PKSB - BACSU - GREMLIN Contacts

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PKSB - Probable polyketide biosynthesis zinc-dependent hydrolase PksB

UniProt:	O34769	Sequences: MNLTYKVHPIKTRYQGWTNYCYIIEDIVSRSAIVVDPSWELSKITTTLSELEAELKAVALTHSHYDHVNLVDPLTKMFNAQVYMSKKEIDYYQFRCRNLISLDDHQTISIGNTRAQCLLTPGHTAGGMCYLFSESIFTGDTVFTEGCGICEDDGSSAEEMFDSIQRIKSEVSPHVRVYPGHSFGKSPGHSIKDLYQHNIYFQIDKKEYFVKFRTRKNQKGIFDFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	225 (180)
Sequences:	14954 (10355)
Seq/√Len:	771.8

ECOLI - YCBL GLO2
BACSU - PKSB YQGX YQJP YRKH YYBB YOBT YFLN
HALSA - Q9HNJ2 Q9HQ50 Q9HRG5 Q9HSD1 Q9HNJ9 O54647 O54661 Q9HS22 Q9HSH2
SULSO - Q7LYK3 Q97U88 Q97VU4 Q97UV2 Q97VU0 Q97UR2 Q97YZ2 Q97XZ1 Q97WC2 Q97Y13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_S	56_K	4.064	1.00
120_T	129_C	3.785	1.00
107_T	114_R	3.005	1.00
60_L	71_V	2.938	1.00
109_S	114_R	2.682	1.00
57_A	83_Y	2.577	1.00
107_T	116_Q	2.543	1.00
115_A	132_F	2.475	1.00
59_A	130_Y	2.426	1.00
117_C	128_M	2.403	1.00
116_Q	133_S	2.313	1.00
86_K	103_D	2.226	1.00
33_I	57_A	2.219	1.00
31_S	54_E	2.198	1.00
45_T	77_M	2.198	1.00
83_Y	100_I	2.139	1.00
32_A	53_A	1.956	1.00
81_Q	100_I	1.898	1.00
35_V	137_F	1.888	1.00
47_T	51_L	1.888	1.00
132_F	135_S	1.856	1.00
117_C	130_Y	1.810	1.00
25_E	53_A	1.803	1.00
57_A	81_Q	1.802	1.00
88_E	126_G	1.774	1.00
156_S	159_E	1.761	1.00
104_D	166_R	1.739	1.00
85_S	119_L	1.735	1.00
83_Y	102_L	1.726	1.00
22_Y	178_Y	1.705	1.00
131_L	175_V	1.637	1.00
103_D	106_Q	1.631	1.00
104_D	167_I	1.626	1.00
162_D	166_R	1.613	1.00
25_E	32_A	1.583	1.00
48_L	55_L	1.530	1.00
73_P	77_M	1.529	1.00
55_L	80_A	1.510	1.00
71_V	82_V	1.480	1.00
45_T	78_F	1.474	1.00
47_T	50_E	1.460	1.00
46_T	50_E	1.442	1.00
116_Q	131_L	1.434	1.00
45_T	49_S	1.419	1.00
168_K	193_D	1.412	1.00
85_S	128_M	1.408	1.00
33_I	59_A	1.387	1.00
35_V	61_T	1.383	1.00
113_T	132_F	1.375	1.00
129_C	136_I	1.356	1.00
100_I	106_Q	1.356	1.00
27_I	30_R	1.333	1.00
72_D	76_K	1.329	1.00
131_L	136_I	1.328	1.00
187_P	190_S	1.286	1.00
161_F	165_Q	1.274	1.00
118_L	131_L	1.267	1.00
72_D	75_T	1.230	1.00
122_G	163_S	1.226	1.00
42_S	46_T	1.220	1.00
49_S	77_M	1.213	1.00
120_T	163_S	1.194	1.00
86_K	101_S	1.193	1.00
41_L	73_P	1.179	1.00
55_L	78_F	1.172	1.00
165_Q	196_Q	1.170	1.00
75_T	82_V	1.170	1.00
125_A	159_E	1.156	1.00
46_T	49_S	1.154	1.00
22_Y	137_F	1.143	1.00
166_R	170_E	1.141	1.00
34_V	55_L	1.140	1.00
149_I	152_D	1.137	1.00
124_T	127_G	1.117	1.00
32_A	55_L	1.102	1.00
75_T	99_L	1.097	1.00
104_D	119_L	1.080	1.00
177_V	185_K	1.078	1.00
89_I	93_Q	1.068	1.00
129_C	141_T	1.066	1.00
89_I	101_S	1.064	1.00
136_I	171_V	1.064	1.00
26_D	112_N	1.056	1.00
23_I	47_T	1.056	1.00
118_L	167_I	1.051	1.00
41_L	70_L	1.045	1.00
37_P	58_V	1.032	1.00
159_E	162_D	1.032	1.00
176_R	184_G	1.018	1.00
157_A	161_F	1.017	1.00
120_T	141_T	1.012	1.00
73_P	76_K	1.007	1.00
59_A	115_A	0.998	1.00
109_S	112_N	0.994	1.00
172_S	175_V	0.990	1.00
127_G	139_G	0.976	1.00
26_D	111_G	0.965	1.00
87_K	119_L	0.962	1.00
61_T	139_G	0.962	1.00
105_H	116_Q	0.956	1.00
33_I	110_I	0.953	1.00
165_Q	168_K	0.952	1.00
12_T	47_T	0.942	1.00
113_T	135_S	0.938	1.00
43_K	47_T	0.933	1.00
150_C	157_A	0.932	1.00
191_I	195_Y	0.931	1.00
41_L	45_T	0.925	1.00
168_K	196_Q	0.925	1.00
190_S	194_L	0.922	1.00
157_A	160_M	0.919	1.00
158_E	162_D	0.915	1.00
40_E	43_K	0.910	1.00
65_Y	69_N	0.908	1.00
102_L	128_M	0.903	1.00
60_L	82_V	0.889	1.00
136_I	177_V	0.873	1.00
167_I	170_E	0.871	1.00
102_L	117_C	0.869	1.00
173_P	195_Y	0.867	1.00
110_I	113_T	0.858	1.00
24_I	35_V	0.847	1.00
30_R	52_E	0.842	1.00
191_I	194_L	0.834	1.00
25_E	47_T	0.833	1.00
150_C	160_M	0.830	1.00
138_T	177_V	0.824	1.00
58_V	80_A	0.824	1.00
21_C	44_I	0.821	1.00
145_E	188_G	0.814	1.00
31_S	57_A	0.813	1.00
71_V	75_T	0.809	1.00
87_K	90_D	0.802	1.00
94_F	98_N	0.798	1.00
19_N	38_S	0.796	1.00
63_S	84_M	0.795	1.00
44_I	48_L	0.793	1.00
142_V	177_V	0.787	1.00
84_M	92_Y	0.787	1.00
189_H	193_D	0.786	1.00
84_M	98_N	0.784	1.00
131_L	171_V	0.783	1.00
141_T	163_S	0.782	1.00
94_F	99_L	0.781	1.00
17_W	65_Y	0.772	1.00
26_D	30_R	0.769	1.00
120_T	127_G	0.769	1.00
144_T	183_F	0.769	1.00
141_T	167_I	0.760	1.00
63_S	88_E	0.759	1.00
141_T	160_M	0.758	1.00
102_L	130_Y	0.758	1.00
34_V	37_P	0.756	1.00
86_K	89_I	0.755	1.00
190_S	193_D	0.754	1.00
57_A	100_I	0.753	1.00
23_I	34_V	0.753	1.00
116_Q	171_V	0.751	1.00
25_E	30_R	0.750	1.00
192_K	196_Q	0.744	1.00
88_E	91_Y	0.743	1.00
127_G	141_T	0.741	1.00
84_M	88_E	0.739	1.00
118_L	129_C	0.739	1.00
173_P	191_I	0.734	1.00
114_R	133_S	0.731	1.00
88_E	124_T	0.728	1.00
40_E	44_I	0.727	1.00
149_I	153_D	0.725	1.00
138_T	179_P	0.725	1.00
25_E	51_L	0.721	1.00
23_I	32_A	0.720	1.00
119_L	128_M	0.717	1.00
42_S	73_P	0.717	1.00
33_I	115_A	0.715	1.00
145_E	189_H	0.714	1.00
173_P	188_G	0.706	1.00
107_T	133_S	0.706	1.00
125_A	154_G	0.704	1.00
58_V	74_L	0.702	1.00
34_V	74_L	0.694	1.00
31_S	111_G	0.690	1.00
143_F	148_G	0.686	1.00
21_C	38_S	0.679	1.00
58_V	82_V	0.678	1.00
87_K	103_D	0.676	1.00
19_N	180_G	0.676	1.00
145_E	148_G	0.673	1.00
56_K	81_Q	0.672	1.00
93_Q	97_R	0.665	1.00
115_A	130_Y	0.665	1.00
164_I	168_K	0.655	1.00
13_R	18_T	0.651	1.00
44_I	47_T	0.650	1.00
26_D	113_T	0.648	1.00
102_L	108_I	0.646	1.00
60_L	68_V	0.644	1.00
26_D	31_S	0.640	1.00
178_Y	184_G	0.639	1.00
118_L	166_R	0.636	1.00
81_Q	99_L	0.633	1.00
43_K	46_T	0.632	1.00
15_Q	21_C	0.629	1.00
34_V	48_L	0.628	1.00
135_S	178_Y	0.625	1.00
108_I	115_A	0.623	1.00
35_V	59_A	0.620	1.00
74_L	78_F	0.619	1.00
165_Q	170_E	0.616	1.00
160_M	164_I	0.611	1.00
129_C	167_I	0.610	1.00
58_V	71_V	0.605	1.00
102_L	106_Q	0.605	1.00
41_L	44_I	0.603	1.00
32_A	54_E	0.596	1.00
32_A	48_L	0.594	1.00
37_P	71_V	0.593	1.00
32_A	56_K	0.588	1.00
70_L	73_P	0.587	1.00
42_S	45_T	0.586	1.00
192_K	195_Y	0.585	1.00
63_S	126_G	0.585	1.00
137_F	178_Y	0.584	1.00
23_I	55_L	0.584	1.00
103_D	119_L	0.582	1.00
24_I	33_I	0.582	1.00
162_D	165_Q	0.582	1.00
146_G	149_I	0.580	1.00
173_P	192_K	0.579	1.00
98_N	101_S	0.579	1.00
30_R	54_E	0.577	1.00
20_Y	182_S	0.575	1.00
131_L	173_P	0.572	1.00
20_Y	180_G	0.569	1.00
76_K	94_F	0.565	1.00
22_Y	180_G	0.564	1.00
24_I	132_F	0.557	1.00
35_V	130_Y	0.556	1.00
23_I	48_L	0.556	1.00
122_G	150_C	0.555	1.00
129_C	138_T	0.547	1.00
121_P	163_S	0.547	1.00
110_I	115_A	0.541	1.00
49_S	52_E	0.540	1.00
147_C	150_C	0.539	1.00
13_R	20_Y	0.536	1.00
176_R	186_S	0.535	1.00
147_C	164_I	0.534	1.00
89_I	92_Y	0.533	1.00
147_C	157_A	0.532	1.00
48_L	78_F	0.532	1.00
190_S	196_Q	0.532	1.00
14_Y	40_E	0.528	1.00
106_Q	117_C	0.522	1.00
140_D	181_H	0.521	1.00
83_Y	106_Q	0.520	1.00
159_E	163_S	0.519	1.00
75_T	79_N	0.519	1.00
14_Y	19_N	0.518	1.00
20_Y	183_F	0.515	1.00
151_E	155_S	0.514	1.00
131_L	172_S	0.514	1.00
135_S	176_R	0.512	1.00
177_V	187_P	0.510	1.00
48_L	53_A	0.509	1.00
42_S	77_M	0.509	1.00
138_T	185_K	0.505	1.00
85_S	88_E	0.505	1.00
59_A	108_I	0.502	1.00
147_C	160_M	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
4yslA	2	0.9956	100	0.318	Contact Map
3r2uA	4	0.9867	100	0.328	Contact Map
4efzA	2	0.9867	100	0.333	Contact Map
2zo4A	1	0.9689	100	0.335	Contact Map
3tp9A	2	0.9689	100	0.336	Contact Map
2p18A	1	0.9511	100	0.34	Contact Map
1qh5A	1	0.9244	100	0.343	Contact Map
2qedA	1	0.9244	100	0.349	Contact Map
4ysbA	2	0.9422	100	0.357	Contact Map
1xm8A	1	0.9378	100	0.359	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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