YYBD - BACSU - GREMLIN Contacts

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YYBD - UPF0039 protein YybD

UniProt:	P37500	Sequences: MNVKKITSEQDLHTAFEIRKAVFVEEQGCPISDEFDEFDTLHGDCQHILAYHQNVPVGTARVRIVGHTGKLERICILKSYRKFGLGKVIVDALERIVKEQGISAFKLHGQTQAAGFYEKLGYRTASEEFMLDGIPHVLMTKQDDSAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (130)
Sequences:	3330 (2555)
Seq/√Len:	224.1

ECOLI - ELAA YIID
BACSU - YYBD YJCF YYAT YITI
HALSA - Q9HPZ8

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_E	122_Y	2.931	1.00
60_A	93_L	2.889	1.00
114_A	124_T	2.648	1.00
108_H	129_F	2.375	1.00
20_K	34_E	2.156	1.00
92_A	95_R	2.105	1.00
18_I	75_C	1.967	1.00
87_K	120_L	1.916	1.00
14_T	51_Y	1.838	1.00
128_E	135_P	1.807	1.00
94_E	141_K	1.780	1.00
18_I	77_L	1.772	1.00
57_V	80_Y	1.765	1.00
111_T	128_E	1.746	1.00
114_A	137_V	1.741	1.00
63_R	72_E	1.728	1.00
90_V	120_L	1.720	1.00
50_A	85_L	1.718	1.00
49_L	56_P	1.694	1.00
125_A	138_L	1.656	1.00
12_L	16_F	1.626	1.00
104_A	140_T	1.625	1.00
21_A	77_L	1.622	1.00
71_L	90_V	1.620	1.00
51_Y	56_P	1.580	1.00
58_G	76_I	1.578	1.00
59_T	75_C	1.570	1.00
21_A	25_E	1.553	1.00
50_A	58_G	1.541	1.00
125_A	140_T	1.512	1.00
118_E	124_T	1.504	1.00
96_I	100_Q	1.500	1.00
94_E	105_F	1.493	1.00
87_K	119_K	1.473	1.00
114_A	118_E	1.443	1.00
130_M	133_G	1.427	1.00
129_F	138_L	1.413	1.00
115_G	118_E	1.375	1.00
87_K	91_D	1.346	1.00
33_D	132_D	1.325	1.00
108_H	138_L	1.325	1.00
130_M	135_P	1.322	1.00
17_E	21_A	1.321	1.00
55_V	79_S	1.312	1.00
126_S	138_L	1.298	1.00
29_C	134_I	1.297	1.00
15_A	49_L	1.290	1.00
29_C	132_D	1.276	1.00
27_Q	110_Q	1.272	1.00
48_I	93_L	1.260	1.00
96_I	99_E	1.259	1.00
48_I	96_I	1.252	1.00
60_A	74_I	1.250	1.00
74_I	90_V	1.237	1.00
20_K	31_I	1.223	1.00
52_H	80_Y	1.219	1.00
68_T	106_K	1.209	1.00
108_H	131_L	1.208	1.00
106_K	138_L	1.200	1.00
46_Q	96_I	1.197	1.00
16_F	35_F	1.184	1.00
65_V	70_K	1.180	1.00
124_T	137_V	1.146	1.00
88_V	92_A	1.145	1.00
52_H	57_V	1.140	1.00
15_A	59_T	1.114	1.00
20_K	24_V	1.111	1.00
21_A	33_D	1.074	1.00
70_K	106_K	1.024	1.00
106_K	140_T	1.023	1.00
98_K	141_K	1.020	1.00
46_Q	100_Q	0.999	1.00
62_V	97_V	0.996	1.00
68_T	104_A	0.980	1.00
37_E	40_T	0.978	1.00
111_T	114_A	0.976	1.00
110_Q	136_H	0.970	1.00
69_G	102_I	0.970	1.00
71_L	74_I	0.968	1.00
20_K	35_F	0.966	1.00
91_D	95_R	0.964	1.00
80_Y	83_F	0.955	1.00
14_T	17_E	0.946	1.00
10_Q	14_T	0.939	1.00
24_V	31_I	0.937	1.00
13_H	16_F	0.936	1.00
40_T	45_C	0.929	1.00
26_E	81_R	0.922	1.00
20_K	25_E	0.914	0.99
104_A	142_Q	0.911	0.99
97_V	105_F	0.894	0.99
95_R	99_E	0.889	0.99
109_G	139_M	0.878	0.99
38_F	63_R	0.861	0.99
51_Y	54_N	0.861	0.99
64_I	102_I	0.857	0.99
52_H	83_F	0.851	0.99
58_G	89_I	0.851	0.99
48_I	60_A	0.838	0.99
113_A	116_F	0.835	0.99
30_P	33_D	0.831	0.99
92_A	96_I	0.827	0.99
9_E	13_H	0.825	0.99
60_A	89_I	0.819	0.99
86_G	116_F	0.810	0.99
71_L	93_L	0.809	0.99
63_R	70_K	0.802	0.99
25_E	30_P	0.801	0.99
70_K	108_H	0.798	0.99
70_K	107_L	0.785	0.98
55_V	77_L	0.776	0.98
57_V	85_L	0.775	0.98
58_G	85_L	0.770	0.98
52_H	55_V	0.761	0.98
91_D	120_L	0.754	0.98
88_V	91_D	0.752	0.98
111_T	135_P	0.744	0.98
122_Y	141_K	0.744	0.98
45_C	63_R	0.743	0.98
123_R	142_Q	0.743	0.98
16_F	20_K	0.742	0.98
18_I	56_P	0.738	0.98
77_L	80_Y	0.729	0.97
17_E	37_E	0.720	0.97
10_Q	40_T	0.710	0.97
21_A	79_S	0.710	0.97
11_D	49_L	0.703	0.97
62_V	96_I	0.700	0.97
84_G	87_K	0.692	0.96
105_F	122_Y	0.691	0.96
85_L	88_V	0.691	0.96
111_T	137_V	0.673	0.96
29_C	131_L	0.672	0.96
30_P	34_E	0.669	0.96
40_T	44_D	0.668	0.96
45_C	64_I	0.666	0.96
124_T	128_E	0.665	0.96
48_I	92_A	0.664	0.96
50_A	88_V	0.662	0.96
11_D	15_A	0.657	0.95
23_F	26_E	0.653	0.95
71_L	122_Y	0.653	0.95
26_E	78_K	0.650	0.95
47_H	59_T	0.650	0.95
39_D	72_E	0.649	0.95
71_L	105_F	0.647	0.95
18_I	59_T	0.646	0.95
23_F	110_Q	0.644	0.95
20_K	30_P	0.631	0.94
69_G	97_V	0.628	0.94
94_E	120_L	0.628	0.94
24_V	34_E	0.627	0.94
107_L	117_Y	0.627	0.94
95_R	98_K	0.626	0.94
83_F	86_G	0.610	0.93
89_I	92_A	0.606	0.93
48_I	62_V	0.603	0.93
58_G	86_G	0.600	0.93
71_L	107_L	0.600	0.93
50_A	57_V	0.600	0.93
13_H	35_F	0.582	0.91
131_L	134_I	0.578	0.91
118_E	123_R	0.572	0.91
72_E	110_Q	0.569	0.90
76_I	85_L	0.559	0.90
13_H	37_E	0.558	0.90
23_F	27_Q	0.556	0.89
12_L	39_D	0.555	0.89
33_D	131_L	0.550	0.89
80_Y	85_L	0.550	0.89
107_L	113_A	0.549	0.89
107_L	139_M	0.548	0.89
26_E	110_Q	0.545	0.88
22_V	81_R	0.539	0.88
112_Q	134_I	0.538	0.88
66_G	70_K	0.535	0.88
86_G	113_A	0.534	0.87
38_F	44_D	0.534	0.87
82_K	87_K	0.532	0.87
61_R	73_R	0.531	0.87
24_V	30_P	0.530	0.87
37_E	44_D	0.526	0.87
63_R	69_G	0.520	0.86
91_D	119_K	0.516	0.86
26_E	73_R	0.516	0.86
73_R	110_Q	0.514	0.85
109_G	117_Y	0.513	0.85
27_Q	73_R	0.512	0.85
69_G	101_G	0.511	0.85
13_H	17_E	0.507	0.85
13_H	40_T	0.504	0.84
27_Q	136_H	0.504	0.84
14_T	56_P	0.502	0.84
101_G	104_A	0.500	0.84
23_F	73_R	0.500	0.84

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
2g0bA	4	0.9864	100	0.407	Contact Map
1q2yA	1	0.9456	99.9	0.427	Contact Map
1kzfA	1	0.9048	99.9	0.436	Contact Map
3p2hA	1	0.932	99.9	0.443	Contact Map
2jdcA	1	0.932	99.9	0.45	Contact Map
1xebA	2	0.9524	99.9	0.452	Contact Map
1ro5A	5	0.9864	99.9	0.455	Contact Map
3efaA	2	0.9592	99.9	0.458	Contact Map
1y9wA	2	0.9388	99.8	0.572	Contact Map
1yvkA	3	0.9252	99.7	0.591	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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