PKSD - BACSU - GREMLIN Contacts

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PKSD - Polyketide biosynthesis acyltransferase homolog PksD

UniProt:	O34877	Sequences: MNEPLVFMFSGQGSQYYHMGKELFKENTVFRQSMLEMDAIAARRIGTSIVEEIYHPGKRVSDPFDSILFSHPAIFMIEYSLYKVLEDRGIYPDYVLGSSLGEFAAAAVSGVSDAEDMLDCILEQAIIIQNSCDKGKMLAILDKPQLLNDHPQLFGNSELISINYDSHFVISGEEDHIRKIMEDLKEKQILCQLLPVSYAFHSSLIDPAESAYAEFLRSKSFQKPSIPIVSSLTGSCLHVMDENFFWNAVRKPMMFREAIRYLESQHTCKFIDLGPSGTLAAFVKQLIPGDSADRCCSIITPFHQELKNLNTVEYFRTPERKFTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	324 (287)
Sequences:	15407 (11387)
Seq/√Len:	672.2

ECOLI - FABD
BACSU - PKSD FABD PKSE PKSC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
158_E	203_S	3.737	1.00
254_M	257_E	3.249	1.00
138_L	181_M	3.033	1.00
178_R	193_L	2.549	1.00
38_D	48_S	2.476	1.00
83_K	86_E	2.449	1.00
113_D	116_D	2.388	1.00
9_F	82_Y	2.346	1.00
247_N	251_K	2.324	1.00
256_R	260_R	2.313	1.00
143_K	146_L	2.307	1.00
130_N	211_A	2.272	1.00
123_E	126_I	2.245	1.00
82_Y	108_V	2.213	1.00
150_H	187_K	2.210	1.00
206_D	250_R	2.110	1.00
144_P	148_N	2.085	1.00
213_A	243_N	2.045	1.00
75_F	117_M	1.954	1.00
6_V	267_T	1.949	1.00
51_E	55_H	1.898	1.00
86_E	91_Y	1.868	1.00
171_S	202_S	1.861	1.00
24_F	35_L	1.859	1.00
173_E	204_L	1.845	1.00
68_L	129_Q	1.827	1.00
231_S	258_A	1.824	1.00
170_I	180_I	1.821	1.00
181_M	193_L	1.804	1.00
37_M	114_A	1.789	1.00
111_V	224_P	1.788	1.00
156_N	173_E	1.787	1.00
34_M	76_M	1.782	1.00
213_A	246_W	1.779	1.00
174_E	193_L	1.755	1.00
33_S	83_K	1.744	1.00
243_N	247_N	1.744	1.00
29_V	87_D	1.737	1.00
123_E	215_F	1.701	1.00
33_S	36_E	1.700	1.00
136_K	177_I	1.692	1.00
183_D	187_K	1.677	1.00
94_Y	267_T	1.668	1.00
173_E	176_H	1.666	1.00
66_S	129_Q	1.659	1.00
181_M	185_K	1.653	1.00
235_S	261_Y	1.635	1.00
34_M	53_I	1.629	1.00
157_S	180_I	1.629	1.00
107_A	117_M	1.627	1.00
174_E	178_R	1.612	1.00
8_M	283_V	1.600	1.00
79_Y	107_A	1.579	1.00
263_E	287_I	1.576	1.00
96_L	258_A	1.572	1.00
78_E	104_A	1.551	1.00
229_V	236_C	1.549	1.00
229_V	261_Y	1.543	1.00
27_N	84_V	1.539	1.00
120_C	216_L	1.534	1.00
150_H	184_L	1.533	1.00
36_E	115_E	1.531	1.00
146_L	149_D	1.524	1.00
31_R	35_L	1.514	1.00
138_L	177_I	1.514	1.00
181_M	191_C	1.509	1.00
40_I	115_E	1.488	1.00
40_I	118_L	1.487	1.00
136_K	174_E	1.485	1.00
261_Y	265_Q	1.484	1.00
156_N	176_H	1.483	1.00
6_V	262_L	1.476	1.00
5_L	93_D	1.465	1.00
259_I	283_V	1.465	1.00
15_Q	19_M	1.452	1.00
160_I	171_S	1.449	1.00
95_V	226_I	1.433	1.00
38_D	50_V	1.421	1.00
142_D	189_I	1.413	1.00
7_F	92_P	1.411	1.00
122_L	126_I	1.406	1.00
21_K	25_K	1.403	1.00
20_G	77_I	1.395	1.00
148_N	152_Q	1.390	1.00
146_L	187_K	1.383	1.00
213_A	217_R	1.374	1.00
48_S	51_E	1.371	1.00
216_L	221_F	1.362	1.00
211_A	214_E	1.356	1.00
4_P	93_D	1.350	1.00
144_P	254_M	1.341	1.00
34_M	80_S	1.335	1.00
35_L	50_V	1.332	1.00
144_P	162_I	1.331	1.00
9_F	108_V	1.329	1.00
229_V	265_Q	1.300	1.00
96_L	262_L	1.295	1.00
229_V	258_A	1.292	1.00
153_L	183_D	1.288	1.00
227_P	236_C	1.286	1.00
140_I	147_L	1.275	1.00
50_V	54_Y	1.270	1.00
178_R	182_E	1.270	1.00
162_I	256_R	1.266	1.00
184_L	189_I	1.250	1.00
5_L	269_K	1.234	1.00
209_E	213_A	1.225	1.00
21_K	54_Y	1.223	1.00
178_R	181_M	1.214	1.00
162_I	168_F	1.186	1.00
142_D	147_L	1.184	1.00
183_D	186_E	1.174	1.00
136_K	193_L	1.174	1.00
259_I	286_L	1.171	1.00
7_F	273_L	1.170	1.00
211_A	215_F	1.158	1.00
36_E	83_K	1.152	1.00
182_E	185_K	1.147	1.00
214_E	217_R	1.145	1.00
94_Y	262_L	1.142	1.00
215_F	218_S	1.129	1.00
27_N	88_R	1.128	1.00
24_F	54_Y	1.125	1.00
63_P	66_S	1.117	1.00
206_D	209_E	1.114	1.00
150_H	183_D	1.108	1.00
4_P	268_C	1.103	1.00
127_I	211_A	1.099	1.00
79_Y	104_A	1.099	1.00
37_M	76_M	1.094	1.00
209_E	250_R	1.093	1.00
270_F	283_V	1.090	1.00
85_L	297_S	1.087	1.00
126_I	130_N	1.086	1.00
141_L	190_L	1.085	1.00
182_E	186_E	1.082	1.00
7_F	82_Y	1.082	1.00
32_Q	36_E	1.076	1.00
140_I	184_L	1.076	1.00
32_Q	35_L	1.075	1.00
164_Y	282_F	1.070	1.00
208_A	249_V	1.068	1.00
123_E	127_I	1.066	1.00
209_E	246_W	1.058	1.00
8_M	96_L	1.057	1.00
138_L	191_C	1.055	1.00
159_L	168_F	1.049	1.00
127_I	208_A	1.048	1.00
149_D	153_L	1.046	1.00
158_E	202_S	1.040	1.00
162_I	252_P	1.040	1.00
261_Y	264_S	1.039	1.00
127_I	215_F	1.038	1.00
179_K	183_D	1.038	1.00
8_M	270_F	1.035	1.00
68_L	125_A	1.034	1.00
159_L	162_I	1.031	1.00
140_I	170_I	1.029	1.00
22_E	26_E	1.028	1.00
212_Y	249_V	1.023	1.00
37_M	118_L	1.022	1.00
6_V	270_F	1.019	1.00
63_P	69_F	1.014	1.00
162_I	257_E	1.010	1.00
85_L	273_L	1.003	1.00
61_S	65_D	0.994	1.00
228_I	240_M	0.986	1.00
147_L	168_F	0.985	1.00
177_I	193_L	0.983	1.00
146_L	189_I	0.983	1.00
28_T	32_Q	0.982	1.00
18_H	21_K	0.976	1.00
134_K	174_E	0.974	1.00
29_V	33_S	0.973	1.00
231_S	248_A	0.972	1.00
149_D	152_Q	0.970	1.00
33_S	80_S	0.970	1.00
95_V	228_I	0.968	1.00
236_C	261_Y	0.963	1.00
82_Y	86_E	0.962	1.00
150_H	180_I	0.961	1.00
162_I	254_M	0.960	1.00
30_F	80_S	0.959	1.00
7_F	90_I	0.955	1.00
98_S	163_N	0.950	1.00
119_D	218_S	0.946	1.00
138_L	193_L	0.932	1.00
103_F	121_I	0.930	1.00
25_K	54_Y	0.929	1.00
95_V	108_V	0.927	1.00
75_F	79_Y	0.927	1.00
179_K	182_E	0.925	1.00
176_H	179_K	0.919	1.00
260_R	264_S	0.914	1.00
210_S	213_A	0.912	1.00
232_L	251_K	0.912	1.00
65_D	195_P	0.911	1.00
157_S	176_H	0.895	1.00
94_Y	265_Q	0.894	1.00
263_E	270_F	0.893	1.00
106_A	245_F	0.893	1.00
75_F	107_A	0.892	1.00
153_L	187_K	0.890	1.00
68_L	126_I	0.888	1.00
94_Y	229_V	0.887	1.00
166_S	285_Q	0.886	1.00
83_K	107_A	0.886	1.00
10_S	78_E	0.885	1.00
100_L	121_I	0.880	1.00
116_D	119_D	0.868	1.00
165_D	286_L	0.862	1.00
47_T	69_F	0.861	1.00
206_D	246_W	0.859	1.00
141_L	166_S	0.857	1.00
164_Y	285_Q	0.857	1.00
144_P	168_F	0.856	1.00
6_V	94_Y	0.854	1.00
84_V	87_D	0.847	1.00
210_S	214_E	0.846	1.00
84_V	88_R	0.840	1.00
206_D	210_S	0.835	1.00
256_R	286_L	0.831	1.00
102_E	231_S	0.831	1.00
112_S	221_F	0.829	1.00
34_M	50_V	0.828	1.00
53_I	77_I	0.825	1.00
237_L	240_M	0.819	1.00
75_F	121_I	0.819	1.00
217_R	242_E	0.809	1.00
36_E	40_I	0.808	1.00
121_I	125_A	0.800	1.00
255_F	283_V	0.800	1.00
147_L	170_I	0.795	1.00
52_E	69_F	0.795	1.00
263_E	268_C	0.793	1.00
20_G	30_F	0.790	1.00
52_E	63_P	0.783	1.00
145_Q	148_N	0.783	1.00
119_D	123_E	0.783	1.00
185_K	191_C	0.782	1.00
111_V	221_F	0.778	1.00
24_F	31_R	0.778	1.00
180_I	184_L	0.778	1.00
33_S	37_M	0.777	1.00
260_R	286_L	0.776	1.00
67_I	200_F	0.776	1.00
112_S	120_C	0.775	1.00
233_T	247_N	0.772	1.00
83_K	114_A	0.771	1.00
120_C	219_K	0.768	1.00
119_D	215_F	0.765	1.00
146_L	166_S	0.764	1.00
110_G	225_S	0.758	1.00
35_L	39_A	0.756	1.00
29_V	32_Q	0.754	1.00
74_I	78_E	0.752	1.00
147_L	151_P	0.752	1.00
30_F	33_S	0.752	1.00
52_E	55_H	0.752	1.00
142_D	146_L	0.748	1.00
283_V	294_R	0.748	1.00
138_L	170_I	0.747	1.00
234_G	257_E	0.746	1.00
154_F	176_H	0.742	1.00
30_F	77_I	0.740	1.00
196_V	200_F	0.737	1.00
260_R	290_D	0.736	1.00
233_T	237_L	0.734	1.00
257_E	260_R	0.731	1.00
14_S	74_I	0.729	1.00
263_E	290_D	0.728	1.00
113_D	222_Q	0.722	1.00
234_G	258_A	0.719	1.00
38_D	49_I	0.717	1.00
116_D	222_Q	0.715	1.00
91_Y	225_S	0.713	1.00
103_F	216_L	0.711	1.00
144_P	257_E	0.710	1.00
49_I	76_M	0.703	1.00
230_S	244_F	0.702	1.00
141_L	189_I	0.699	1.00
116_D	219_K	0.696	1.00
68_L	72_P	0.694	1.00
62_D	65_D	0.694	1.00
12_Q	196_V	0.693	1.00
96_L	255_F	0.693	1.00
259_I	270_F	0.693	1.00
214_E	218_S	0.690	1.00
228_I	237_L	0.688	1.00
205_I	249_V	0.687	1.00
5_L	271_I	0.686	1.00
79_Y	108_V	0.683	1.00
229_V	262_L	0.680	1.00
31_R	50_V	0.679	1.00
24_F	34_M	0.676	1.00
40_I	119_D	0.672	1.00
107_A	114_A	0.671	1.00
281_A	284_K	0.668	1.00
149_D	187_K	0.668	1.00
260_R	263_E	0.663	1.00
130_N	208_A	0.662	1.00
203_S	206_D	0.662	1.00
75_F	104_A	0.654	1.00
143_K	166_S	0.654	1.00
233_T	244_F	0.649	1.00
277_G	281_A	0.649	1.00
75_F	118_L	0.648	1.00
232_L	247_N	0.645	1.00
6_V	268_C	0.644	1.00
200_F	249_V	0.641	1.00
76_M	118_L	0.641	1.00
100_L	200_F	0.638	1.00
230_S	237_L	0.636	1.00
270_F	290_D	0.636	1.00
140_I	191_C	0.635	1.00
81_L	273_L	0.633	1.00
10_S	274_G	0.631	1.00
36_E	114_A	0.631	1.00
79_Y	83_K	0.630	1.00
128_I	205_I	0.627	1.00
28_T	31_R	0.627	1.00
94_Y	236_C	0.626	1.00
131_S	205_I	0.626	1.00
230_S	233_T	0.625	1.00
263_E	288_P	0.623	1.00
70_S	74_I	0.622	1.00
103_F	219_K	0.620	1.00
154_F	180_I	0.617	1.00
56_P	63_P	0.615	1.00
258_A	261_Y	0.614	1.00
114_A	118_L	0.614	1.00
134_K	173_E	0.612	1.00
146_L	150_H	0.612	1.00
228_I	239_V	0.612	1.00
156_N	203_S	0.611	1.00
120_C	212_Y	0.608	1.00
157_S	170_I	0.608	1.00
154_F	183_D	0.605	1.00
156_N	179_K	0.604	1.00
127_I	130_N	0.602	1.00
151_P	159_L	0.602	1.00
165_D	256_R	0.601	1.00
65_D	70_S	0.599	1.00
208_A	212_Y	0.599	1.00
235_S	257_E	0.598	1.00
107_A	112_S	0.594	1.00
139_A	167_H	0.594	1.00
143_K	147_L	0.593	1.00
71_H	124_Q	0.593	1.00
102_E	230_S	0.591	1.00
175_D	178_R	0.590	1.00
33_S	114_A	0.590	1.00
12_Q	71_H	0.588	1.00
192_Q	195_P	0.588	1.00
25_K	31_R	0.585	1.00
98_S	253_M	0.584	1.00
145_Q	149_D	0.583	1.00
128_I	198_Y	0.582	1.00
55_H	62_D	0.581	1.00
147_L	184_L	0.581	1.00
148_N	162_I	0.580	1.00
24_F	50_V	0.580	1.00
204_L	207_P	0.579	1.00
30_F	84_V	0.579	1.00
80_S	84_V	0.578	1.00
79_Y	118_L	0.578	1.00
207_P	210_S	0.577	1.00
106_A	111_V	0.576	1.00
170_I	177_I	0.575	1.00
29_V	84_V	0.575	1.00
35_L	38_D	0.573	1.00
78_E	273_L	0.572	1.00
246_W	250_R	0.569	1.00
262_L	267_T	0.568	1.00
33_S	79_Y	0.566	1.00
33_S	107_A	0.566	1.00
155_G	173_E	0.566	1.00
272_D	279_L	0.566	1.00
112_S	117_M	0.565	1.00
115_E	119_D	0.563	1.00
215_F	219_K	0.560	1.00
104_A	107_A	0.559	1.00
236_C	265_Q	0.558	1.00
49_I	73_A	0.557	1.00
232_L	244_F	0.557	1.00
134_K	207_P	0.556	1.00
148_N	252_P	0.555	1.00
36_E	39_A	0.555	1.00
12_Q	200_F	0.552	1.00
144_P	159_L	0.552	1.00
92_P	226_I	0.551	1.00
72_P	125_A	0.550	1.00
164_Y	167_H	0.550	1.00
209_E	247_N	0.549	1.00
288_P	291_S	0.548	1.00
29_V	83_K	0.548	1.00
82_Y	273_L	0.548	1.00
86_E	225_S	0.546	1.00
137_M	196_V	0.544	1.00
51_E	56_P	0.544	1.00
221_F	242_E	0.541	1.00
232_L	248_A	0.539	1.00
184_L	187_K	0.537	1.00
69_F	72_P	0.533	1.00
222_Q	225_S	0.531	1.00
118_L	122_L	0.531	1.00
136_K	178_R	0.528	1.00
92_P	95_V	0.527	1.00
12_Q	128_I	0.527	1.00
4_P	267_T	0.526	1.00
123_E	211_A	0.525	0.99
113_D	220_S	0.525	0.99
47_T	52_E	0.523	0.99
210_S	246_W	0.520	0.99
137_M	171_S	0.519	0.99
52_E	62_D	0.519	0.99
109_S	228_I	0.519	0.99
161_S	169_V	0.514	0.99
112_S	116_D	0.514	0.99
10_S	276_S	0.512	0.99
75_F	114_A	0.510	0.99
157_S	177_I	0.508	0.99
208_A	211_A	0.508	0.99
22_E	25_K	0.506	0.99
199_A	205_I	0.506	0.99
293_D	296_C	0.505	0.99
131_S	208_A	0.504	0.99
280_A	296_C	0.504	0.99
281_A	285_Q	0.503	0.99
199_A	204_L	0.500	0.99

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
4mz0A	2	0.966	100	0.044	Contact Map
2qo3A	2	0.9938	100	0.045	Contact Map
2hg4A	2	0.9846	100	0.059	Contact Map
4rl1A	1	0.9599	100	0.063	Contact Map
4qbuA	1	0.9846	100	0.072	Contact Map
3tzyA	1	0.9846	100	0.079	Contact Map
3ptwA	1	0.9506	100	0.093	Contact Map
2vz8A	2	0.9691	100	0.102	Contact Map
3hhdA	2	0.9691	100	0.116	Contact Map
3g87A	1	0.8642	100	0.127	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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