KCY - HALSA - GREMLIN Contacts

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KCY - Cytidylate kinase

UniProt:	Q9HPA5	Sequences: MLVTISGPPGSGKSTVASTLADHLSYEHISGGDIFRGLAEDRDLTLAEFNELAEEDPQIDKDLDRRLRETARGRDDIVLESRLAGWMAGEYADIKIWLDAPMSVRARRIAEREDKTPAAARAETEAREESETQRYEEYYAIDFDDITIYDLSVNTARWGPDAVTDIVLDAVDAYQAERDEGPTPIENVRYQF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	192 (167)
Sequences:	9230 (5597)
Seq/√Len:	433.1

ECOLI - KAD AROL AROK
BACSU - KAD AROK YQAC
HALSA - KCY KAD KAD6 Y2452
SULSO - KCY KAD6 Y1041

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
129_E	133_Q	3.895	1.00
23_H	168_L	3.139	1.00
102_M	132_T	2.703	1.00
19_T	164_T	2.630	1.00
99_D	152_S	2.476	1.00
121_R	125_E	2.368	1.00
50_N	54_E	2.348	1.00
104_V	107_R	2.241	1.00
66_R	71_A	2.111	1.00
157_R	166_I	1.879	1.00
37_G	41_D	1.875	1.00
107_R	111_E	1.853	1.00
24_L	168_L	1.848	1.00
159_G	162_A	1.828	1.00
126_A	129_E	1.821	1.00
98_L	155_T	1.806	1.00
146_I	152_S	1.791	1.00
97_W	152_S	1.759	1.00
126_A	130_S	1.746	1.00
104_V	156_A	1.740	1.00
66_R	69_E	1.709	1.00
65_R	69_E	1.685	1.00
101_P	156_A	1.650	1.00
23_H	164_T	1.643	1.00
151_L	170_A	1.623	1.00
44_L	47_A	1.622	1.00
145_D	152_S	1.615	1.00
19_T	22_D	1.599	1.00
39_A	53_A	1.593	1.00
60_D	82_R	1.592	1.00
48_E	51_E	1.586	1.00
110_A	114_D	1.585	1.00
117_P	120_A	1.582	1.00
24_L	172_D	1.566	1.00
109_I	124_T	1.564	1.00
166_I	169_D	1.557	1.00
19_T	161_D	1.540	1.00
102_M	125_E	1.524	1.00
130_S	134_R	1.511	1.00
157_R	162_A	1.498	1.00
111_E	114_D	1.496	1.00
5_I	17_A	1.480	1.00
38_L	65_R	1.468	1.00
51_E	55_E	1.451	1.00
16_V	167_V	1.440	1.00
64_D	68_R	1.439	1.00
168_L	172_D	1.423	1.00
122_A	126_A	1.414	1.00
165_D	169_D	1.391	1.00
44_L	48_E	1.365	1.00
106_A	125_E	1.357	1.00
94_I	151_L	1.350	1.00
26_Y	76_D	1.333	1.00
16_V	164_T	1.312	1.00
39_A	50_N	1.308	1.00
62_D	66_R	1.304	1.00
42_R	47_A	1.303	1.00
15_T	160_P	1.296	1.00
96_I	167_V	1.253	1.00
164_T	168_L	1.225	1.00
132_T	136_E	1.224	1.00
136_E	142_D	1.216	1.00
11_S	100_A	1.190	1.00
86_W	147_T	1.181	1.00
39_A	49_F	1.177	1.00
97_W	141_I	1.175	1.00
19_T	23_H	1.174	1.00
155_T	163_V	1.159	1.00
142_D	146_I	1.141	1.00
95_K	150_D	1.134	1.00
63_L	67_L	1.129	1.00
18_S	22_D	1.122	1.00
60_D	63_L	1.122	1.00
29_I	79_L	1.119	1.00
60_D	66_R	1.104	1.00
96_I	170_A	1.097	1.00
120_A	123_E	1.097	1.00
94_I	170_A	1.095	1.00
166_I	170_A	1.093	1.00
32_G	36_R	1.082	1.00
122_A	125_E	1.073	1.00
61_K	64_D	1.060	1.00
125_E	129_E	1.059	1.00
71_A	89_G	1.052	1.00
2_L	89_G	1.049	1.00
47_A	50_N	1.046	1.00
52_L	57_P	1.044	1.00
128_E	132_T	1.043	1.00
113_E	116_T	1.040	1.00
98_L	167_V	1.035	1.00
20_L	167_V	1.035	1.00
6_S	141_I	1.034	1.00
38_L	43_D	1.032	1.00
51_E	54_E	1.013	1.00
49_F	52_L	1.010	1.00
165_D	168_L	1.004	1.00
103_S	121_R	1.003	1.00
162_A	165_D	0.996	1.00
102_M	129_E	0.996	1.00
100_A	155_T	0.988	1.00
20_L	164_T	0.987	1.00
87_M	90_E	0.986	1.00
114_D	117_P	0.980	1.00
43_D	46_L	0.977	1.00
111_E	115_K	0.969	1.00
153_V	170_A	0.966	1.00
38_L	41_D	0.962	1.00
2_L	93_D	0.959	1.00
106_A	121_R	0.958	1.00
103_S	107_R	0.931	1.00
57_P	126_A	0.929	1.00
119_A	123_E	0.928	1.00
110_A	121_R	0.921	1.00
70_T	74_R	0.918	1.00
142_D	145_D	0.914	1.00
30_S	33_D	0.908	1.00
65_R	68_R	0.907	1.00
23_H	172_D	0.899	1.00
60_D	64_D	0.891	1.00
86_W	90_E	0.884	1.00
60_D	71_A	0.881	1.00
97_W	132_T	0.878	1.00
49_F	53_A	0.870	1.00
8_P	131_E	0.862	1.00
160_P	164_T	0.860	1.00
79_L	84_A	0.858	1.00
62_D	65_R	0.855	1.00
4_T	84_A	0.849	1.00
18_S	28_H	0.847	1.00
162_A	166_I	0.833	1.00
153_V	163_V	0.828	1.00
39_A	46_L	0.822	1.00
38_L	62_D	0.822	1.00
6_S	95_K	0.818	1.00
4_T	92_A	0.815	1.00
157_R	163_V	0.812	1.00
131_E	135_Y	0.806	1.00
48_E	52_L	0.805	1.00
110_A	120_A	0.799	1.00
111_E	116_T	0.785	1.00
47_A	51_E	0.785	1.00
34_I	38_L	0.783	1.00
101_P	104_V	0.782	1.00
97_W	150_D	0.779	1.00
10_G	109_I	0.771	1.00
113_E	117_P	0.768	1.00
143_F	147_T	0.764	1.00
18_S	21_A	0.762	1.00
110_A	113_E	0.750	1.00
48_E	61_K	0.748	1.00
61_K	65_R	0.748	1.00
154_N	157_R	0.746	1.00
103_S	125_E	0.744	1.00
91_Y	149_Y	0.739	1.00
87_M	137_E	0.738	1.00
145_D	148_I	0.734	1.00
104_V	157_R	0.730	1.00
34_I	64_D	0.721	1.00
161_D	165_D	0.721	1.00
45_T	48_E	0.717	1.00
123_E	126_A	0.715	1.00
92_A	149_Y	0.713	1.00
69_E	72_R	0.713	1.00
14_S	80_E	0.710	1.00
27_E	75_D	0.710	1.00
8_P	105_R	0.706	1.00
102_M	128_E	0.701	1.00
94_I	171_V	0.692	1.00
16_V	163_V	0.689	1.00
35_F	39_A	0.684	1.00
3_V	94_I	0.678	1.00
35_F	63_L	0.667	1.00
17_A	28_H	0.666	1.00
106_A	110_A	0.665	1.00
84_A	88_A	0.660	1.00
89_G	143_F	0.657	0.99
29_I	77_I	0.657	0.99
3_V	171_V	0.656	0.99
60_D	67_L	0.654	0.99
16_V	160_P	0.648	0.99
12_G	15_T	0.648	0.99
134_R	138_Y	0.643	0.99
66_R	70_T	0.640	0.99
52_L	130_S	0.633	0.99
118_A	121_R	0.630	0.99
5_I	78_V	0.622	0.99
2_L	77_I	0.617	0.99
76_D	93_D	0.612	0.99
99_D	141_I	0.607	0.99
21_A	28_H	0.607	0.99
27_E	66_R	0.607	0.99
26_Y	77_I	0.607	0.99
20_L	78_V	0.604	0.99
52_L	55_E	0.603	0.99
20_L	168_L	0.603	0.99
102_M	121_R	0.599	0.99
42_R	50_N	0.594	0.99
86_W	145_D	0.593	0.99
57_P	136_E	0.592	0.99
153_V	166_I	0.590	0.99
154_N	166_I	0.588	0.99
67_L	71_A	0.587	0.99
155_T	167_V	0.587	0.99
9_P	123_E	0.586	0.99
52_L	56_D	0.584	0.99
38_L	46_L	0.579	0.99
5_I	20_L	0.576	0.99
135_Y	138_Y	0.569	0.99
37_G	66_R	0.569	0.99
66_R	72_R	0.568	0.99
103_S	106_A	0.566	0.99
19_T	160_P	0.566	0.99
8_P	11_S	0.565	0.98
46_L	49_F	0.562	0.98
27_E	77_I	0.560	0.98
77_I	92_A	0.560	0.98
64_D	67_L	0.556	0.98
90_E	143_F	0.551	0.98
130_S	133_Q	0.549	0.98
12_G	108_R	0.547	0.98
5_I	98_L	0.545	0.98
31_G	34_I	0.544	0.98
10_G	124_T	0.541	0.98
119_A	122_A	0.540	0.98
35_F	53_A	0.539	0.98
50_N	130_S	0.537	0.98
7_G	10_G	0.536	0.98
7_G	11_S	0.536	0.98
86_W	143_F	0.535	0.98
127_R	131_E	0.531	0.98
121_R	124_T	0.529	0.98
129_E	132_T	0.528	0.98
112_R	116_T	0.524	0.98
86_W	138_Y	0.523	0.98
23_H	165_D	0.523	0.98
20_L	171_V	0.521	0.97
67_L	72_R	0.520	0.97
85_G	88_A	0.518	0.97
99_D	154_N	0.517	0.97
57_P	61_K	0.516	0.97
64_D	137_E	0.515	0.97
116_T	119_A	0.509	0.97
2_L	91_Y	0.509	0.97
141_I	150_D	0.507	0.97
147_T	150_D	0.506	0.97
79_L	89_G	0.505	0.97
37_G	69_E	0.504	0.97
118_A	127_R	0.503	0.97
42_R	56_D	0.501	0.97
83_L	88_A	0.500	0.97

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
4qbgB	1	0.8958	100	0.384	Contact Map
2xb4A	4	0.8698	99.9	0.404	Contact Map
3tlxA	1	0.8802	99.9	0.407	Contact Map
4jzkA	1	0.875	99.9	0.408	Contact Map
1akyA	1	0.8906	99.9	0.408	Contact Map
3be4A	1	0.8594	99.9	0.411	Contact Map
2c95A	1	0.901	99.9	0.415	Contact Map
3gmtA	1	0.7865	99.9	0.416	Contact Map
4pzlA	2	0.8854	99.9	0.418	Contact Map
1zd8A	1	0.8906	99.9	0.42	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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