RIMI - BACSU - GREMLIN Contacts

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RIMI - Putative ribosomal-protein-alanine acetyltransferase

UniProt:	O05517	Sequences: MKTKAAVRNMRLEDIDHVYEIEASSFTSPWTKDSFYHELLENPYAHYLVIEKDGHLAGYCGIWIVMDDAQITNIAIKPEYRGQSLGETLFRSAVELCKEKDARRLSLEVRVSNHPAQGLYKKFGMQPGGIRKNYYTDNGEDALIMWVTINE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	151 (130)
Sequences:	12760 (10130)
Seq/√Len:	888.4

ECOLI - RIMI YJGM MNAT YPEA PHNO YEDL YAFP YJAB YIAC YHHY YHBS RIML YJHQ ATDA
BACSU - RIMI PAIA YQJY YYAR YHFO YWNH YTMI YUAI YESJ YBFA YHDJ YSNE YBBJ SPSD YYCN BLTD YDGE YVBK YITH YITI YRKN YYAT YOKL YOAA YYBD YOBR YNAD
HALSA - Q9HMF0 Q9HSL3 Q9HMI8 Q9HQD2 Q9HRK6
SULSO - Y209 Q7LXZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_V	125_M	3.182	1.00
8_R	51_E	3.145	1.00
24_S	77_K	2.975	1.00
87_E	123_F	2.627	1.00
60_C	93_A	2.508	1.00
87_E	122_K	2.399	1.00
8_R	14_D	2.253	1.00
50_I	85_L	2.215	1.00
62_I	93_A	2.162	1.00
57_A	80_Y	2.115	1.00
127_P	130_I	2.093	1.00
91_R	123_F	2.013	1.00
117_Q	121_K	1.859	1.00
121_K	127_P	1.848	1.00
69_A	97_C	1.790	1.00
94_V	105_L	1.775	1.00
10_M	18_V	1.763	1.00
48_L	92_S	1.747	1.00
58_G	76_I	1.733	1.00
52_K	80_Y	1.726	1.00
92_S	95_E	1.667	1.00
81_R	115_P	1.621	1.00
80_Y	83_Q	1.618	1.00
25_S	75_A	1.614	1.00
19_Y	23_A	1.606	1.00
96_L	99_E	1.604	1.00
49_V	56_L	1.591	1.00
118_G	121_K	1.556	1.00
17_H	20_E	1.524	1.00
16_D	32_K	1.509	1.00
90_F	123_F	1.504	1.00
96_L	100_K	1.503	1.00
47_Y	61_G	1.478	1.00
64_I	102_A	1.450	1.00
24_S	78_P	1.448	1.00
107_L	120_Y	1.342	1.00
46_H	96_L	1.336	1.00
14_D	51_E	1.323	1.00
17_H	56_L	1.308	1.00
10_M	49_V	1.298	1.00
55_H	77_K	1.286	1.00
20_E	24_S	1.253	1.00
111_V	130_I	1.244	1.00
87_E	91_R	1.239	1.00
48_L	96_L	1.231	1.00
92_S	96_L	1.224	1.00
68_D	106_S	1.211	1.00
117_Q	127_P	1.210	1.00
55_H	79_E	1.190	1.00
76_I	85_L	1.179	1.00
46_H	100_K	1.172	1.00
52_K	57_A	1.160	1.00
51_E	56_L	1.158	1.00
52_K	83_Q	1.152	1.00
51_E	54_G	1.129	1.00
105_L	125_M	1.076	1.00
97_C	105_L	1.074	1.00
22_E	35_F	1.061	1.00
88_T	91_R	1.057	1.00
21_I	25_S	1.052	1.00
24_S	79_E	1.052	1.00
114_H	117_Q	1.051	1.00
63_W	72_T	1.038	1.00
62_I	97_C	1.035	1.00
60_C	89_L	1.030	1.00
22_E	59_Y	1.026	1.00
32_K	36_Y	1.008	1.00
109_V	113_N	1.008	1.00
116_A	120_Y	0.992	1.00
68_D	104_R	0.991	1.00
7_V	88_T	0.976	1.00
71_I	90_F	0.972	1.00
82_G	115_P	0.964	1.00
95_E	99_E	0.962	1.00
26_F	75_A	0.959	1.00
60_C	71_I	0.956	1.00
69_A	102_A	0.956	1.00
7_V	92_S	0.955	1.00
97_C	102_A	0.944	1.00
70_Q	106_S	0.941	1.00
11_R	14_D	0.941	1.00
19_Y	32_K	0.937	1.00
84_S	87_E	0.935	1.00
106_S	128_G	0.914	1.00
12_L	36_Y	0.913	1.00
113_N	116_A	0.897	1.00
35_F	38_E	0.896	1.00
15_I	19_Y	0.896	1.00
21_I	77_K	0.896	1.00
114_H	118_G	0.893	1.00
20_E	77_K	0.886	1.00
6_A	51_E	0.885	1.00
77_K	80_Y	0.879	1.00
64_I	100_K	0.867	1.00
17_H	55_H	0.863	1.00
55_H	80_Y	0.850	1.00
52_K	55_H	0.829	1.00
34_S	38_E	0.826	1.00
22_E	26_F	0.824	1.00
31_T	34_S	0.821	1.00
25_S	81_R	0.820	1.00
16_D	20_E	0.810	1.00
7_V	48_L	0.808	1.00
94_V	123_F	0.808	1.00
104_R	128_G	0.803	1.00
90_F	119_L	0.801	1.00
119_L	123_F	0.792	1.00
25_S	78_P	0.788	1.00
88_T	92_S	0.787	1.00
21_I	56_L	0.782	1.00
22_E	73_N	0.780	1.00
109_V	116_A	0.769	1.00
107_L	116_A	0.769	1.00
57_A	85_L	0.766	1.00
28_S	31_T	0.760	1.00
10_M	47_Y	0.755	1.00
38_E	61_G	0.749	1.00
18_V	59_Y	0.745	1.00
91_R	95_E	0.737	1.00
109_V	117_Q	0.732	1.00
9_N	48_L	0.729	1.00
94_V	98_K	0.725	1.00
20_E	55_H	0.724	1.00
10_M	15_I	0.723	1.00
9_N	46_H	0.722	1.00
12_L	15_I	0.715	1.00
46_H	62_I	0.708	1.00
61_G	72_T	0.704	1.00
65_V	68_D	0.695	1.00
70_Q	108_E	0.690	1.00
50_I	57_A	0.676	1.00
86_G	119_L	0.655	1.00
42_N	45_A	0.654	1.00
90_F	125_M	0.651	1.00
8_R	49_V	0.651	1.00
46_H	64_I	0.646	1.00
115_P	118_G	0.645	1.00
50_I	58_G	0.637	1.00
26_F	73_N	0.636	1.00
47_Y	51_E	0.633	1.00
62_I	69_A	0.631	1.00
76_I	86_G	0.630	1.00
85_L	88_T	0.629	1.00
90_F	120_Y	0.629	1.00
58_G	85_L	0.618	1.00
62_I	96_L	0.616	1.00
21_I	75_A	0.615	1.00
17_H	21_I	0.610	1.00
121_K	126_Q	0.609	1.00
116_A	119_L	0.607	1.00
30_W	33_D	0.606	1.00
34_S	63_W	0.605	1.00
64_I	69_A	0.605	1.00
33_D	37_H	0.604	1.00
37_H	41_E	0.596	1.00
118_G	122_K	0.593	1.00
71_I	125_M	0.593	1.00
61_G	73_N	0.592	1.00
58_G	89_L	0.592	1.00
82_G	118_G	0.591	1.00
82_G	122_K	0.591	1.00
10_M	14_D	0.589	1.00
74_I	120_Y	0.586	1.00
16_D	19_Y	0.585	1.00
8_R	11_R	0.576	1.00
76_I	89_L	0.571	1.00
15_I	36_Y	0.568	1.00
20_E	23_A	0.566	1.00
48_L	51_E	0.566	1.00
78_P	81_R	0.565	1.00
80_Y	85_L	0.561	1.00
35_F	39_L	0.558	1.00
36_Y	39_L	0.553	1.00
34_S	37_H	0.552	1.00
38_E	45_A	0.552	1.00
95_E	98_K	0.549	1.00
92_S	99_E	0.546	1.00
60_C	74_I	0.544	1.00
7_V	89_L	0.542	1.00
17_H	77_K	0.540	1.00
114_H	121_K	0.538	1.00
108_E	135_Y	0.535	1.00
6_A	54_G	0.529	1.00
9_N	96_L	0.523	1.00
57_A	77_K	0.522	1.00
91_R	94_V	0.517	1.00
90_F	94_V	0.516	1.00
59_Y	75_A	0.515	1.00
12_L	41_E	0.514	1.00
50_I	89_L	0.512	1.00
74_I	90_F	0.511	1.00
109_V	120_Y	0.505	1.00
18_V	56_L	0.502	1.00
63_W	70_Q	0.500	1.00
38_E	42_N	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
4kvxA	1	0.947	99.9	0.285	Contact Map
4r3lA	1	0.9536	99.9	0.291	Contact Map
4pv6C	3	0.9868	99.9	0.297	Contact Map
3dr6A	2	0.9801	99.9	0.3	Contact Map
2reeA	1	0.9801	99.9	0.301	Contact Map
2ob0A	1	0.9868	99.9	0.305	Contact Map
2cntA	1	0.9669	99.9	0.306	Contact Map
2j8mA	2	0.9801	99.9	0.31	Contact Map
2r7hA	2	0.9669	99.9	0.314	Contact Map
1mk4A	2	0.9603	99.9	0.318	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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