YRAI - BACSU - GREMLIN Contacts

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YRAI - Uncharacterized protein YraI

UniProt:	O07909	Sequences: MNKLKRLSMLTVMIASVFIFSSHALAAQYYTVSTSSGAPVNMRSGPGTSWGIVTTIPSGTRIPIYCYKTGTTVTGKYGTSNIWNYTERTLASGEIVPGFVSDTYMYTGSDGPVVPKCSW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	119 (89)
Sequences:	768 (687)
Seq/√Len:	72.8

ECOLI - YGIM
BACSU - YRAI YRAJ YFHK YWSB

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_G	50_W	4.462	1.00
47_G	50_W	3.385	1.00
66_C	74_T	2.769	1.00
104_Y	107_T	2.574	1.00
41_N	55_T	2.420	1.00
62_I	75_G	2.381	1.00
73_V	86_T	2.306	1.00
40_V	88_R	2.292	1.00
73_V	89_T	2.188	1.00
56_I	62_I	2.111	1.00
104_Y	108_G	2.025	1.00
54_T	77_Y	1.830	1.00
42_M	75_G	1.827	1.00
85_Y	88_R	1.799	1.00
105_M	108_G	1.709	1.00
42_M	56_I	1.667	1.00
41_N	52_I	1.639	1.00
44_S	51_G	1.613	0.99
62_I	89_T	1.577	0.99
63_P	76_K	1.525	0.99
64_I	73_V	1.511	0.99
74_T	81_N	1.501	0.99
75_G	82_I	1.494	0.99
37_G	40_V	1.458	0.99
103_T	107_T	1.442	0.99
71_T	86_T	1.431	0.99
40_V	84_N	1.421	0.99
39_P	57_P	1.386	0.98
33_S	64_I	1.296	0.97
66_C	69_T	1.222	0.96
53_V	82_I	1.181	0.96
40_V	85_Y	1.172	0.95
39_P	55_T	1.171	0.95
106_Y	109_S	1.159	0.95
77_Y	82_I	1.141	0.95
34_T	92_S	1.119	0.94
83_W	86_T	1.100	0.93
103_T	108_G	1.075	0.93
42_M	54_T	1.061	0.92
42_M	53_V	1.054	0.92
53_V	77_Y	1.051	0.92
57_P	60_T	1.043	0.92
64_I	89_T	1.032	0.91
36_S	90_L	1.025	0.91
68_K	91_A	1.023	0.91
40_V	43_R	0.998	0.90
48_T	85_Y	0.991	0.89
56_I	84_N	0.989	0.89
71_T	85_Y	0.954	0.87
103_T	106_Y	0.954	0.87
69_T	83_W	0.936	0.86
84_N	87_E	0.933	0.86
74_T	83_W	0.920	0.85
105_M	109_S	0.894	0.84
43_R	88_R	0.893	0.84
33_S	62_I	0.889	0.83
41_N	47_G	0.871	0.82
31_T	91_A	0.870	0.82
61_R	92_S	0.869	0.82
33_S	73_V	0.845	0.80
35_S	38_A	0.806	0.77
104_Y	109_S	0.798	0.76
76_K	82_I	0.794	0.76
56_I	60_T	0.789	0.75
46_P	69_T	0.780	0.75
103_T	109_S	0.776	0.74
21_S	24_A	0.775	0.74
42_M	84_N	0.769	0.74
84_N	89_T	0.761	0.73
66_C	83_W	0.747	0.71
40_V	54_T	0.742	0.71
59_G	97_P	0.735	0.70
34_T	59_G	0.712	0.68
99_F	102_D	0.705	0.67
93_G	99_F	0.697	0.66
21_S	25_L	0.694	0.66
75_G	84_N	0.690	0.65
65_Y	74_T	0.687	0.65
59_G	93_G	0.677	0.64
27_A	83_W	0.676	0.64
70_G	85_Y	0.667	0.63
60_T	66_C	0.665	0.62
32_V	63_P	0.662	0.62
33_S	91_A	0.661	0.62
43_R	46_P	0.657	0.61
35_S	39_P	0.653	0.61
102_D	106_Y	0.639	0.59
42_M	82_I	0.636	0.59
85_Y	89_T	0.626	0.58
25_L	76_K	0.625	0.58
69_T	73_V	0.623	0.57
83_W	87_E	0.616	0.57
95_I	98_G	0.613	0.56
42_M	77_Y	0.607	0.55
52_I	60_T	0.597	0.54
20_F	71_T	0.586	0.53
95_I	100_V	0.586	0.53
22_S	26_A	0.579	0.52
45_G	83_W	0.576	0.52
49_S	87_E	0.574	0.51
30_Y	36_S	0.574	0.51
45_G	70_G	0.569	0.51
37_G	71_T	0.568	0.51
27_A	47_G	0.564	0.50
38_A	49_S	0.564	0.50
24_A	98_G	0.564	0.50
100_V	103_T	0.560	0.50
96_V	101_S	0.556	0.49
44_S	81_N	0.555	0.49
23_H	51_G	0.555	0.49
101_S	104_Y	0.554	0.49
57_P	90_L	0.553	0.49
58_S	96_V	0.549	0.48
49_S	96_V	0.548	0.48
34_T	37_G	0.547	0.48
35_S	42_M	0.540	0.47
66_C	70_G	0.535	0.47
35_S	62_I	0.533	0.46
76_K	79_T	0.532	0.46
22_S	25_L	0.531	0.46
39_P	59_G	0.528	0.46
26_A	88_R	0.525	0.45
23_H	28_Q	0.525	0.45
46_P	63_P	0.524	0.45
95_I	102_D	0.524	0.45
27_A	44_S	0.523	0.45
48_T	51_G	0.518	0.45
102_D	105_M	0.511	0.44
52_I	79_T	0.511	0.44
99_F	103_T	0.510	0.44
77_Y	80_S	0.507	0.43
22_S	28_Q	0.505	0.43
48_T	71_T	0.504	0.43
53_V	97_P	0.500	0.42

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
2kt8A	1	0.6303	99.4	0.493	Contact Map
2kq8A	1	0.5882	99.3	0.5	Contact Map
2krsA	1	0.6134	99.3	0.508	Contact Map
3npfA	2	0.8151	98.9	0.588	Contact Map
4krtA	1	0.7143	98.8	0.602	Contact Map
3h41A	1	0.9496	98.7	0.61	Contact Map
2hbwA	1	0.7227	98.4	0.647	Contact Map
3m1uA	2	0.9496	98	0.685	Contact Map
4mt7A	1	0	94.1	0.79	Contact Map
1xovA	1	0.9664	93.9	0.792	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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