YOAB - ECOLI - GREMLIN Contacts

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YOAB - RutC family protein YoaB

UniProt:	P0AEB7	Sequences: MTIVRIDAEARWSDVVIHNNTLYYTGVPENLDADAFEQTANTLAQIDAVLEKQGSNKSSILDATIFLADKNDFAAMNKAWDAWVVAGHAPVRCTVQAGLMNPKYKVEIKIVAAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13514
Length:	114 (106)
Sequences:	7427 (4619)
Seq/√Len:	448.6

ECOLI - YOAB RUTC YJGH TDCF RIDA
BACSU - RIDA
HALSA - Q9HNH7
SULSO - Y3206

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_A	82_A	3.088	1.00
47_D	57_K	2.966	1.00
34_D	37_E	2.614	1.00
55_S	59_S	2.611	1.00
36_F	75_A	2.346	1.00
62_D	109_K	2.318	1.00
36_F	78_K	2.247	1.00
66_F	95_V	2.031	1.00
40_A	44_A	1.994	1.00
65_I	76_M	1.944	1.00
46_I	110_I	1.937	1.00
27_V	104_Y	1.898	1.00
44_A	83_W	1.809	1.00
38_Q	105_K	1.798	1.00
96_Q	99_L	1.791	1.00
72_D	105_K	1.737	1.00
47_D	51_E	1.695	1.00
70_K	96_Q	1.649	1.00
41_N	45_Q	1.604	1.00
30_N	33_A	1.575	1.00
18_H	61_L	1.539	1.00
63_A	110_I	1.532	1.00
22_L	55_S	1.467	1.00
18_H	113_A	1.463	1.00
40_A	83_W	1.452	1.00
56_N	59_S	1.441	1.00
99_L	103_K	1.426	1.00
28_P	104_Y	1.384	1.00
44_A	47_D	1.384	1.00
41_N	44_A	1.382	1.00
50_L	112_A	1.324	1.00
67_L	76_M	1.317	1.00
35_A	39_T	1.291	1.00
23_Y	111_V	1.265	1.00
77_N	92_R	1.255	1.00
68_A	72_D	1.253	1.00
67_L	94_T	1.239	1.00
22_L	53_Q	1.217	1.00
60_I	110_I	1.194	1.00
72_D	75_A	1.179	1.00
79_A	82_A	1.177	1.00
75_A	78_K	1.168	1.00
93_C	109_K	1.151	1.00
80_W	92_R	1.138	1.00
17_I	20_N	1.134	1.00
50_L	55_S	1.110	1.00
85_V	89_A	1.090	1.00
68_A	99_L	1.085	1.00
64_T	109_K	1.076	1.00
36_F	40_A	1.061	1.00
39_T	76_M	1.051	1.00
66_F	97_A	1.051	1.00
26_G	107_E	1.049	1.00
40_A	79_A	1.048	1.00
17_I	22_L	1.045	1.00
63_A	80_W	1.021	1.00
21_T	113_A	1.014	1.00
17_I	55_S	1.007	1.00
66_F	93_C	0.997	1.00
28_P	42_T	0.991	1.00
47_D	83_W	0.989	1.00
68_A	105_K	0.977	1.00
24_Y	49_V	0.976	1.00
85_V	88_H	0.970	1.00
24_Y	110_I	0.948	1.00
35_A	76_M	0.941	1.00
60_I	84_V	0.940	1.00
36_F	79_A	0.938	1.00
66_F	109_K	0.930	1.00
35_A	72_D	0.921	1.00
21_T	61_L	0.894	1.00
78_K	81_D	0.879	1.00
15_V	49_V	0.870	1.00
86_A	89_A	0.855	1.00
43_L	83_W	0.850	1.00
51_E	56_N	0.837	1.00
69_D	72_D	0.837	1.00
73_F	94_T	0.823	1.00
71_N	99_L	0.823	1.00
7_D	52_K	0.816	1.00
78_K	82_A	0.812	1.00
50_L	60_I	0.805	1.00
63_A	84_V	0.803	1.00
63_A	108_I	0.803	1.00
37_E	40_A	0.765	1.00
15_V	53_Q	0.760	1.00
43_L	108_I	0.756	1.00
68_A	98_G	0.753	1.00
34_D	75_A	0.752	1.00
14_D	49_V	0.750	1.00
42_T	46_I	0.747	1.00
57_K	60_I	0.744	1.00
74_A	78_K	0.739	1.00
68_A	103_K	0.733	1.00
48_A	51_E	0.732	1.00
43_L	57_K	0.729	1.00
57_K	83_W	0.728	1.00
101_N	104_Y	0.724	1.00
11_R	81_D	0.722	1.00
35_A	79_A	0.717	1.00
79_A	83_W	0.708	1.00
48_A	52_K	0.707	1.00
30_N	41_N	0.705	1.00
16_V	91_V	0.695	1.00
24_Y	46_I	0.694	1.00
20_N	113_A	0.693	1.00
36_F	82_A	0.690	1.00
58_S	85_V	0.688	1.00
42_T	108_I	0.686	1.00
15_V	22_L	0.684	1.00
35_A	75_A	0.683	1.00
45_Q	48_A	0.682	1.00
39_T	106_V	0.679	1.00
31_L	41_N	0.671	1.00
62_D	93_C	0.668	1.00
62_D	111_V	0.666	1.00
35_A	106_V	0.664	1.00
18_H	23_Y	0.658	1.00
65_I	92_R	0.650	1.00
81_D	89_A	0.649	1.00
50_L	57_K	0.648	1.00
64_T	93_C	0.631	0.99
11_R	77_N	0.630	0.99
21_T	111_V	0.630	0.99
18_H	21_T	0.627	0.99
68_A	97_A	0.621	0.99
27_V	42_T	0.610	0.99
64_T	111_V	0.607	0.99
44_A	48_A	0.607	0.99
70_K	99_L	0.605	0.99
34_D	105_K	0.601	0.99
28_P	38_Q	0.600	0.99
43_L	80_W	0.596	0.99
17_I	53_Q	0.594	0.99
60_I	63_A	0.585	0.99
77_N	80_W	0.581	0.99
49_V	52_K	0.577	0.99
65_I	108_I	0.571	0.99
16_V	61_L	0.568	0.99
25_T	91_V	0.567	0.99
31_L	48_A	0.566	0.99
69_D	105_K	0.564	0.99
72_D	96_Q	0.554	0.98
14_D	52_K	0.552	0.98
74_A	102_P	0.551	0.98
62_D	91_V	0.547	0.98
24_Y	93_C	0.538	0.98
69_D	96_Q	0.537	0.98
13_S	16_V	0.534	0.98
67_L	70_K	0.531	0.98
29_E	33_A	0.531	0.98
7_D	14_D	0.524	0.98
14_D	45_Q	0.524	0.98
67_L	72_D	0.520	0.98
19_N	113_A	0.519	0.98
58_S	88_H	0.510	0.97
34_D	38_Q	0.509	0.97
55_S	113_A	0.502	0.97
73_F	77_N	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
3kjjA	3	0.9912	100	0.174	Contact Map
3k12A	3	0.9912	100	0.177	Contact Map
3gtzA	3	0.9825	100	0.201	Contact Map
3m1xA	3	0.9825	100	0.206	Contact Map
3r0pA	5	0.9912	100	0.208	Contact Map
1xrgA	3	0.9912	100	0.21	Contact Map
3l7qA	3	0.9912	100	0.21	Contact Map
2b33A	3	0.9912	100	0.211	Contact Map
3vczA	5	1	100	0.211	Contact Map
3quwA	3	0.9737	100	0.212	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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