_L	230_A	0.752	1.00
57_Y	60_H	0.752	1.00
81_F	84_F	0.750	1.00
271_I	274_T	0.749	1.00
66_K	71_S	0.749	1.00
249_A	274_T	0.748	1.00
150_E	170_G	0.741	1.00
180_I	184_A	0.739	1.00
75_L	96_S	0.738	1.00
12_V	16_R	0.737	1.00
156_T	196_R	0.734	1.00
112_L	243_T	0.729	1.00
271_I	275_Q	0.728	1.00
55_I	58_L	0.726	1.00
154_L	208_L	0.718	1.00
51_R	89_K	0.717	1.00
270_D	274_T	0.717	1.00
10_H	13_M	0.716	1.00
123_T	229_I	0.715	1.00
259_L	271_I	0.709	1.00
6_K	27_E	0.709	1.00
189_E	193_T	0.708	1.00
192_M	196_R	0.704	1.00
249_A	268_H	0.704	1.00
69_K	72_A	0.704	1.00
124_P	135_K	0.703	1.00
265_M	285_L	0.703	1.00
253_L	281_T	0.700	1.00
225_N	229_I	0.698	1.00
226_L	241_P	0.698	1.00
226_L	244_L	0.695	1.00
227_K	230_A	0.694	1.00
6_K	38_T	0.692	1.00
220_Q	227_K	0.692	1.00
141_L	148_V	0.690	1.00
134_D	229_I	0.687	1.00
160_H	164_G	0.686	1.00
85_L	91_T	0.685	1.00
140_L	146_I	0.683	1.00
189_E	192_M	0.681	1.00
195_A	210_L	0.680	1.00
192_M	195_A	0.674	1.00
54_I	78_I	0.674	1.00
28_R	31_K	0.673	1.00
120_L	138_L	0.672	1.00
89_K	98_H	0.672	1.00
257_A	288_V	0.671	1.00
52_I	88_E	0.671	1.00
281_T	284_R	0.669	1.00
261_A	265_M	0.669	1.00
222_F	241_P	0.669	1.00
242_H	246_H	0.668	1.00
61_L	64_S	0.666	1.00
72_A	76_A	0.666	1.00
221_G	225_N	0.664	1.00
239_L	243_T	0.661	1.00
186_S	190_E	0.661	1.00
32_S	57_Y	0.660	1.00
139_E	184_A	0.658	1.00
117_V	121_L	0.656	1.00
52_I	56_Q	0.655	1.00
144_T	181_G	0.650	1.00
86_L	97_V	0.649	1.00
58_L	71_S	0.648	1.00
13_M	27_E	0.641	1.00
133_R	191_Y	0.641	1.00
125_K	139_E	0.639	1.00
282_K	285_L	0.638	1.00
158_D	169_F	0.636	1.00
186_S	189_E	0.635	1.00
12_V	26_Y	0.634	1.00
136_A	140_L	0.634	1.00
79_R	96_S	0.634	1.00
49_V	54_I	0.632	1.00
83_Q	86_L	0.626	1.00
170_G	175_E	0.622	1.00
115_N	119_R	0.620	1.00
119_R	122_D	0.616	1.00
138_L	244_L	0.614	1.00
33_Y	78_I	0.613	1.00
146_I	150_E	0.612	1.00
40_T	56_Q	0.611	1.00
260_R	275_Q	0.611	1.00
79_R	101_T	0.609	1.00
187_A	190_E	0.608	1.00
253_L	260_R	0.607	1.00
33_Y	64_S	0.607	1.00
253_L	258_D	0.607	1.00
30_L	38_T	0.607	1.00
30_L	34_S	0.606	1.00
57_Y	78_I	0.606	1.00
114_L	247_S	0.605	1.00
84_F	90_V	0.604	1.00
109_P	240_T	0.604	1.00
68_G	72_A	0.604	1.00
30_L	81_F	0.604	1.00
121_L	135_K	0.604	1.00
82_H	86_L	0.602	1.00
30_L	77_S	0.602	1.00
139_E	143_A	0.601	1.00
115_N	118_E	0.600	1.00
283_T	286_K	0.599	1.00
257_A	262_V	0.598	1.00
243_T	246_H	0.597	1.00
111_V	250_T	0.595	1.00
136_A	184_A	0.595	1.00
147_R	169_F	0.595	1.00
117_V	247_S	0.592	1.00
188_I	208_L	0.591	1.00
9_I	12_V	0.588	1.00
253_L	259_L	0.587	1.00
7_D	10_H	0.587	1.00
153_E	216_Q	0.582	1.00
263_Q	273_T	0.582	1.00
259_L	274_T	0.580	1.00
262_V	278_T	0.580	1.00
33_Y	57_Y	0.580	1.00
86_L	89_K	0.579	1.00
60_H	63_D	0.578	1.00
26_Y	29_D	0.569	1.00
136_A	188_I	0.569	1.00
59_K	63_D	0.566	1.00
80_S	83_Q	0.562	1.00
269_A	273_T	0.561	1.00
229_I	233_A	0.559	1.00
31_K	34_S	0.556	1.00
46_W	85_L	0.555	1.00
159_V	188_I	0.551	1.00
190_E	193_T	0.549	1.00
51_R	98_H	0.548	1.00
141_L	244_L	0.547	1.00
191_Y	194_K	0.546	1.00
96_S	99_I	0.544	1.00
133_R	136_A	0.544	1.00
80_S	84_F	0.538	1.00
138_L	226_L	0.537	1.00
156_T	188_I	0.533	1.00
78_I	96_S	0.531	1.00
86_L	93_K	0.531	1.00
72_A	101_T	0.530	1.00
263_Q	266_L	0.529	1.00
79_R	97_V	0.528	1.00
150_E	267_G	0.526	1.00
106_R	276_I	0.526	1.00
86_L	98_H	0.526	1.00
112_L	117_V	0.524	1.00
252_L	265_M	0.524	1.00
73_R	77_S	0.523	1.00
140_L	188_I	0.523	1.00
253_L	280_V	0.521	1.00
51_R	88_E	0.520	1.00
155_K	205_S	0.519	1.00
18_L	22_T	0.517	1.00
161_L	180_I	0.515	1.00
260_R	271_I	0.514	1.00
159_V	208_L	0.514	1.00
75_L	99_I	0.512	1.00
109_P	246_H	0.509	1.00
220_Q	224_K	0.509	1.00
146_I	154_L	0.508	1.00
263_Q	270_D	0.506	1.00
11_Y	84_F	0.505	1.00
82_H	94_D	0.501	1.00
7_D	84_F	0.501	1.00
131_G	135_K	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	0.9088	100	0.148	Contact Map
2a3vA	3	0.9392	100	0.212	Contact Map
1z1bA	3	0.9257	100	0.213	Contact Map
1z19A	3	0.9358	100	0.222	Contact Map
1xo0A	3	0.9662	100	0.228	Contact Map
4a8eA	2	0.8851	100	0.245	Contact Map
3nkhA	2	0.6453	100	0.396	Contact Map
1ae9A	4	0.5676	100	0.465	Contact Map
1aihA	2	0.5541	99.9	0.515	Contact Map
4e0gA	2	0.9122	99.9	0.552	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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