PYRH - HALSA - GREMLIN Contacts

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PYRH - Uridylate kinase

UniProt:	Q9HNN8	Sequences: MRVVVSIGGSVLAPGLDADQVDAHADAINELTDAGCEVGAVVGGGGVARDYIGTARELGANEIELDDIGVDVTRLNARLLIAALGGDAAPSPAEDYEDAGEAMRRGDIAVMGGVVAGQTTDAVSAALAEYTDADLLLYATSVPGVFSADPNEDADAEHFTRMTAGELVDIIADIEMNAGSSAPVDLLAAKLIERSGVRTIVLDGTDPRRIVDAVRFGEHDGTDVIPDGTDNQMTYWADNQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	241 (202)
Sequences:	10253 (5766)
Seq/√Len:	405.7

ECOLI - PROB PYRH AK1H AK2H AK3
BACSU - PYRH PROB PROJ AK2 AK1 AK3
HALSA - PYRH
SULSO - PYRH Q97ZL7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
148_A	153_D	4.528	1.00
144_G	158_H	2.614	1.00
29_N	33_D	2.426	1.00
26_D	87_D	2.384	1.00
128_A	136_L	2.372	1.00
90_P	107_D	2.259	1.00
29_N	89_A	2.251	1.00
165_G	193_E	2.121	1.00
48_A	51_Y	2.107	1.00
39_G	131_T	2.052	1.00
147_S	157_E	2.022	1.00
137_L	202_L	1.986	1.00
135_L	200_I	1.980	1.00
45_G	48_A	1.979	1.00
29_N	87_D	1.970	1.00
93_A	96_Y	1.861	1.00
11_V	204_G	1.852	1.00
22_D	87_D	1.835	1.00
30_E	211_V	1.826	1.00
81_I	91_S	1.815	1.00
46_G	50_D	1.794	1.00
143_P	206_D	1.789	1.00
32_T	89_A	1.783	1.00
166_E	170_I	1.774	1.00
143_P	203_D	1.764	1.00
147_S	153_D	1.750	1.00
211_V	215_R	1.735	1.00
9_G	48_A	1.731	1.00
89_A	108_I	1.717	1.00
32_T	106_G	1.707	1.00
46_G	49_R	1.704	1.00
129_E	197_V	1.696	1.00
149_D	152_E	1.676	1.00
148_A	155_D	1.633	1.00
167_L	189_A	1.594	1.00
23_A	26_D	1.574	1.00
141_S	151_N	1.572	1.00
64_E	67_D	1.556	1.00
47_V	50_D	1.546	1.00
200_I	213_A	1.532	1.00
22_D	86_G	1.528	1.00
125_A	136_L	1.523	1.00
32_T	37_E	1.520	1.00
125_A	192_I	1.516	1.00
5_V	28_I	1.515	1.00
140_T	201_V	1.485	1.00
102_A	107_D	1.483	1.00
30_E	207_P	1.449	1.00
192_I	199_T	1.443	1.00
168_V	190_K	1.429	1.00
167_L	170_I	1.405	1.00
147_S	159_F	1.397	1.00
45_G	49_R	1.394	1.00
23_A	27_A	1.389	1.00
98_D	102_A	1.389	1.00
25_A	83_A	1.387	1.00
143_P	146_F	1.362	1.00
30_E	33_D	1.353	1.00
27_A	208_R	1.352	1.00
65_L	69_G	1.348	1.00
209_R	212_D	1.346	1.00
4_V	133_A	1.343	1.00
206_D	212_D	1.342	1.00
100_G	104_R	1.335	1.00
83_A	87_D	1.333	1.00
101_E	104_R	1.325	1.00
92_P	107_D	1.324	1.00
39_G	42_V	1.292	1.00
34_A	215_R	1.284	1.00
101_E	105_R	1.284	1.00
84_L	91_S	1.283	1.00
150_P	156_A	1.265	1.00
73_T	92_P	1.258	1.00
26_D	29_N	1.254	1.00
24_H	80_L	1.249	1.00
203_D	206_D	1.245	1.00
22_D	83_A	1.237	1.00
210_I	213_A	1.233	1.00
20_Q	23_A	1.212	1.00
111_M	114_V	1.208	1.00
32_T	108_I	1.206	1.00
28_I	40_A	1.205	1.00
129_E	195_S	1.204	1.00
159_F	170_I	1.200	1.00
202_L	213_A	1.197	1.00
30_E	34_A	1.196	1.00
72_V	76_N	1.193	1.00
22_D	26_D	1.161	1.00
42_V	77_A	1.155	1.00
102_A	109_A	1.130	1.00
206_D	209_R	1.125	1.00
148_A	156_A	1.125	1.00
70_V	112_G	1.123	1.00
92_P	102_A	1.111	1.00
27_A	207_P	1.103	1.00
202_L	209_R	1.096	1.00
10_S	13_A	1.090	1.00
124_S	136_L	1.080	1.00
146_F	156_A	1.077	1.00
145_V	162_M	1.075	1.00
84_L	89_A	1.071	1.00
147_S	156_A	1.066	1.00
71_D	75_L	1.042	1.00
42_V	80_L	1.042	1.00
143_P	158_H	1.042	1.00
190_K	194_R	1.042	1.00
37_E	106_G	1.034	1.00
99_A	103_M	1.032	1.00
39_G	103_M	1.023	1.00
73_T	76_N	1.020	1.00
158_H	203_D	1.017	1.00
26_D	30_E	1.009	1.00
47_V	115_V	1.004	1.00
3_V	36_C	1.000	1.00
21_V	83_A	0.997	1.00
106_G	109_A	0.990	1.00
137_L	200_I	0.986	1.00
165_G	168_V	0.983	1.00
85_G	90_P	0.976	1.00
132_D	195_S	0.976	1.00
122_A	191_L	0.975	1.00
20_Q	205_T	0.964	1.00
165_G	169_D	0.956	1.00
31_L	34_A	0.952	1.00
145_V	201_V	0.945	1.00
107_D	110_V	0.943	1.00
83_A	86_G	0.934	1.00
9_G	177_N	0.932	1.00
148_A	154_A	0.924	1.00
19_D	22_D	0.921	1.00
139_A	202_L	0.921	1.00
18_A	22_D	0.919	1.00
63_I	111_M	0.916	1.00
166_E	169_D	0.916	1.00
122_A	187_L	0.915	1.00
37_E	104_R	0.914	1.00
25_A	84_L	0.914	1.00
29_N	32_T	0.912	1.00
84_L	87_D	0.909	1.00
74_R	77_A	0.902	1.00
164_A	189_A	0.901	1.00
159_F	162_M	0.897	1.00
29_N	84_L	0.897	1.00
128_A	197_V	0.890	1.00
136_L	192_I	0.886	1.00
30_E	208_R	0.885	1.00
7_I	40_A	0.880	1.00
103_M	109_A	0.878	1.00
21_V	80_L	0.872	1.00
46_G	51_Y	0.860	1.00
32_T	38_V	0.856	1.00
31_L	137_L	0.853	1.00
14_P	19_D	0.852	1.00
137_L	210_I	0.847	1.00
23_A	204_G	0.846	1.00
5_V	31_L	0.846	1.00
37_E	42_V	0.844	1.00
180_S	193_E	0.844	1.00
26_D	207_P	0.843	1.00
145_V	159_F	0.843	1.00
211_V	214_V	0.842	1.00
67_D	101_E	0.840	1.00
54_T	57_E	0.829	1.00
31_L	214_V	0.825	1.00
143_P	208_R	0.825	1.00
44_G	72_V	0.823	1.00
45_G	50_D	0.817	1.00
146_F	150_P	0.815	1.00
14_P	20_Q	0.814	1.00
25_A	87_D	0.809	1.00
135_L	198_R	0.807	1.00
31_L	36_C	0.806	1.00
68_I	79_L	0.806	1.00
23_A	207_P	0.804	1.00
77_A	80_L	0.803	1.00
149_D	156_A	0.791	1.00
146_F	158_H	0.787	1.00
5_V	137_L	0.782	1.00
82_A	86_G	0.779	1.00
71_D	74_R	0.779	1.00
27_A	30_E	0.775	1.00
47_V	51_Y	0.771	1.00
125_A	191_L	0.770	1.00
208_R	212_D	0.770	1.00
187_L	190_K	0.765	1.00
28_I	84_L	0.762	1.00
193_E	199_T	0.757	1.00
138_Y	141_S	0.744	1.00
127_L	131_T	0.741	1.00
152_E	182_A	0.734	1.00
76_N	80_L	0.730	1.00
14_P	18_A	0.730	1.00
141_S	205_T	0.728	1.00
98_D	101_E	0.722	1.00
208_R	211_V	0.720	1.00
28_I	108_I	0.714	1.00
34_A	211_V	0.713	1.00
3_V	214_V	0.713	1.00
3_V	135_L	0.711	1.00
188_A	192_I	0.710	1.00
192_I	197_V	0.710	1.00
31_L	38_V	0.706	1.00
51_Y	54_T	0.706	1.00
102_A	105_R	0.706	1.00
25_A	29_N	0.705	1.00
46_G	182_A	0.705	1.00
187_L	191_L	0.703	1.00
36_C	134_D	0.690	1.00
163_T	166_E	0.687	1.00
141_S	150_P	0.687	1.00
36_C	42_V	0.687	1.00
81_I	85_G	0.684	1.00
92_P	109_A	0.684	1.00
191_L	195_S	0.680	1.00
168_V	186_L	0.676	0.99
7_I	11_V	0.674	0.99
69_G	72_V	0.670	0.99
11_V	141_S	0.667	0.99
10_S	45_G	0.661	0.99
39_G	133_A	0.661	0.99
118_Q	188_A	0.656	0.99
69_G	76_N	0.655	0.99
51_Y	55_A	0.654	0.99
7_I	12_L	0.652	0.99
146_F	184_V	0.652	0.99
63_I	67_D	0.651	0.99
82_A	85_G	0.646	0.99
97_E	101_E	0.645	0.99
157_E	161_R	0.638	0.99
178_A	186_L	0.633	0.99
60_A	65_L	0.626	0.99
184_V	188_A	0.625	0.99
184_V	199_T	0.624	0.99
10_S	141_S	0.623	0.99
33_D	89_A	0.623	0.99
212_D	215_R	0.620	0.99
102_A	106_G	0.616	0.99
112_G	116_A	0.614	0.99
24_H	28_I	0.612	0.99
90_P	106_G	0.611	0.99
85_G	91_S	0.611	0.99
28_I	38_V	0.610	0.99
153_D	156_A	0.605	0.99
29_N	108_I	0.599	0.99
129_E	191_L	0.597	0.99
140_T	199_T	0.597	0.99
70_V	74_R	0.596	0.99
20_Q	24_H	0.588	0.99
184_V	201_V	0.587	0.99
47_V	72_V	0.584	0.98
88_A	91_S	0.583	0.98
68_I	78_R	0.580	0.98
69_G	73_T	0.580	0.98
21_V	25_A	0.579	0.98
26_D	86_G	0.578	0.98
68_I	75_L	0.577	0.98
38_V	42_V	0.576	0.98
100_G	132_D	0.572	0.98
99_A	102_A	0.569	0.98
10_S	140_T	0.569	0.98
98_D	111_M	0.569	0.98
138_Y	184_V	0.565	0.98
8_G	121_D	0.562	0.98
81_I	97_E	0.559	0.98
25_A	80_L	0.557	0.98
5_V	38_V	0.557	0.98
113_G	116_A	0.554	0.98
112_G	115_V	0.553	0.98
98_D	107_D	0.552	0.98
23_A	208_R	0.549	0.98
20_Q	204_G	0.548	0.98
114_V	119_T	0.544	0.98
11_V	20_Q	0.537	0.97
96_Y	99_A	0.531	0.97
189_A	199_T	0.531	0.97
3_V	38_V	0.529	0.97
48_A	54_T	0.528	0.97
84_L	108_I	0.528	0.97
160_T	210_I	0.527	0.97
13_A	18_A	0.521	0.97
67_D	74_R	0.519	0.97
85_G	92_P	0.519	0.97
149_D	153_D	0.516	0.97
99_A	110_V	0.515	0.97
185_D	191_L	0.513	0.97
24_H	204_G	0.510	0.96
100_G	103_M	0.509	0.96
207_P	211_V	0.508	0.96
49_R	117_G	0.508	0.96
47_V	75_L	0.508	0.96
26_D	33_D	0.507	0.96
67_D	71_D	0.507	0.96
27_A	206_D	0.506	0.96
12_L	76_N	0.505	0.96
32_T	90_P	0.505	0.96
145_V	193_E	0.503	0.96
19_D	26_D	0.502	0.96
27_A	211_V	0.502	0.96
97_E	100_G	0.502	0.96
55_A	58_L	0.502	0.96
142_V	146_F	0.502	0.96
66_D	114_V	0.501	0.96
113_G	126_A	0.500	0.96

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
4q1tA	4	0.9129	100	0.288	Contact Map
2j5vA	2	0.8299	100	0.309	Contact Map
3l76A	2	0.917	100	0.323	Contact Map
2j4jA	5	0.9295	100	0.325	Contact Map
2brxA	5	0.8963	100	0.331	Contact Map
3ab4A	7	0.917	100	0.34	Contact Map
2va1A	5	0.8838	100	0.349	Contact Map
3nwyA	5	0.888	100	0.35	Contact Map
3c1mA	3	0.917	100	0.353	Contact Map
1z9dA	5	0.888	100	0.354	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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