PYRH - SULSO - GREMLIN Contacts

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PYRH - Uridylate kinase

UniProt:	Q97ZE2	Sequences: MMNIILKISGKFFDEDNVDNLIVLRQSIKELADNGFRVGIVTGGGSTARRYIKLAREIGIGEAYLDLLGIWASRLNAYLVMFSLQDLAYMHVPQSLEEFIQDWSHGKVVVTGGFQPGQSTAAVAALVAEASSSKTLVVATNVDGVYEKDPRIYADVKLIPHLTTQDLRKILEGSQSVQAGTYELLDPLAIKIVERSKIRVIVMNYRKLNRIIDILKGEEVSSIIEPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	227 (206)
Sequences:	10522 (5730)
Seq/√Len:	399.2

ECOLI - PYRH PROB AK2H AK1H AK3
BACSU - PYRH PROB PROJ AK2 AK1 AK3
HALSA - PYRH Q9HMV1
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_K	153_Y	4.597	1.00
3_N	37_R	3.743	1.00
213_D	218_E	3.135	1.00
144_G	158_L	2.676	1.00
26_Q	87_L	2.506	1.00
29_K	33_D	2.469	1.00
128_A	136_L	2.401	1.00
29_K	89_Y	2.321	1.00
39_G	131_S	2.236	1.00
90_M	107_K	2.221	1.00
135_T	201_I	2.153	1.00
165_Q	194_E	2.146	1.00
147_E	157_K	2.124	1.00
29_K	87_L	1.989	1.00
89_Y	108_V	1.977	1.00
10_G	48_A	1.915	1.00
137_V	203_M	1.909	1.00
12_F	205_Y	1.908	1.00
22_I	87_L	1.873	1.00
143_D	207_K	1.836	1.00
30_E	212_I	1.830	1.00
32_A	89_Y	1.816	1.00
143_D	204_N	1.789	1.00
81_M	91_H	1.776	1.00
201_I	214_I	1.758	1.00
147_E	153_Y	1.754	1.00
168_R	191_K	1.716	1.00
77_A	111_T	1.716	1.00
148_K	155_D	1.709	1.00
212_I	216_K	1.674	1.00
129_E	198_I	1.672	1.00
24_L	80_V	1.647	1.00
32_A	106_G	1.623	1.00
149_D	152_I	1.618	1.00
125_A	136_L	1.595	1.00
22_I	86_D	1.589	1.00
167_L	190_I	1.585	1.00
6_L	28_I	1.573	1.00
23_V	26_Q	1.571	1.00
141_N	151_R	1.549	1.00
193_V	200_V	1.533	1.00
47_T	50_R	1.528	1.00
32_A	37_R	1.512	1.00
140_T	202_V	1.510	1.00
102_D	107_K	1.507	1.00
125_A	193_V	1.496	1.00
25_R	83_S	1.485	1.00
42_T	77_A	1.459	1.00
96_L	100_I	1.444	1.00
42_T	80_V	1.435	1.00
92_V	107_K	1.421	1.00
143_D	146_Y	1.397	1.00
23_V	27_S	1.390	1.00
100_I	104_S	1.382	1.00
30_E	33_D	1.374	1.00
5_I	133_S	1.357	1.00
147_E	159_I	1.353	1.00
27_S	209_N	1.312	1.00
32_A	108_V	1.312	1.00
22_I	83_S	1.308	1.00
20_N	23_V	1.297	1.00
98_E	102_D	1.294	1.00
34_N	216_K	1.260	1.00
21_L	80_V	1.258	1.00
129_E	196_S	1.250	1.00
99_F	111_T	1.237	1.00
28_I	40_I	1.218	1.00
203_M	210_R	1.214	1.00
48_A	51_Y	1.198	1.00
84_L	91_H	1.186	1.00
207_K	213_D	1.185	1.00
101_Q	104_S	1.181	1.00
96_L	132_S	1.181	1.00
204_N	207_K	1.180	1.00
26_Q	29_K	1.173	1.00
166_D	173_G	1.169	1.00
145_V	162_L	1.161	1.00
207_K	210_R	1.159	1.00
30_E	209_N	1.159	1.00
101_Q	105_H	1.155	1.00
92_V	102_D	1.149	1.00
150_P	156_V	1.146	1.00
46_S	50_R	1.139	1.00
30_E	34_N	1.136	1.00
124_A	136_L	1.121	1.00
83_S	87_L	1.120	1.00
210_R	213_D	1.119	1.00
65_L	69_G	1.104	1.00
22_I	26_Q	1.099	1.00
148_K	156_V	1.084	1.00
74_R	77_A	1.084	1.00
21_L	83_S	1.076	1.00
27_S	208_L	1.074	1.00
102_D	109_V	1.072	1.00
37_R	106_G	1.065	1.00
147_E	156_V	1.063	1.00
143_D	158_L	1.062	1.00
4_I	36_F	1.060	1.00
47_T	115_Q	1.058	1.00
20_N	206_R	1.057	1.00
30_E	208_L	1.051	1.00
203_M	214_I	1.045	1.00
122_A	192_I	1.042	1.00
132_S	196_S	1.036	1.00
39_G	103_W	1.032	1.00
211_I	214_I	1.021	1.00
111_T	114_F	1.021	1.00
3_N	100_I	1.018	1.00
191_K	195_R	1.009	1.00
70_I	92_V	1.004	1.00
165_Q	169_K	1.003	1.00
37_R	104_S	0.991	1.00
28_I	108_V	0.989	1.00
48_A	52_I	0.987	1.00
38_V	42_T	0.980	1.00
84_L	89_Y	0.979	1.00
158_L	204_N	0.977	1.00
146_Y	156_V	0.967	1.00
212_I	215_L	0.967	1.00
26_Q	30_E	0.961	1.00
18_V	22_I	0.957	1.00
71_W	75_L	0.957	1.00
26_Q	208_L	0.954	1.00
11_K	45_G	0.939	1.00
29_K	84_L	0.937	1.00
11_K	14_D	0.928	1.00
167_L	170_I	0.927	1.00
31_L	34_N	0.919	1.00
44_G	72_A	0.918	1.00
145_V	202_V	0.918	1.00
137_V	201_I	0.913	1.00
25_R	84_L	0.909	1.00
94_Q	98_E	0.906	1.00
159_I	162_L	0.901	1.00
94_Q	97_E	0.894	1.00
31_L	36_F	0.889	1.00
148_K	154_A	0.886	1.00
85_Q	90_M	0.883	1.00
29_K	32_A	0.875	1.00
122_A	188_L	0.874	1.00
19_D	22_I	0.873	1.00
83_S	86_D	0.869	1.00
3_N	134_K	0.868	1.00
209_N	213_D	0.867	1.00
164_T	190_I	0.866	1.00
99_F	103_W	0.863	1.00
139_A	203_M	0.863	1.00
128_A	198_I	0.859	1.00
161_H	216_K	0.858	1.00
32_A	38_V	0.855	1.00
15_E	19_D	0.854	1.00
21_L	79_L	0.853	1.00
78_Y	82_F	0.853	1.00
8_I	40_I	0.843	1.00
135_T	199_R	0.834	1.00
138_V	141_N	0.832	1.00
125_A	192_I	0.825	1.00
146_Y	150_P	0.821	1.00
165_Q	168_R	0.821	1.00
181_T	194_E	0.820	1.00
46_S	183_E	0.815	1.00
60_I	65_L	0.815	1.00
6_L	31_L	0.813	1.00
100_I	132_S	0.813	1.00
29_K	108_V	0.807	1.00
25_R	87_L	0.806	1.00
143_D	210_R	0.805	1.00
15_E	20_N	0.796	1.00
197_K	217_G	0.794	1.00
52_I	56_R	0.792	1.00
146_Y	158_L	0.791	1.00
137_V	211_I	0.784	1.00
136_L	193_V	0.779	1.00
50_R	54_L	0.777	1.00
145_V	159_I	0.775	1.00
93_P	96_L	0.775	1.00
31_L	137_V	0.772	1.00
92_V	109_V	0.772	1.00
31_L	38_V	0.771	1.00
8_I	12_F	0.771	1.00
127_V	131_S	0.768	1.00
31_L	215_L	0.766	1.00
28_I	84_L	0.766	1.00
209_N	212_I	0.765	1.00
82_F	85_Q	0.764	1.00
6_L	137_V	0.762	1.00
25_R	80_V	0.759	1.00
163_T	166_D	0.746	1.00
152_I	183_E	0.742	1.00
95_S	98_E	0.742	1.00
167_L	171_L	0.738	1.00
53_K	81_M	0.737	1.00
159_I	173_G	0.737	1.00
106_G	109_V	0.736	1.00
15_E	18_V	0.729	1.00
188_L	191_K	0.726	1.00
194_E	200_V	0.726	1.00
95_S	102_D	0.725	1.00
95_S	99_F	0.724	1.00
28_I	38_V	0.724	1.00
46_S	49_R	0.720	1.00
66_D	114_F	0.718	1.00
193_V	198_I	0.716	1.00
97_E	101_Q	0.716	1.00
63_A	67_L	0.713	1.00
23_V	205_Y	0.709	1.00
82_F	86_D	0.707	1.00
188_L	192_I	0.707	1.00
118_Q	189_A	0.707	1.00
4_I	135_T	0.704	1.00
68_L	79_L	0.701	1.00
64_Y	101_Q	0.698	1.00
53_K	57_E	0.695	1.00
166_D	169_K	0.685	0.99
27_S	30_E	0.685	0.99
55_A	65_L	0.683	0.99
68_L	71_W	0.682	0.99
12_F	141_N	0.681	0.99
23_V	208_L	0.681	0.99
39_G	42_T	0.680	0.99
169_K	173_G	0.677	0.99
11_K	141_N	0.675	0.99
45_G	50_R	0.675	0.99
34_N	212_I	0.670	0.99
160_P	211_I	0.669	0.99
49_R	52_I	0.668	0.99
98_E	101_Q	0.667	0.99
33_D	89_Y	0.661	0.99
81_M	85_Q	0.661	0.99
149_D	156_V	0.659	0.99
3_N	6_L	0.659	0.99
109_V	112_G	0.657	0.99
189_A	193_V	0.657	0.99
192_I	196_S	0.652	0.99
172_E	187_P	0.651	0.99
95_S	130_A	0.650	0.99
113_G	116_P	0.650	0.99
24_L	28_I	0.649	0.99
211_I	215_L	0.647	0.99
102_D	105_H	0.646	0.99
25_R	29_K	0.645	0.99
53_K	56_R	0.644	0.99
84_L	108_V	0.643	0.99
168_R	172_E	0.641	0.99
36_F	134_K	0.641	0.99
88_A	91_H	0.639	0.99
40_I	80_V	0.638	0.99
4_I	215_L	0.634	0.99
170_I	173_G	0.631	0.99
169_K	172_E	0.623	0.99
39_G	127_V	0.622	0.99
103_W	109_V	0.621	0.99
90_M	106_G	0.620	0.99
140_T	200_V	0.619	0.99
8_I	13_F	0.615	0.99
51_Y	55_A	0.614	0.99
185_L	189_A	0.612	0.99
39_G	133_S	0.610	0.99
168_R	171_L	0.609	0.99
185_L	200_V	0.607	0.99
157_K	161_H	0.601	0.99
213_D	216_K	0.597	0.99
153_Y	156_V	0.597	0.99
4_I	38_V	0.596	0.99
68_L	75_L	0.595	0.99
129_E	192_I	0.592	0.99
26_Q	86_D	0.587	0.98
94_Q	103_W	0.586	0.98
21_L	25_R	0.586	0.98
11_K	140_T	0.586	0.98
79_L	82_F	0.585	0.98
85_Q	91_H	0.584	0.98
95_S	101_Q	0.581	0.98
81_M	97_E	0.581	0.98
167_L	172_E	0.580	0.98
99_F	130_A	0.572	0.98
49_R	117_G	0.571	0.98
59_G	62_E	0.571	0.98
185_L	202_V	0.569	0.98
6_L	38_V	0.566	0.98
20_N	24_L	0.565	0.98
60_I	64_Y	0.563	0.98
114_F	119_S	0.563	0.98
96_L	130_A	0.558	0.98
168_R	187_P	0.554	0.98
45_G	183_E	0.552	0.98
84_L	87_L	0.548	0.98
99_F	109_V	0.545	0.98
141_N	150_P	0.544	0.97
27_S	207_K	0.543	0.97
38_V	108_V	0.536	0.97
167_L	173_G	0.531	0.97
158_L	210_R	0.529	0.97
190_I	200_V	0.527	0.97
50_R	53_K	0.527	0.97
26_Q	33_D	0.522	0.97
146_Y	185_L	0.521	0.97
20_N	205_Y	0.517	0.97
52_I	69_G	0.514	0.96
208_L	212_I	0.513	0.96
45_G	49_R	0.512	0.96
14_D	48_A	0.511	0.96
52_I	65_L	0.508	0.96
85_Q	92_V	0.507	0.96
6_L	139_A	0.506	0.96
135_T	214_I	0.506	0.96
115_Q	119_S	0.503	0.96
142_V	146_Y	0.502	0.96
68_L	78_Y	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	0.9163	100	0.24	Contact Map
2j5vA	2	0.8282	100	0.256	Contact Map
3ab4A	7	0.9515	100	0.265	Contact Map
3l76A	2	0.9515	100	0.266	Contact Map
2brxA	5	0.9515	100	0.278	Contact Map
2j4jA	5	0.9912	100	0.282	Contact Map
2akoA	2	0.9383	100	0.292	Contact Map
3c1mA	3	0.9515	100	0.293	Contact Map
2j0wA	2	0.9427	100	0.301	Contact Map
3nwyA	5	0.9427	100	0.306	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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