YLBB - BACSU - GREMLIN Contacts

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YLBB - Uncharacterized protein YlbB

UniProt:	O34682	Sequences: MTKIKDLMTADLQYCTVLDNVYEAAVKMKDANVGAIPVVDEDGETLVGIVTDRDLVLRGIAIKKPNSQKITDAMTEKPVSVEEDASVDEVLHLMASHQLRRIPVTKNKKLTGIVTLGDLSLSEQTNERAGSALSDISEGDNREEGFFH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	148 (121)
Sequences:	12675 (9528)
Seq/√Len:	866.2

ECOLI - KDSD GUTQ IMDH
BACSU - YLBB ACUB YHCV CCPN YKUL YTOI IMDH MGTE
HALSA - Q9HRK9 Q9HQD0 Q9HPF4 Q9HNT8 Q9HMW8 Q9HNB6 Q9HR38 Q9HPN8 IMDH
SULSO - Q97U20 Q97VN1 Q7LXY4 Q97U00 Q981B7 Q97VD7 Q97U50 Q7LXN6 Q97V95 Q97Z58 Q97U23

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_D	23_E	2.854	1.00
35_A	101_R	2.592	1.00
83_E	106_K	2.400	1.00
81_V	104_V	2.374	1.00
17_V	71_T	2.234	1.00
85_A	89_E	2.168	1.00
81_V	85_A	2.054	1.00
79_V	97_H	2.052	1.00
68_Q	72_D	1.973	1.00
16_T	19_D	1.958	1.00
24_A	70_I	1.921	1.00
82_E	85_A	1.902	1.00
15_C	19_D	1.818	1.00
15_C	24_A	1.798	1.00
15_C	36_I	1.757	1.00
4_I	90_V	1.743	1.00
17_V	47_V	1.732	1.00
15_C	38_V	1.713	1.00
83_E	111_T	1.706	1.00
81_V	90_V	1.651	1.00
69_K	72_D	1.640	1.00
37_P	46_L	1.626	1.00
100_R	116_L	1.621	1.00
79_V	99_L	1.606	1.00
24_A	50_V	1.544	1.00
13_Q	31_A	1.499	1.00
103_P	110_L	1.496	1.00
27_K	31_A	1.469	1.00
17_V	40_D	1.438	1.00
90_V	102_I	1.424	1.00
5_K	83_E	1.423	1.00
16_T	41_E	1.421	1.00
40_D	45_T	1.402	1.00
26_V	30_D	1.369	1.00
24_A	36_I	1.345	1.00
18_L	71_T	1.344	1.00
50_V	55_L	1.337	1.00
20_N	23_E	1.314	1.00
85_A	93_L	1.300	1.00
15_C	70_I	1.281	1.00
19_D	27_K	1.274	1.00
93_L	97_H	1.257	1.00
92_H	96_S	1.244	1.00
22_Y	26_V	1.236	1.00
52_D	56_V	1.228	1.00
22_Y	66_N	1.225	1.00
14_Y	39_V	1.221	1.00
81_V	102_I	1.213	1.00
80_S	105_T	1.211	1.00
13_Q	27_K	1.199	1.00
79_V	93_L	1.176	1.00
64_K	67_S	1.172	1.00
50_V	73_A	1.153	1.00
23_E	26_V	1.148	1.00
7_L	87_V	1.134	1.00
46_L	110_L	1.131	1.00
90_V	114_V	1.128	1.00
40_D	47_V	1.126	1.00
50_V	70_I	1.122	1.00
82_E	106_K	1.115	1.00
68_Q	73_A	1.113	1.00
106_K	109_K	1.106	1.00
21_V	73_A	1.097	1.00
5_K	84_D	1.090	1.00
35_A	49_I	1.087	1.00
38_V	74_M	1.078	1.00
27_K	30_D	1.059	1.00
7_L	114_V	1.054	1.00
86_S	89_E	1.045	1.00
52_D	100_R	1.044	1.00
89_E	93_L	1.035	1.00
49_I	103_P	1.029	1.00
39_V	47_V	1.008	1.00
33_V	36_I	0.987	1.00
54_D	75_T	0.976	1.00
56_V	100_R	0.976	1.00
25_A	55_L	0.970	1.00
15_C	27_K	0.965	1.00
46_L	78_P	0.962	1.00
13_Q	33_V	0.954	1.00
37_P	110_L	0.935	1.00
48_G	74_M	0.934	1.00
87_V	119_L	0.931	1.00
34_G	52_D	0.931	1.00
35_A	100_R	0.923	1.00
106_K	111_T	0.920	1.00
46_L	103_P	0.905	1.00
101_R	113_I	0.885	1.00
81_V	93_L	0.880	1.00
18_L	69_K	0.876	1.00
9_T	118_D	0.866	1.00
65_P	68_Q	0.856	1.00
93_L	102_I	0.849	1.00
94_M	102_I	0.849	1.00
24_A	28_M	0.849	1.00
34_G	100_R	0.842	1.00
101_R	115_T	0.839	1.00
22_Y	67_S	0.839	1.00
45_T	109_K	0.825	1.00
66_N	69_K	0.818	1.00
27_K	36_I	0.814	1.00
37_P	103_P	0.808	1.00
45_T	108_K	0.795	1.00
89_E	92_H	0.794	1.00
16_T	39_V	0.788	1.00
70_I	74_M	0.783	1.00
16_T	40_D	0.777	1.00
4_I	81_V	0.771	1.00
40_D	43_G	0.764	1.00
100_R	117_G	0.758	1.00
8_M	104_V	0.756	1.00
12_L	37_P	0.753	1.00
23_E	27_K	0.751	1.00
95_A	121_L	0.746	1.00
47_V	74_M	0.741	1.00
28_M	36_I	0.735	1.00
35_A	113_I	0.724	1.00
53_R	100_R	0.717	1.00
34_G	116_L	0.704	1.00
34_G	53_R	0.691	1.00
105_T	108_K	0.686	1.00
39_V	43_G	0.670	1.00
49_I	78_P	0.667	1.00
35_A	51_T	0.665	1.00
39_V	46_L	0.651	1.00
120_S	124_Q	0.649	1.00
9_T	12_L	0.647	1.00
42_D	109_K	0.646	1.00
71_T	74_M	0.646	1.00
91_L	119_L	0.637	1.00
49_I	101_R	0.634	1.00
4_I	114_V	0.633	1.00
108_K	111_T	0.629	1.00
34_G	101_R	0.624	1.00
105_T	110_L	0.623	1.00
29_K	62_I	0.622	1.00
101_R	116_L	0.616	1.00
8_M	111_T	0.605	1.00
82_E	108_K	0.604	1.00
117_G	121_L	0.597	1.00
49_I	113_I	0.591	1.00
33_V	37_P	0.587	1.00
21_V	59_G	0.587	1.00
13_Q	36_I	0.585	1.00
80_S	108_K	0.585	1.00
61_A	65_P	0.585	1.00
29_K	57_L	0.584	1.00
11_D	110_L	0.579	1.00
118_D	121_L	0.578	1.00
37_P	47_V	0.576	1.00
55_L	59_G	0.574	1.00
33_V	118_D	0.572	1.00
20_N	69_K	0.566	1.00
116_L	120_S	0.558	1.00
62_I	65_P	0.554	1.00
94_M	116_L	0.553	1.00
4_I	7_L	0.553	1.00
19_D	36_I	0.552	1.00
49_I	75_T	0.552	1.00
17_V	41_E	0.546	1.00
85_A	90_V	0.545	1.00
33_V	115_T	0.544	1.00
52_D	117_G	0.543	1.00
75_T	78_P	0.541	1.00
7_L	122_S	0.532	1.00
58_R	61_A	0.530	1.00
14_Y	43_G	0.529	1.00
34_G	37_P	0.529	1.00
55_L	60_I	0.523	1.00
25_A	52_D	0.523	1.00
5_K	8_M	0.521	1.00
119_L	123_E	0.520	1.00
78_P	103_P	0.518	1.00
113_I	118_D	0.517	1.00
103_P	113_I	0.516	1.00
103_P	111_T	0.510	1.00
62_I	68_Q	0.508	1.00
22_Y	65_P	0.507	1.00
57_L	95_A	0.503	1.00
64_K	68_Q	0.502	1.00
4_I	8_M	0.501	1.00
41_E	45_T	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
2o16A	2	0.8986	99.9	0.301	Contact Map
3l2bA	2	0.7838	99.9	0.314	Contact Map
3orgA	2	0.7838	99.9	0.334	Contact Map
4cooA	2	0.8446	99.9	0.337	Contact Map
3pc3A	2	0.8514	99.9	0.338	Contact Map
1y5hA	2	0.8243	99.8	0.347	Contact Map
3fhmA	2	0.8446	99.8	0.351	Contact Map
4nocA	2	0.8446	99.8	0.352	Contact Map
2rc3A	3	0.8311	99.8	0.352	Contact Map
4esyA	2	0.8446	99.8	0.356	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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