YWQD - BACSU - GREMLIN Contacts

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YWQD - Tyrosine-protein kinase YwqD

UniProt:	P96716	Sequences: MALRKNRGSRMQRNVIAMTEPKSLNSEQYRTIRTNIEFASVDRQMKSVMITSACPGEGKSTTAANLAVVFAQQGKKVLLIDADLRKPTVHTAFFLENTVGLTSVLLKKSSMEQAVQASNEKHLDVLTSGPIPPNPAELLSSKWMKELAYEACAAYDMVIFDTPPILAVADAQILGNVADGSVLVISSGKTEKEQAAKAKEALATCKSKLLGAIMNGKKLSKHSEYGYYGTKDNFMQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	237 (185)
Sequences:	14999 (10269)
Seq/√Len:	755.0

ECOLI - ETK WZC MRP MIND BCSQ
BACSU - YWQD YVEL SALA YLXH SOJ MIND
HALSA - Q9HHZ7 Q9HQY5 Q9HNF1 Q9HQJ7 Q9HHU2 O54573 Q9HHL5 O51969 O51991
SULSO - Q97ZW4 Q97VX7 Q981B3 Q97WA2 Q97YM8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_D	155_Y	4.327	1.00
186_S	216_G	4.285	1.00
63_A	159_I	3.794	1.00
70_F	157_M	3.300	1.00
75_K	157_M	3.180	1.00
49_M	178_A	3.054	1.00
47_S	152_C	2.681	1.00
49_M	162_T	2.603	1.00
117_A	124_D	2.562	1.00
78_L	155_Y	2.348	1.00
180_G	210_L	2.284	1.00
76_K	156_D	2.107	1.00
71_A	123_L	2.106	1.00
62_T	213_I	2.049	1.00
63_A	79_L	2.044	1.00
145_K	177_V	2.034	1.00
104_V	114_A	2.032	1.00
82_A	160_F	1.996	1.00
75_K	156_D	1.981	1.00
187_S	214_M	1.972	1.00
112_E	154_A	1.953	1.00
110_S	113_Q	1.941	1.00
46_K	180_G	1.896	1.00
50_I	66_L	1.862	1.00
64_A	89_V	1.851	1.00
64_A	93_F	1.838	1.00
79_L	89_V	1.759	1.00
82_A	101_L	1.738	1.00
47_S	160_F	1.706	1.00
109_S	114_A	1.682	1.00
92_A	190_T	1.665	1.00
78_L	151_A	1.646	1.00
80_I	160_F	1.611	1.00
62_T	215_N	1.602	1.00
58_G	215_N	1.601	1.00
214_M	228_Y	1.592	1.00
70_F	159_I	1.563	1.00
183_L	198_A	1.563	1.00
148_A	160_F	1.548	1.00
95_L	125_V	1.529	1.00
199_K	203_A	1.476	1.00
67_A	159_I	1.439	1.00
70_F	77_V	1.424	1.00
182_V	213_I	1.421	1.00
103_S	130_P	1.421	1.00
180_G	211_G	1.416	1.00
64_A	92_A	1.409	1.00
67_A	79_L	1.366	1.00
50_I	182_V	1.365	1.00
100_G	129_G	1.361	1.00
147_L	151_A	1.352	1.00
152_C	179_D	1.346	1.00
65_N	68_V	1.337	1.00
184_V	215_N	1.336	1.00
52_S	57_E	1.311	1.00
60_S	89_V	1.309	1.00
109_S	113_Q	1.300	1.00
114_A	126_L	1.296	1.00
100_G	103_S	1.260	1.00
68_V	72_Q	1.259	1.00
115_V	124_D	1.252	1.00
71_A	122_H	1.240	1.00
50_I	63_A	1.237	1.00
116_Q	127_T	1.234	1.00
52_S	59_K	1.203	1.00
47_S	178_A	1.202	1.00
145_K	149_Y	1.194	1.00
99_V	109_S	1.183	1.00
150_E	154_A	1.181	1.00
104_V	147_L	1.162	1.00
144_M	147_L	1.134	1.00
99_V	103_S	1.118	1.00
76_K	154_A	1.118	1.00
186_S	189_K	1.115	1.00
137_E	141_S	1.112	1.00
93_F	123_L	1.111	1.00
62_T	184_V	1.109	1.00
187_S	217_K	1.088	1.00
54_C	57_E	1.063	1.00
102_T	106_L	1.062	1.00
67_A	123_L	1.047	1.00
146_E	150_E	1.047	1.00
60_S	161_D	1.043	1.00
87_P	90_H	1.029	1.00
90_H	127_T	1.022	1.00
191_E	194_Q	1.017	1.00
59_K	83_D	1.011	1.00
165_I	198_A	1.004	1.00
53_A	57_E	0.999	1.00
202_L	207_S	0.994	1.00
78_L	158_V	0.993	1.00
185_I	195_A	0.984	1.00
180_G	208_K	0.979	1.00
88_T	92_A	0.977	1.00
54_C	194_Q	0.968	1.00
188_G	191_E	0.965	1.00
82_A	173_I	0.955	1.00
143_W	146_E	0.950	1.00
84_L	169_A	0.948	1.00
104_V	126_L	0.945	1.00
221_K	224_E	0.944	1.00
111_M	126_L	0.941	1.00
144_M	148_A	0.938	1.00
84_L	102_T	0.935	1.00
138_L	142_K	0.926	1.00
62_T	66_L	0.908	1.00
53_A	183_L	0.898	1.00
90_H	97_N	0.897	1.00
46_K	179_D	0.895	1.00
89_V	125_V	0.895	1.00
49_M	174_L	0.889	1.00
81_D	90_H	0.882	1.00
89_V	92_A	0.879	1.00
149_Y	152_C	0.875	1.00
111_M	115_V	0.874	1.00
67_A	89_V	0.872	1.00
50_I	62_T	0.870	1.00
99_V	114_A	0.865	1.00
74_G	122_H	0.860	1.00
112_E	150_E	0.859	1.00
138_L	141_S	0.858	1.00
181_S	207_S	0.857	1.00
139_L	142_K	0.851	1.00
82_A	144_M	0.849	1.00
48_V	157_M	0.836	1.00
51_T	198_A	0.830	1.00
160_F	178_A	0.827	1.00
69_V	73_Q	0.820	1.00
47_S	148_A	0.816	1.00
115_V	155_Y	0.816	1.00
103_S	108_K	0.813	1.00
120_E	123_L	0.812	1.00
185_I	212_A	0.808	1.00
46_K	152_C	0.800	1.00
68_V	123_L	0.797	1.00
111_M	114_A	0.795	1.00
68_V	120_E	0.793	1.00
115_V	126_L	0.790	1.00
181_S	202_L	0.786	1.00
175_G	207_S	0.780	1.00
124_D	127_T	0.779	1.00
51_T	170_D	0.779	1.00
162_T	173_I	0.778	1.00
147_L	150_E	0.777	1.00
110_S	150_E	0.769	1.00
78_L	115_V	0.763	1.00
137_E	140_S	0.763	1.00
81_D	87_P	0.763	1.00
77_V	156_D	0.762	1.00
146_E	149_Y	0.760	1.00
118_S	121_K	0.759	1.00
76_K	124_D	0.759	1.00
183_L	209_L	0.756	1.00
69_V	72_Q	0.756	1.00
83_D	86_K	0.755	1.00
47_S	158_V	0.753	1.00
222_H	226_G	0.752	1.00
112_E	116_Q	0.750	1.00
101_L	126_L	0.748	1.00
51_T	181_S	0.748	1.00
77_V	159_I	0.747	1.00
49_M	181_S	0.743	1.00
126_L	147_L	0.738	1.00
151_A	154_A	0.732	1.00
99_V	113_Q	0.725	1.00
200_E	203_A	0.723	1.00
111_M	150_E	0.721	1.00
101_L	104_V	0.721	1.00
77_V	157_M	0.720	1.00
113_Q	116_Q	0.713	1.00
162_T	174_L	0.709	1.00
197_K	200_E	0.708	1.00
88_T	190_T	0.705	1.00
48_V	159_I	0.704	1.00
222_H	225_Y	0.704	1.00
83_D	164_P	0.703	1.00
55_P	167_A	0.698	1.00
79_L	123_L	0.698	1.00
51_T	162_T	0.693	1.00
115_V	118_S	0.691	1.00
60_S	88_T	0.690	1.00
85_R	170_D	0.688	1.00
196_A	200_E	0.686	1.00
80_I	158_V	0.679	1.00
200_E	204_T	0.677	1.00
214_M	217_K	0.677	1.00
53_A	198_A	0.675	1.00
169_A	173_I	0.674	1.00
172_Q	175_G	0.671	1.00
119_N	122_H	0.667	1.00
71_A	77_V	0.665	1.00
47_S	179_D	0.663	1.00
103_S	106_L	0.661	1.00
134_N	137_E	0.659	1.00
76_K	122_H	0.653	1.00
190_T	195_A	0.646	1.00
77_V	123_L	0.645	1.00
91_T	193_E	0.644	1.00
88_T	91_T	0.644	1.00
89_V	93_F	0.640	1.00
79_L	159_I	0.640	1.00
102_T	138_L	0.639	1.00
180_G	209_L	0.637	1.00
142_K	146_E	0.634	1.00
186_S	190_T	0.628	1.00
78_L	126_L	0.627	1.00
58_G	161_D	0.622	1.00
198_A	202_L	0.621	1.00
118_S	125_V	0.620	1.00
223_S	227_Y	0.618	1.00
142_K	145_K	0.609	1.00
59_K	161_D	0.608	1.00
70_F	73_Q	0.608	1.00
104_V	111_M	0.601	1.00
219_L	222_H	0.598	1.00
155_Y	158_V	0.593	1.00
68_V	71_A	0.593	1.00
57_E	190_T	0.592	1.00
166_L	194_Q	0.589	1.00
114_A	118_S	0.589	1.00
152_C	158_V	0.588	1.00
64_A	79_L	0.586	1.00
93_F	125_V	0.585	1.00
185_I	214_M	0.584	1.00
187_S	224_E	0.583	1.00
53_A	201_A	0.583	1.00
66_L	182_V	0.583	1.00
104_V	107_K	0.581	1.00
76_K	155_Y	0.581	1.00
54_C	190_T	0.578	1.00
192_K	196_A	0.577	1.00
137_E	142_K	0.576	1.00
55_P	86_K	0.575	1.00
46_K	210_L	0.571	1.00
148_A	177_V	0.569	1.00
50_I	159_I	0.569	1.00
88_T	194_Q	0.568	1.00
102_T	134_N	0.566	1.00
65_N	69_V	0.561	1.00
144_M	174_L	0.560	1.00
148_A	151_A	0.558	1.00
169_A	172_Q	0.552	1.00
131_I	134_N	0.550	1.00
103_S	107_K	0.549	1.00
87_P	128_S	0.547	1.00
45_M	179_D	0.545	1.00
115_V	151_A	0.544	1.00
132_P	135_P	0.543	1.00
201_A	204_T	0.543	1.00
172_Q	201_A	0.542	1.00
45_M	158_V	0.541	1.00
137_E	168_V	0.540	1.00
53_A	166_L	0.538	1.00
171_A	201_A	0.538	1.00
102_T	129_G	0.537	1.00
111_M	151_A	0.536	1.00
183_L	199_K	0.534	1.00
196_A	199_K	0.532	1.00
60_S	64_A	0.531	1.00
111_M	154_A	0.526	1.00
195_A	199_K	0.526	1.00
124_D	154_A	0.525	1.00
168_V	171_A	0.524	1.00
48_V	180_G	0.521	1.00
136_A	167_A	0.521	1.00
116_Q	125_V	0.519	1.00
81_D	89_V	0.516	1.00
78_L	124_D	0.515	1.00
162_T	170_D	0.512	1.00
53_A	190_T	0.510	1.00
150_E	153_A	0.509	1.00
225_Y	228_Y	0.509	1.00
99_V	116_Q	0.508	1.00
56_G	86_K	0.508	1.00
141_S	144_M	0.507	1.00
91_T	189_K	0.503	1.00
87_P	131_I	0.502	1.00
57_E	87_P	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
3cioA	2	0.9747	100	0.179	Contact Map
3la6A	4	0.9789	100	0.179	Contact Map
4jlvA	1	0.8608	100	0.202	Contact Map
4jmpA	1	0.8861	100	0.203	Contact Map
4rz3A	2	0.8101	100	0.324	Contact Map
4pfsA	1	0.8059	100	0.336	Contact Map
3pg5A	2	0.7848	100	0.337	Contact Map
1g3qA	1	0.8017	100	0.357	Contact Map
3ea0A	2	0.8186	100	0.359	Contact Map
1wcv1	2	0.789	100	0.363	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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