BDBA - BACSU - GREMLIN Contacts

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BDBA - SPBc2 prophage-derived disulfide bond formation protein A

UniProt:	P68569	Sequences: MKKWIVLFLVLIAAAISIFVYVSTGSEKPFYNDINLTQYQKEVDSKKPKFIYVYETSCPPCQEIKPELNEVIKKEKLKVQALNIEEKENYNTEFLDKYNLNKTPTILYYKDGKEKDRLEGYRSASQIEKFFDKNGDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	137 (108)
Sequences:	6539 (4214)
Seq/√Len:	405.5

ECOLI - THIO2 THIO YBBN
BACSU - BDBA YDFQ THIO YTPP YDBP YUSE YNEN STOA
HALSA - O46709 Q9HQ69 Q9HMD0
SULSO - Q980E5 Q97WI4 Q980T5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_E	95_L	3.440	1.00
40_Q	97_K	2.626	1.00
70_E	124_A	2.547	1.00
123_S	126_Q	2.304	1.00
34_I	82_L	2.278	1.00
107_L	117_R	2.265	1.00
58_C	61_C	2.111	1.00
67_E	124_A	2.010	1.00
98_Y	109_Y	1.976	1.00
36_L	93_E	1.937	1.00
49_K	80_Q	1.928	1.00
74_K	128_E	1.906	1.00
121_Y	126_Q	1.895	1.00
85_E	88_E	1.876	1.00
52_Y	83_N	1.871	1.00
74_K	124_A	1.864	1.00
36_L	94_F	1.832	1.00
48_P	108_Y	1.828	1.00
84_I	94_F	1.737	1.00
67_E	70_E	1.706	1.00
50_F	68_L	1.663	1.00
30_F	73_K	1.644	1.00
35_N	38_Q	1.643	1.00
68_L	81_A	1.575	1.00
71_V	81_A	1.553	1.00
86_E	103_T	1.534	1.00
49_K	82_L	1.505	1.00
36_L	91_N	1.505	1.00
30_F	76_K	1.449	1.00
128_E	132_D	1.439	1.00
38_Q	42_E	1.438	1.00
50_F	106_I	1.416	1.00
52_Y	65_K	1.390	1.00
75_E	132_D	1.387	1.00
42_E	80_Q	1.382	1.00
71_V	124_A	1.365	1.00
107_L	114_E	1.345	1.00
56_T	85_E	1.340	1.00
88_E	91_N	1.321	1.00
40_Q	44_D	1.316	1.00
47_K	80_Q	1.312	1.00
32_N	42_E	1.289	1.00
114_E	117_R	1.283	1.00
42_E	49_K	1.254	1.00
34_I	42_E	1.245	1.00
75_E	128_E	1.226	1.00
126_Q	129_K	1.195	1.00
71_V	128_E	1.183	1.00
64_I	106_I	1.165	1.00
51_I	109_Y	1.158	1.00
116_D	134_N	1.152	1.00
64_I	127_I	1.145	1.00
65_K	69_N	1.135	1.00
33_D	83_N	1.091	1.00
64_I	67_E	1.027	1.00
108_Y	130_F	1.012	1.00
39_Y	43_V	0.990	1.00
35_N	91_N	0.983	1.00
65_K	83_N	0.975	1.00
39_Y	53_V	0.961	1.00
92_T	96_D	0.949	1.00
92_T	95_L	0.946	1.00
118_L	130_F	0.935	1.00
71_V	127_I	0.922	1.00
54_Y	83_N	0.918	1.00
56_T	87_K	0.917	1.00
125_S	129_K	0.909	1.00
69_N	83_N	0.896	1.00
124_A	128_E	0.890	1.00
53_V	100_L	0.886	1.00
108_Y	131_F	0.857	1.00
50_F	81_A	0.855	1.00
52_Y	60_P	0.843	1.00
118_L	122_R	0.839	1.00
79_V	131_F	0.838	1.00
71_V	75_E	0.837	1.00
67_E	71_V	0.829	1.00
54_Y	85_E	0.810	1.00
53_V	107_L	0.800	1.00
53_V	98_Y	0.794	1.00
31_Y	68_L	0.789	1.00
75_E	81_A	0.786	1.00
48_P	110_K	0.782	1.00
64_I	68_L	0.782	1.00
29_P	69_N	0.775	1.00
52_Y	64_I	0.764	1.00
67_E	123_S	0.746	1.00
32_N	80_Q	0.744	1.00
101_N	117_R	0.735	1.00
68_L	131_F	0.727	1.00
60_P	102_K	0.715	1.00
129_K	132_D	0.713	1.00
60_P	63_E	0.704	1.00
116_D	130_F	0.702	1.00
91_N	94_F	0.695	1.00
39_Y	51_I	0.695	1.00
84_I	91_N	0.689	1.00
50_F	108_Y	0.679	0.99
25_G	28_K	0.678	0.99
34_I	51_I	0.676	0.99
46_K	111_D	0.672	0.99
31_Y	72_I	0.666	0.99
50_F	127_I	0.657	0.99
32_N	49_K	0.650	0.99
130_F	134_N	0.649	0.99
86_E	100_L	0.649	0.99
93_E	97_K	0.647	0.99
43_V	49_K	0.647	0.99
39_Y	94_F	0.646	0.99
34_I	38_Q	0.645	0.99
57_S	62_Q	0.643	0.99
38_Q	41_K	0.641	0.99
59_P	63_E	0.638	0.99
39_Y	98_Y	0.637	0.99
54_Y	58_C	0.634	0.99
53_V	109_Y	0.633	0.99
46_K	49_K	0.630	0.99
63_E	67_E	0.627	0.99
122_R	126_Q	0.623	0.99
31_Y	83_N	0.623	0.99
55_E	58_C	0.621	0.99
108_Y	134_N	0.612	0.99
42_E	46_K	0.606	0.99
55_E	66_P	0.595	0.99
48_P	78_K	0.594	0.99
93_E	96_D	0.589	0.99
84_I	95_L	0.588	0.99
47_K	78_K	0.587	0.99
72_I	81_A	0.580	0.98
59_P	62_Q	0.574	0.98
95_L	98_Y	0.572	0.98
122_R	130_F	0.565	0.98
59_P	102_K	0.564	0.98
68_L	127_I	0.563	0.98
109_Y	114_E	0.562	0.98
120_G	126_Q	0.560	0.98
57_S	87_K	0.560	0.98
55_E	87_K	0.559	0.98
100_L	105_T	0.559	0.98
33_D	88_E	0.558	0.98
50_F	131_F	0.556	0.98
51_I	82_L	0.552	0.98
94_F	97_K	0.552	0.98
106_I	127_I	0.549	0.98
53_V	86_E	0.543	0.98
45_S	48_P	0.541	0.98
124_A	127_I	0.539	0.97
73_K	76_K	0.539	0.97
61_C	66_P	0.532	0.97
52_Y	61_C	0.531	0.97
55_E	61_C	0.530	0.97
29_P	33_D	0.523	0.97
64_I	122_R	0.522	0.97
99_N	107_L	0.520	0.97
47_K	111_D	0.520	0.97
34_I	84_I	0.515	0.97
70_E	74_K	0.514	0.97
75_E	79_V	0.513	0.97
54_Y	103_T	0.511	0.97
48_P	111_D	0.502	0.96
118_L	126_Q	0.502	0.96
118_L	121_Y	0.500	0.96

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
2r2jA	2	0.7591	99.8	0.267	Contact Map
3f8uA	2	0.781	99.8	0.267	Contact Map
2b5eA	1	0.854	99.8	0.274	Contact Map
4ekzA	1	0.9343	99.8	0.303	Contact Map
3ed3A	1	0.8467	99.8	0.308	Contact Map
3apoA	1	0.8686	99.8	0.309	Contact Map
1sjiA	2	0.8467	99.8	0.311	Contact Map
3us3A	2	0.8613	99.8	0.324	Contact Map
2pptA	2	0.9781	99.8	0.325	Contact Map
3t58A	1	0.8467	99.8	0.326	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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