YBDM - BACSU - GREMLIN Contacts

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YBDM - Probable serine/threonine-protein kinase YbdM

UniProt:	O31435	Sequences: MALKLLKKLLFDRPLKNGVILNHQYKIEECLGMGGYGLVYLCTDILAQTPYVLKQLRPTKAKKEKEKVRFQQEIKLLKNIHHPQIPGFIDEFIIDGQAYYVMQFIEGENIEELLFFRKQPFTELMALQLISQLLEIIEYLHDRLIFHSDIRTPNIIINDGRLCLIDFGLAKQLTPEEMEEIKVRKQDDFFDLGETLLFLLYSQYKGKKKKNGTWLEELTLTKEVTLLLKRLLGIEEEYQHTASIREDLNRAIQSVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	256 (223)
Sequences:	94843 (58256)
Seq/√Len:	3901.1

ECOLI - YEGI
BACSU - YBDM PRKC PKN1 YRZF
HALSA - Q9HR00
SULSO - Q97U18 Q97U41 Q97WD5 Q97ZY9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
156_I	165_I	3.104	1.00
41_L	50_P	3.096	1.00
130_I	196_L	3.071	1.00
29_E	41_L	2.780	1.00
30_C	38_L	2.535	1.00
189_F	231_L	2.485	1.00
42_C	51_Y	2.372	1.00
42_C	53_L	2.345	1.00
138_E	242_A	2.321	1.00
230_R	239_Q	2.315	1.00
138_E	142_D	2.308	1.00
123_E	221_T	2.267	1.00
44_D	47_A	2.220	1.00
230_R	247_D	2.173	1.00
81_H	87_G	2.123	1.00
231_L	244_I	2.117	1.00
30_C	33_M	2.113	1.00
111_E	153_P	2.099	1.00
132_Q	162_L	2.049	1.00
26_K	45_I	2.034	1.00
158_N	161_R	2.012	1.00
82_H	139_Y	2.010	1.00
132_Q	161_R	1.992	1.00
134_L	192_L	1.924	1.00
133_L	155_I	1.903	1.00
26_K	43_T	1.894	1.00
137_I	192_L	1.890	1.00
103_Q	163_C	1.887	1.00
155_I	162_L	1.886	1.00
41_L	104_F	1.874	1.00
193_G	231_L	1.849	1.00
122_T	125_M	1.765	1.00
28_E	43_T	1.764	1.00
89_I	103_Q	1.753	1.00
43_T	50_P	1.705	1.00
109_N	112_E	1.680	1.00
158_N	163_C	1.659	1.00
174_T	187_D	1.651	1.00
24_Q	44_D	1.648	1.00
87_G	103_Q	1.617	1.00
30_C	40_Y	1.539	1.00
150_I	195_T	1.537	1.00
137_I	241_T	1.519	1.00
126_A	200_L	1.482	1.00
130_I	199_L	1.481	1.00
137_I	150_I	1.461	1.00
138_E	245_R	1.446	1.00
134_L	244_I	1.446	1.00
189_F	241_T	1.431	1.00
135_E	245_R	1.430	1.00
84_Q	136_I	1.428	1.00
53_L	101_V	1.426	1.00
43_T	48_Q	1.422	1.00
240_H	243_S	1.404	1.00
128_Q	132_Q	1.403	1.00
28_E	41_L	1.397	1.00
130_I	192_L	1.392	1.00
227_L	247_D	1.384	1.00
200_L	224_V	1.382	1.00
226_L	247_D	1.381	1.00
33_M	38_L	1.373	1.00
142_D	242_A	1.362	1.00
84_Q	135_E	1.361	1.00
239_Q	247_D	1.357	1.00
105_I	158_N	1.352	1.00
49_T	89_I	1.344	1.00
145_I	170_A	1.333	1.00
136_I	164_L	1.330	1.00
111_E	115_F	1.321	1.00
131_S	135_E	1.303	1.00
155_I	195_T	1.286	1.00
129_L	162_L	1.277	1.00
239_Q	244_I	1.272	1.00
225_T	229_K	1.262	1.00
55_Q	97_Q	1.258	1.00
227_L	239_Q	1.254	1.00
196_L	227_L	1.252	1.00
148_S	183_V	1.247	1.00
126_A	199_L	1.246	1.00
105_I	163_C	1.233	1.00
114_L	198_F	1.222	1.00
141_H	241_T	1.214	1.00
214_W	217_E	1.212	1.00
134_L	245_R	1.210	1.00
139_Y	143_R	1.184	1.00
51_Y	101_V	1.183	1.00
228_L	232_L	1.178	1.00
39_V	52_V	1.176	1.00
241_T	244_I	1.176	1.00
152_T	195_T	1.165	1.00
131_S	245_R	1.158	1.00
134_L	241_T	1.153	1.00
111_E	198_F	1.152	1.00
79_N	172_Q	1.146	1.00
149_D	154_N	1.144	1.00
50_P	104_F	1.143	1.00
198_F	204_Y	1.143	1.00
55_Q	99_Y	1.114	1.00
27_I	40_Y	1.105	1.00
152_T	198_F	1.090	1.00
53_L	99_Y	1.085	1.00
147_H	150_I	1.071	1.00
227_L	231_L	1.067	1.00
133_L	162_L	1.067	1.00
194_E	232_L	1.066	1.00
51_Y	89_I	1.065	1.00
227_L	244_I	1.065	1.00
177_E	187_D	1.056	1.00
40_Y	55_Q	1.055	1.00
105_I	156_I	1.054	1.00
174_T	177_E	1.052	1.00
226_L	230_R	1.048	1.00
157_I	162_L	1.042	1.00
108_E	165_I	1.039	1.00
88_F	91_E	1.036	1.00
186_Q	240_H	1.035	1.00
86_P	165_I	1.022	1.00
76_L	170_A	1.019	1.00
230_R	233_G	1.017	1.00
92_F	99_Y	1.015	1.00
86_P	102_M	1.015	1.00
58_P	93_I	1.014	1.00
79_N	143_R	1.000	1.00
192_L	231_L	0.994	1.00
154_N	166_D	0.991	1.00
52_V	104_F	0.989	1.00
28_E	50_P	0.987	1.00
144_L	185_K	0.986	1.00
67_K	71_Q	0.982	1.00
50_P	106_E	0.969	1.00
86_P	105_I	0.966	1.00
128_Q	161_R	0.963	1.00
194_E	204_Y	0.963	1.00
135_E	138_E	0.962	1.00
113_L	121_F	0.961	1.00
138_E	241_T	0.958	1.00
92_F	101_V	0.954	1.00
233_G	239_Q	0.951	1.00
183_V	187_D	0.950	1.00
113_L	157_I	0.942	1.00
230_R	243_S	0.933	1.00
133_L	195_T	0.929	1.00
31_L	104_F	0.928	1.00
145_I	172_Q	0.923	1.00
85_I	140_L	0.916	1.00
77_L	88_F	0.903	1.00
44_D	49_T	0.895	1.00
71_Q	75_K	0.893	1.00
192_L	241_T	0.886	1.00
81_H	139_Y	0.884	1.00
105_I	165_I	0.880	1.00
243_S	246_E	0.875	1.00
125_M	128_Q	0.874	1.00
25_Y	90_D	0.872	1.00
151_R	154_N	0.871	1.00
150_I	164_L	0.870	1.00
107_G	160_G	0.866	1.00
27_I	42_C	0.864	1.00
88_F	100_Y	0.859	1.00
133_L	150_I	0.858	1.00
177_E	183_V	0.856	1.00
109_N	153_P	0.853	1.00
121_F	129_L	0.847	1.00
194_E	198_F	0.841	1.00
140_L	167_F	0.840	1.00
84_Q	161_R	0.837	1.00
108_E	112_E	0.836	1.00
113_L	125_M	0.833	1.00
197_L	201_Y	0.832	1.00
231_L	239_Q	0.832	1.00
137_I	141_H	0.832	1.00
84_Q	132_Q	0.831	1.00
80_I	145_I	0.827	1.00
193_G	232_L	0.826	1.00
129_L	157_I	0.820	1.00
192_L	196_L	0.806	1.00
200_L	220_L	0.800	1.00
203_Q	207_K	0.799	1.00
114_L	199_L	0.798	1.00
123_E	126_A	0.796	1.00
190_F	232_L	0.794	1.00
214_W	225_T	0.782	1.00
222_K	226_L	0.778	1.00
151_R	166_D	0.775	1.00
38_L	57_R	0.774	1.00
74_I	91_E	0.772	1.00
242_A	246_E	0.771	1.00
186_Q	237_E	0.770	1.00
189_F	244_I	0.763	1.00
108_E	113_L	0.763	1.00
80_I	139_Y	0.762	1.00
133_L	192_L	0.762	1.00
190_F	194_E	0.760	1.00
38_L	55_Q	0.759	1.00
194_E	197_L	0.759	1.00
111_E	152_T	0.757	1.00
139_Y	142_D	0.757	1.00
42_C	101_V	0.757	1.00
140_L	145_I	0.756	1.00
77_L	102_M	0.754	1.00
197_L	232_L	0.753	1.00
125_M	160_G	0.749	1.00
127_L	224_V	0.749	1.00
222_K	225_T	0.748	1.00
34_G	37_G	0.744	1.00
241_T	245_R	0.742	1.00
24_Q	46_L	0.740	1.00
25_Y	101_V	0.736	1.00
213_T	217_E	0.734	1.00
213_T	216_E	0.732	1.00
82_H	135_E	0.729	1.00
32_G	39_V	0.729	1.00
216_E	225_T	0.727	1.00
194_E	205_K	0.723	1.00
176_E	187_D	0.720	1.00
133_L	136_I	0.719	1.00
24_Q	90_D	0.718	1.00
126_A	196_L	0.717	1.00
88_F	102_M	0.713	1.00
80_I	140_L	0.712	1.00
72_Q	75_K	0.711	1.00
189_F	239_Q	0.707	1.00
193_G	228_L	0.704	1.00
108_E	117_R	0.700	1.00
75_K	78_K	0.699	1.00
83_P	161_R	0.692	1.00
33_M	57_R	0.689	1.00
32_G	52_V	0.680	1.00
76_L	145_I	0.679	1.00
239_Q	243_S	0.675	1.00
44_D	48_Q	0.672	1.00
106_E	158_N	0.671	1.00
85_I	139_Y	0.671	1.00
82_H	85_I	0.664	1.00
113_L	129_L	0.660	1.00
229_K	233_G	0.658	1.00
123_E	127_L	0.657	1.00
71_Q	93_I	0.655	1.00
190_F	233_G	0.652	1.00
74_I	78_K	0.652	1.00
148_S	171_K	0.651	1.00
134_L	189_F	0.651	1.00
197_L	228_L	0.647	1.00
105_I	157_I	0.647	1.00
220_L	224_V	0.645	1.00
83_P	135_E	0.644	1.00
173_L	185_K	0.641	1.00
28_E	42_C	0.635	1.00
110_I	199_L	0.634	1.00
110_I	195_T	0.630	1.00
118_K	125_M	0.622	1.00
34_G	52_V	0.621	1.00
27_I	55_Q	0.621	1.00
214_W	218_L	0.613	1.00
196_L	224_V	0.613	1.00
22_N	25_Y	0.613	1.00
141_H	188_D	0.611	1.00
122_T	126_A	0.611	1.00
174_T	178_M	0.611	1.00
192_L	244_I	0.610	1.00
94_I	97_Q	0.607	1.00
121_F	126_A	0.607	1.00
197_L	206_G	0.607	1.00
179_E	234_I	0.604	1.00
105_I	108_E	0.602	1.00
87_G	163_C	0.601	1.00
204_Y	207_K	0.599	1.00
68_V	71_Q	0.599	1.00
187_D	191_D	0.599	1.00
141_H	185_K	0.596	1.00
221_T	224_V	0.596	1.00
27_I	53_L	0.593	1.00
132_Q	135_E	0.593	1.00
44_D	51_Y	0.590	1.00
58_P	61_A	0.588	1.00
76_L	172_Q	0.588	1.00
93_I	98_A	0.586	1.00
49_T	87_G	0.586	1.00
25_Y	51_Y	0.586	1.00
107_G	158_N	0.583	1.00
196_L	228_L	0.581	1.00
27_I	30_C	0.581	1.00
74_I	88_F	0.580	1.00
75_K	79_N	0.574	1.00
103_Q	158_N	0.564	1.00
47_A	78_K	0.561	1.00
140_L	164_L	0.561	1.00
66_E	69_R	0.559	1.00
73_E	77_L	0.559	1.00
129_L	199_L	0.556	1.00
67_K	93_I	0.556	1.00
197_L	205_K	0.554	1.00
104_F	108_E	0.553	1.00
220_L	225_T	0.550	1.00
124_L	127_L	0.550	1.00
56_L	70_F	0.549	1.00
54_K	73_E	0.548	1.00
90_D	101_V	0.542	1.00
108_E	156_I	0.541	1.00
123_E	200_L	0.539	1.00
72_Q	76_L	0.539	1.00
243_S	247_D	0.538	1.00
129_L	155_I	0.537	1.00
189_F	193_G	0.536	1.00
129_L	133_L	0.535	1.00
123_E	220_L	0.533	1.00
114_L	152_T	0.532	1.00
244_I	247_D	0.532	1.00
54_K	166_D	0.531	1.00
68_V	72_Q	0.530	1.00
37_G	56_L	0.530	1.00
146_F	183_V	0.530	1.00
226_L	229_K	0.529	1.00
86_P	163_C	0.527	1.00
217_E	220_L	0.524	1.00
130_I	137_I	0.523	1.00
146_F	185_K	0.522	1.00
146_F	184_R	0.519	1.00
149_D	166_D	0.518	1.00
85_I	167_F	0.518	1.00
126_A	130_I	0.517	1.00
127_L	131_S	0.517	1.00
213_T	229_K	0.516	1.00
73_E	76_L	0.512	1.00
215_L	218_L	0.506	1.00
225_T	228_L	0.506	1.00
85_I	136_I	0.505	1.00
24_Q	45_I	0.505	1.00
146_F	187_D	0.504	1.00
65_K	68_V	0.503	1.00
123_E	224_V	0.503	1.00
223_E	226_L	0.501	1.00
57_R	60_K	0.500	1.00
58_P	94_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
4lqsA	1	0.9336	100	0.177	Contact Map
3zonA	1	0.8906	100	0.18	Contact Map
4c0tA	1	0.9219	100	0.187	Contact Map
4oliA	1	0.9062	100	0.19	Contact Map
4e5wA	2	0.9531	100	0.19	Contact Map
4dc2A	1	0.9062	100	0.191	Contact Map
3cblA	1	0.9883	100	0.195	Contact Map
4fl3A	1	0.9688	100	0.195	Contact Map
4qoxA	1	0.9648	100	0.196	Contact Map
4aszA	1	0.9336	100	0.196	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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