RIMI - ECOLI - GREMLIN Contacts

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RIMI - Ribosomal-protein-alanine acetyltransferase

UniProt:	P0A944	Sequences: MNTISSLETTDLPAAYHIEQRAHAFPWSEKTFASNQGERYLNFQLTQNGKMAAFAITQVVLDEATLFNIAVDPDYQRQGLGRALLEHLIDELEKRGVATLWLEVRASNAAAIALYESLGFNEATIRRNYYPTTDGREDAIIMALPISM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10850
Length:	148 (128)
Sequences:	11454 (9002)
Seq/√Len:	795.7

ECOLI - RIMI MNAT YJGM YPEA YEDL PHNO YAFP YIAC YJAB YHHY RIML ATDA RIMJ YJHQ
BACSU - RIMI YWNH YQJY YYAR PAIA YUAI YHFO YHDJ YTMI YSNE YESJ YBFA YVBK SPSD YBBJ YDGE YYCN BLTD YNAD YOAA YOKL YITI YJCK YOBR YDAF YDHI YRKN YYAT YITH YYBD YKKB YXBD YJDG
HALSA - Q9HMF0 Q9HSL3 Q9HMI8 Q9HQD2 Q9HRK6 Q9HRY5 Q9HNJ3 Q9HMZ2 Q9HRY6
SULSO - Q7LXZ8 Y209 Q97UX1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
89_I	120_F	3.130	1.00
21_R	72_D	3.075	1.00
5_S	46_T	2.930	1.00
55_A	88_L	2.518	1.00
82_R	117_S	2.445	1.00
82_R	118_L	2.398	1.00
45_L	80_L	2.336	1.00
122_E	125_I	2.258	1.00
5_S	11_D	2.239	1.00
57_T	88_L	2.066	1.00
86_E	118_L	2.061	1.00
52_A	75_Y	2.035	1.00
112_I	116_E	1.825	1.00
89_I	100_L	1.811	1.00
53_A	71_V	1.801	1.00
7_L	15_A	1.790	1.00
116_E	122_E	1.782	1.00
13_P	29_E	1.775	1.00
43_F	87_H	1.772	1.00
113_A	116_E	1.731	1.00
22_A	70_A	1.693	1.00
75_Y	78_Q	1.646	1.00
44_Q	51_M	1.644	1.00
21_R	73_P	1.588	1.00
87_H	90_D	1.584	1.00
91_E	94_K	1.584	1.00
16_Y	20_Q	1.572	1.00
64_A	92_L	1.567	1.00
47_Q	75_Y	1.527	1.00
42_N	56_I	1.516	1.00
85_L	118_L	1.507	1.00
76_Q	110_A	1.498	1.00
14_A	17_H	1.448	1.00
112_I	122_E	1.399	1.00
91_E	95_R	1.371	1.00
11_D	46_T	1.358	1.00
7_L	44_Q	1.348	1.00
102_L	115_Y	1.332	1.00
106_A	125_I	1.327	1.00
29_E	33_A	1.322	1.00
59_V	97_V	1.262	1.00
50_K	72_D	1.256	1.00
71_V	80_L	1.247	1.00
14_A	51_M	1.233	1.00
82_R	86_E	1.197	1.00
50_K	74_D	1.190	1.00
47_Q	78_Q	1.184	1.00
17_H	21_R	1.178	1.00
41_L	91_E	1.169	1.00
43_F	91_E	1.164	1.00
16_Y	29_E	1.161	1.00
46_T	51_M	1.159	1.00
41_L	95_R	1.149	1.00
28_S	31_T	1.128	1.00
63_E	101_W	1.127	1.00
21_R	74_D	1.114	1.00
87_H	91_E	1.082	1.00
109_A	112_I	1.076	1.00
83_A	86_E	1.071	1.00
47_Q	52_A	1.046	1.00
9_T	33_A	1.042	1.00
79_G	82_R	1.031	1.00
46_T	49_G	1.026	1.00
109_A	113_A	1.007	1.00
104_V	108_N	1.001	1.00
55_A	84_L	0.993	1.00
92_L	100_L	0.989	1.00
64_A	97_V	0.980	1.00
23_H	70_A	0.979	1.00
4_I	87_H	0.977	1.00
57_T	92_L	0.972	1.00
111_A	115_Y	0.971	1.00
55_A	66_L	0.968	1.00
100_L	120_F	0.966	1.00
18_I	22_A	0.961	1.00
9_T	37_G	0.957	1.00
77_R	110_A	0.949	1.00
22_A	76_Q	0.941	1.00
90_D	94_K	0.931	1.00
4_I	83_A	0.928	1.00
72_D	75_Y	0.925	1.00
66_L	85_L	0.916	1.00
14_A	50_K	0.906	1.00
108_N	111_A	0.903	1.00
19_E	54_F	0.884	1.00
63_E	99_T	0.880	1.00
101_W	123_A	0.877	1.00
18_I	72_D	0.874	1.00
65_T	101_W	0.873	1.00
58_Q	67_F	0.868	1.00
4_I	43_F	0.867	1.00
30_K	34_S	0.860	1.00
19_E	23_H	0.859	1.00
13_P	17_H	0.856	1.00
52_A	80_L	0.849	1.00
8_E	11_D	0.837	1.00
19_E	32_F	0.829	1.00
22_A	73_P	0.828	1.00
114_L	118_L	0.822	1.00
83_A	87_H	0.820	1.00
33_A	37_G	0.813	1.00
47_Q	50_K	0.808	1.00
18_I	51_M	0.802	1.00
7_L	42_N	0.799	1.00
50_K	75_Y	0.797	1.00
17_H	50_K	0.793	1.00
104_V	111_A	0.792	1.00
17_H	72_D	0.788	1.00
92_L	97_V	0.785	1.00
89_I	118_L	0.783	1.00
102_L	111_A	0.777	1.00
99_T	123_A	0.772	1.00
41_L	57_T	0.768	1.00
35_N	56_I	0.768	1.00
19_E	68_N	0.765	1.00
65_T	103_E	0.754	1.00
85_L	114_L	0.743	1.00
59_V	95_R	0.730	1.00
66_L	120_F	0.725	1.00
89_I	93_E	0.720	1.00
86_E	90_D	0.716	1.00
12_L	16_Y	0.708	1.00
30_K	33_A	0.703	1.00
116_E	121_N	0.703	1.00
6_S	43_F	0.694	1.00
5_S	8_E	0.689	1.00
35_N	40_Y	0.687	1.00
77_R	113_A	0.685	1.00
5_S	44_Q	0.675	1.00
45_L	52_A	0.675	1.00
71_V	81_G	0.675	1.00
23_H	68_N	0.666	1.00
7_L	11_D	0.666	1.00
56_I	67_F	0.666	1.00
15_A	54_F	0.659	1.00
28_S	32_F	0.642	1.00
12_L	36_Q	0.641	1.00
80_L	83_A	0.640	1.00
18_I	70_A	0.633	1.00
34_S	38_E	0.633	1.00
110_A	113_A	0.631	1.00
73_P	76_Q	0.624	1.00
25_F	31_T	0.621	1.00
41_L	59_V	0.618	1.00
14_A	72_D	0.613	1.00
87_H	94_K	0.607	1.00
109_A	116_E	0.606	1.00
77_R	117_S	0.604	1.00
45_L	84_L	0.603	1.00
6_S	41_L	0.601	1.00
75_Y	80_L	0.600	1.00
55_A	69_I	0.598	1.00
71_V	84_L	0.594	1.00
53_A	84_L	0.594	1.00
31_T	58_Q	0.592	1.00
7_L	12_L	0.589	1.00
9_T	12_L	0.583	1.00
12_L	29_E	0.582	1.00
53_A	80_L	0.582	1.00
27_W	32_F	0.582	1.00
86_E	89_I	0.579	1.00
32_F	35_N	0.576	1.00
85_L	115_Y	0.576	1.00
57_T	91_E	0.575	1.00
69_I	115_Y	0.571	1.00
59_V	64_A	0.569	1.00
13_P	16_Y	0.565	1.00
60_V	63_E	0.563	1.00
32_F	56_I	0.559	1.00
27_W	35_N	0.559	1.00
81_G	114_L	0.553	1.00
34_S	37_G	0.548	1.00
14_A	46_T	0.545	1.00
90_D	93_E	0.545	1.00
69_I	85_L	0.544	1.00
57_T	64_A	0.543	1.00
98_A	131_P	0.542	1.00
58_Q	65_T	0.537	1.00
111_A	114_L	0.536	1.00
106_A	112_I	0.534	1.00
54_F	70_A	0.530	1.00
45_L	53_A	0.530	1.00
16_Y	32_F	0.527	1.00
103_E	130_Y	0.525	1.00
54_F	68_N	0.524	1.00
31_T	35_N	0.522	1.00
15_A	51_M	0.520	1.00
56_I	68_N	0.516	1.00
6_S	91_E	0.514	1.00
32_F	54_F	0.508	1.00
15_A	44_Q	0.500	1.00
69_I	81_G	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
2cntA	1	1	99.9	0.24	Contact Map
2ob0A	1	0.9932	99.9	0.263	Contact Map
3dr6A	2	1	99.9	0.278	Contact Map
2j8mA	2	1	99.9	0.28	Contact Map
4kvxA	1	0.9595	99.9	0.283	Contact Map
3kkwA	1	0.9865	99.9	0.29	Contact Map
2reeA	1	1	99.9	0.29	Contact Map
4l8aA	1	0.9865	99.9	0.296	Contact Map
4r3lA	1	0.9662	99.9	0.302	Contact Map
2r7hA	2	0.973	99.9	0.303	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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