KAPD - BACSU - GREMLIN Contacts

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KAPD - Probable 3'-5' exonuclease KapD

UniProt:	O05231	Sequences: MTTNSLLIIDFEFTMPDGKYSPQNFFPEIIEAGIVKSIDDEVVETFSSYVRPKKFPKLTKRCKSFLKITQKQVDEGMRFEDFIRKLNELDPEKNSTIITWGNMDMKVLKQNCMFNHIPFPFKGEMRDLSLEYKNFFGDRTLTGLWKAAEEYGDSGTGTHHKALDDALTAYKLFKLVEQDKQYLEKPKPPTIGERIDLTELLKRAT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (165)
Sequences:	8432 (5683)
Seq/√Len:	442.4

ECOLI - DPO3E EXOX
BACSU - KAPD DPO3 DING

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_T	167_L	2.811	1.00
141_L	146_K	2.762	1.00
31_E	161_K	2.664	1.00
53_K	78_R	2.630	1.00
98_I	101_G	2.366	1.00
99_T	128_L	2.288	1.00
63_K	69_T	2.204	1.00
34_I	86_L	2.155	1.00
51_R	75_E	2.090	1.00
48_S	77_M	2.081	1.00
48_S	85_K	2.073	1.00
62_C	66_L	2.073	1.00
69_T	72_Q	2.069	1.00
5_S	38_I	2.051	1.00
57_K	70_Q	1.952	1.00
58_L	73_V	1.902	1.00
136_F	151_Y	1.814	1.00
143_G	146_K	1.774	1.00
28_E	51_R	1.738	1.00
11_F	29_I	1.702	1.00
31_E	47_S	1.701	1.00
77_M	82_F	1.698	1.00
70_Q	74_D	1.635	1.00
60_K	64_S	1.617	1.00
148_A	168_T	1.582	1.00
148_A	153_D	1.550	1.00
48_S	82_F	1.537	1.00
78_R	81_D	1.520	1.00
50_V	82_F	1.503	1.00
5_S	36_K	1.502	1.00
105_M	125_M	1.501	1.00
33_G	166_A	1.492	1.00
7_L	34_I	1.457	1.00
13_F	103_M	1.432	1.00
36_K	44_E	1.427	1.00
61_R	64_S	1.421	1.00
79_F	83_I	1.415	1.00
47_S	161_K	1.414	1.00
8_I	169_A	1.408	1.00
35_V	163_L	1.407	1.00
5_S	94_N	1.405	1.00
175_L	178_Q	1.401	1.00
58_L	63_K	1.379	1.00
28_E	111_N	1.376	1.00
42_V	45_T	1.372	1.00
49_Y	72_Q	1.368	1.00
37_S	40_D	1.366	1.00
101_G	125_M	1.356	1.00
47_S	163_L	1.350	1.00
145_W	159_H	1.339	1.00
175_L	179_D	1.338	1.00
139_R	150_E	1.334	1.00
35_V	166_A	1.334	1.00
136_F	176_V	1.329	1.00
7_L	94_N	1.327	1.00
58_L	70_Q	1.289	1.00
84_R	117_I	1.272	1.00
17_D	20_Y	1.249	1.00
158_T	164_D	1.236	1.00
46_F	85_K	1.234	1.00
28_E	53_K	1.231	1.00
36_K	94_N	1.226	1.00
110_Q	114_F	1.224	1.00
111_N	114_F	1.222	1.00
11_F	108_L	1.221	1.00
32_A	86_L	1.208	1.00
79_F	111_N	1.193	1.00
37_S	42_V	1.184	1.00
28_E	114_F	1.168	1.00
77_M	81_D	1.167	1.00
49_Y	161_K	1.163	1.00
28_E	54_K	1.155	1.00
36_K	89_L	1.152	1.00
30_I	66_L	1.147	1.00
155_G	168_T	1.143	1.00
48_S	76_G	1.141	1.00
44_E	89_L	1.133	1.00
77_M	85_K	1.115	1.00
62_C	65_F	1.087	1.00
155_G	159_H	1.086	1.00
20_Y	27_P	1.079	1.00
132_Y	147_A	1.075	1.00
153_D	171_K	1.073	1.00
167_L	171_K	1.070	1.00
30_I	58_L	1.068	1.00
129_S	133_K	1.065	1.00
7_L	36_K	1.058	1.00
128_L	173_F	1.056	1.00
68_I	72_Q	1.047	1.00
170_Y	174_K	1.028	1.00
97_I	173_F	1.021	1.00
166_A	170_Y	1.020	1.00
132_Y	142_T	1.019	1.00
27_P	54_K	1.011	1.00
6_L	173_F	1.006	1.00
147_A	172_L	0.994	1.00
63_K	70_Q	0.991	1.00
136_F	179_D	0.990	1.00
159_H	164_D	0.989	1.00
111_N	115_N	0.988	1.00
87_N	112_C	0.980	1.00
161_K	164_D	0.969	1.00
15_M	27_P	0.969	1.00
135_F	176_V	0.967	1.00
27_P	107_V	0.962	1.00
52_P	73_V	0.940	1.00
86_L	90_D	0.934	1.00
49_Y	76_G	0.933	1.00
109_K	119_F	0.930	1.00
60_K	63_K	0.924	1.00
37_S	170_Y	0.923	1.00
68_I	73_V	0.923	1.00
61_R	65_F	0.918	1.00
46_F	89_L	0.912	1.00
129_S	142_T	0.911	1.00
51_R	78_R	0.911	1.00
29_I	50_V	0.905	1.00
53_K	80_E	0.896	1.00
105_M	109_K	0.880	1.00
72_Q	76_G	0.878	1.00
9_I	98_I	0.878	1.00
33_G	162_A	0.872	1.00
151_Y	172_L	0.870	1.00
33_G	47_S	0.864	1.00
8_I	170_Y	0.859	1.00
110_Q	113_M	0.856	1.00
9_I	96_T	0.852	1.00
37_S	174_K	0.852	1.00
164_D	167_L	0.844	1.00
76_G	82_F	0.844	1.00
45_T	163_L	0.839	1.00
85_K	88_E	0.837	1.00
84_R	88_E	0.834	1.00
83_I	112_C	0.829	1.00
80_E	115_N	0.825	1.00
171_K	174_K	0.821	1.00
59_T	62_C	0.812	1.00
132_Y	176_V	0.811	1.00
58_L	62_C	0.808	1.00
49_Y	68_I	0.802	1.00
37_S	41_E	0.801	1.00
148_A	155_G	0.797	1.00
163_L	167_L	0.789	1.00
86_L	89_L	0.784	1.00
160_H	165_D	0.774	1.00
38_I	43_V	0.772	1.00
95_S	126_R	0.768	1.00
153_D	172_L	0.767	1.00
138_D	142_T	0.763	1.00
72_Q	75_E	0.761	1.00
8_I	166_A	0.760	1.00
70_Q	73_V	0.754	1.00
9_I	86_L	0.749	1.00
34_I	89_L	0.741	1.00
82_F	86_L	0.735	1.00
32_A	50_V	0.734	1.00
88_E	91_P	0.729	1.00
148_A	172_L	0.726	1.00
151_Y	176_V	0.721	1.00
30_I	62_C	0.718	1.00
33_G	163_L	0.708	1.00
171_K	175_L	0.706	1.00
18_G	106_K	0.705	1.00
83_I	87_N	0.704	1.00
143_G	159_H	0.697	1.00
35_V	170_Y	0.692	1.00
144_L	172_L	0.687	1.00
144_L	169_A	0.684	1.00
28_E	79_F	0.683	1.00
147_A	151_Y	0.683	1.00
46_F	86_L	0.681	1.00
29_I	107_V	0.680	1.00
136_F	150_E	0.680	1.00
109_K	120_P	0.680	1.00
42_V	167_L	0.679	1.00
148_A	159_H	0.678	1.00
36_K	43_V	0.677	1.00
119_F	122_K	0.677	1.00
168_T	171_K	0.675	1.00
31_E	163_L	0.672	1.00
32_A	82_F	0.669	1.00
173_F	177_E	0.666	1.00
8_I	173_F	0.664	1.00
132_Y	136_F	0.661	1.00
79_F	115_N	0.660	1.00
79_F	82_F	0.656	1.00
9_I	90_D	0.655	1.00
18_G	107_V	0.654	1.00
80_E	84_R	0.653	1.00
100_W	103_M	0.649	0.99
151_Y	179_D	0.648	0.99
29_I	111_N	0.646	0.99
71_K	74_D	0.641	0.99
12_E	165_D	0.637	0.99
63_K	72_Q	0.636	0.99
35_V	45_T	0.631	0.99
91_P	94_N	0.628	0.99
35_V	42_V	0.626	0.99
52_P	79_F	0.621	0.99
102_N	106_K	0.619	0.99
16_P	61_R	0.618	0.99
155_G	164_D	0.617	0.99
82_F	85_K	0.608	0.99
48_S	86_L	0.606	0.99
146_K	149_E	0.604	0.99
11_F	107_V	0.602	0.99
127_D	131_E	0.600	0.99
16_P	59_T	0.597	0.99
99_T	147_A	0.595	0.99
15_M	107_V	0.587	0.99
128_L	147_A	0.582	0.99
172_L	175_L	0.581	0.99
156_T	164_D	0.581	0.99
121_F	124_E	0.580	0.99
51_R	54_K	0.579	0.99
133_K	142_T	0.578	0.99
151_Y	175_L	0.577	0.99
85_K	89_L	0.574	0.99
132_Y	150_E	0.573	0.99
127_D	130_L	0.573	0.99
128_L	132_Y	0.573	0.99
174_K	178_Q	0.570	0.99
163_L	166_A	0.567	0.99
102_N	130_L	0.566	0.99
166_A	169_A	0.564	0.99
27_P	59_T	0.555	0.98
50_V	79_F	0.555	0.98
142_T	150_E	0.555	0.98
17_D	27_P	0.552	0.98
30_I	73_V	0.551	0.98
145_W	155_G	0.536	0.98
136_F	142_T	0.535	0.98
145_W	149_E	0.530	0.98
15_M	62_C	0.529	0.98
13_F	107_V	0.529	0.98
131_E	176_V	0.528	0.98
83_I	111_N	0.520	0.98
9_I	108_L	0.516	0.97
40_D	177_E	0.516	0.97
169_A	172_L	0.515	0.97
129_S	132_Y	0.515	0.97
117_I	120_P	0.514	0.97
29_I	79_F	0.514	0.97
19_K	110_Q	0.513	0.97
87_N	117_I	0.512	0.97
156_T	171_K	0.511	0.97
57_K	60_K	0.504	0.97
98_I	169_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
1zbuA	1	0.9902	100	0.241	Contact Map
4qozB	1	0.9805	100	0.245	Contact Map
3cg7A	2	0.9854	100	0.261	Contact Map
1w0hA	1	0.9122	100	0.266	Contact Map
2xriA	1	0.8829	100	0.277	Contact Map
2guiA	1	0.8341	100	0.333	Contact Map
3mxmB	2	0.9122	100	0.338	Contact Map
4rg8A	1	0.922	100	0.341	Contact Map
2qxfA	1	0.9317	100	0.343	Contact Map
2p1jA	2	0.8341	100	0.348	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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