YKKB - BACSU - GREMLIN Contacts

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YKKB - Uncharacterized protein YkkB

UniProt:	P49855	Sequences: MNAKTKLVTDRIRLRCMEDRDQATLFGLLFNDPDVMTYYSGLKDKRQTREWVNWNQRNEKGYGVSLWIAEDKRTGEFLGQCGIVPQQIENQTVMEIGYMFARRHWGNGYAQEAARACLDYGFNERQFGKMAALIDPGNKASIRVAEKIGMHYSKTIRKWNKPIAVYERKSYN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (152)
Sequences:	19411 (14963)
Seq/√Len:	1213.7

ECOLI - RIMJ RIML ATDA YHHY MNAT
BACSU - YKKB YJDG YOAA YJCK YDAF YNAD YOKL YWNH
HALSA - Q9HMZ2 Q9HRY6 Q9HNJ3 Q9HRY5 Q9HSL3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_Q	147_K	2.832	1.00
132_A	145_A	2.810	1.00
15_R	70_E	2.728	1.00
71_D	74_T	2.441	1.00
15_R	21_D	2.411	1.00
8_V	72_K	2.297	1.00
34_D	102_R	2.294	1.00
134_I	142_I	2.287	1.00
94_M	127_F	2.173	1.00
152_Y	155_T	2.166	1.00
83_I	121_G	2.127	1.00
134_I	145_A	2.098	1.00
11_R	112_E	2.097	1.00
9_T	116_A	2.019	1.00
143_R	146_E	1.932	1.00
142_I	146_E	1.913	1.00
96_I	114_A	1.799	1.00
32_D	102_R	1.792	1.00
119_D	123_N	1.787	1.00
17_M	68_I	1.778	1.00
118_L	150_M	1.766	1.00
68_I	77_F	1.751	1.00
9_T	112_E	1.708	1.00
23_A	45_K	1.704	1.00
24_T	77_F	1.663	1.00
118_L	130_M	1.659	1.00
81_C	113_A	1.626	1.00
101_A	104_H	1.619	1.00
128_G	158_K	1.619	1.00
22_Q	49_R	1.608	1.00
114_A	148_I	1.590	1.00
70_E	75_G	1.563	1.00
142_I	152_Y	1.562	1.00
44_D	47_Q	1.542	1.00
13_R	72_K	1.531	1.00
45_K	49_R	1.519	1.00
51_W	55_N	1.498	1.00
100_F	110_A	1.497	1.00
116_A	119_D	1.492	1.00
98_Y	145_A	1.418	1.00
139_K	142_I	1.404	1.00
146_E	152_Y	1.394	1.00
7_L	116_A	1.391	1.00
69_A	100_F	1.355	1.00
69_A	113_A	1.334	1.00
19_D	53_N	1.315	1.00
111_Q	144_V	1.312	1.00
136_P	155_T	1.311	1.00
98_Y	141_S	1.307	1.00
120_Y	124_E	1.271	1.00
71_D	78_L	1.268	1.00
129_K	153_S	1.241	1.00
8_V	13_R	1.235	1.00
22_Q	52_V	1.233	1.00
57_R	61_G	1.217	1.00
78_L	104_H	1.213	1.00
13_R	70_E	1.209	1.00
81_C	117_C	1.191	1.00
24_T	76_E	1.188	1.00
121_G	130_M	1.169	1.00
110_A	144_V	1.138	1.00
80_Q	99_M	1.113	1.00
76_E	103_R	1.112	1.00
9_T	12_I	1.111	1.00
26_F	45_K	1.110	1.00
71_D	109_Y	1.108	1.00
22_Q	45_K	1.107	1.00
93_V	131_A	1.107	1.00
132_A	150_M	1.098	1.00
7_L	14_L	1.089	1.00
7_L	120_Y	1.078	1.00
121_G	125_R	1.077	1.00
35_V	105_W	1.061	1.00
49_R	53_N	1.057	1.00
95_E	133_L	1.044	1.00
76_E	104_H	1.029	1.00
29_L	99_M	1.029	1.00
67_W	117_C	1.028	1.00
111_Q	115_R	1.026	1.00
105_W	140_A	1.012	1.00
102_R	105_W	1.000	1.00
141_S	145_A	0.996	1.00
24_T	27_G	0.995	1.00
145_A	150_M	0.985	1.00
153_S	157_R	0.977	1.00
144_V	148_I	0.969	1.00
19_D	49_R	0.966	1.00
29_L	101_A	0.957	1.00
19_D	56_Q	0.954	1.00
71_D	107_N	0.953	1.00
67_W	120_Y	0.951	1.00
43_K	47_Q	0.951	1.00
17_M	80_Q	0.949	1.00
71_D	76_E	0.939	1.00
120_Y	125_R	0.937	1.00
87_Q	91_Q	0.919	1.00
58_N	64_V	0.917	1.00
42_L	48_T	0.915	1.00
106_G	140_A	0.890	1.00
70_E	77_F	0.890	1.00
118_L	148_I	0.881	1.00
34_D	37_T	0.880	1.00
115_R	119_D	0.874	1.00
139_K	143_R	0.874	1.00
13_R	75_G	0.867	1.00
12_I	113_A	0.867	1.00
12_I	109_Y	0.866	1.00
46_R	49_R	0.865	1.00
111_Q	148_I	0.861	1.00
98_Y	110_A	0.854	1.00
115_R	148_I	0.851	1.00
93_V	129_K	0.850	1.00
50_E	54_W	0.845	1.00
26_F	48_T	0.844	1.00
58_N	63_G	0.843	1.00
121_G	127_F	0.842	1.00
83_I	117_C	0.842	1.00
27_G	101_A	0.839	1.00
21_D	70_E	0.838	1.00
139_K	146_E	0.822	1.00
112_E	116_A	0.822	1.00
100_F	109_Y	0.817	1.00
38_Y	135_D	0.817	1.00
34_D	105_W	0.811	1.00
22_Q	26_F	0.810	1.00
27_G	103_R	0.807	1.00
71_D	104_H	0.805	1.00
93_V	159_W	0.795	1.00
24_T	101_A	0.794	1.00
104_H	107_N	0.792	1.00
69_A	81_C	0.782	1.00
9_T	14_L	0.780	1.00
23_A	27_G	0.780	1.00
38_Y	137_G	0.776	1.00
133_L	156_I	0.763	1.00
76_E	101_A	0.760	1.00
27_G	76_E	0.747	1.00
19_D	22_Q	0.740	1.00
32_D	101_A	0.727	1.00
16_C	59_E	0.726	1.00
36_M	39_Y	0.724	1.00
106_G	143_R	0.718	1.00
36_M	41_G	0.716	1.00
114_A	144_V	0.714	1.00
106_G	111_Q	0.714	1.00
55_N	66_L	0.711	1.00
50_E	53_N	0.710	1.00
111_Q	140_A	0.708	1.00
47_Q	50_E	0.708	1.00
54_W	58_N	0.706	1.00
156_I	159_W	0.702	1.00
95_E	131_A	0.698	1.00
53_N	57_R	0.697	1.00
15_R	68_I	0.693	1.00
10_D	112_E	0.693	1.00
78_L	109_Y	0.679	1.00
11_R	108_G	0.676	1.00
134_I	141_S	0.673	1.00
98_Y	114_A	0.663	1.00
56_Q	59_E	0.662	1.00
69_A	109_Y	0.661	1.00
69_A	110_A	0.652	1.00
27_G	31_N	0.652	1.00
30_F	99_M	0.652	1.00
26_F	31_N	0.652	1.00
59_E	65_S	0.651	1.00
66_L	82_G	0.651	1.00
136_P	142_I	0.648	1.00
43_K	48_T	0.648	1.00
46_R	50_E	0.647	1.00
92_T	128_G	0.636	1.00
110_A	114_A	0.634	1.00
143_R	147_K	0.627	1.00
54_W	57_R	0.620	1.00
48_T	52_V	0.618	1.00
29_L	77_F	0.614	1.00
100_F	105_W	0.614	1.00
132_A	141_S	0.613	1.00
118_L	122_F	0.612	1.00
140_A	143_R	0.612	1.00
18_E	21_D	0.610	1.00
106_G	144_V	0.609	1.00
81_C	114_A	0.608	1.00
100_F	104_H	0.607	1.00
15_R	18_E	0.604	1.00
131_A	156_I	0.604	1.00
84_V	95_E	0.603	1.00
131_A	159_W	0.603	1.00
98_Y	144_V	0.602	1.00
30_F	80_Q	0.599	1.00
69_A	79_G	0.596	1.00
32_D	105_W	0.596	1.00
151_H	157_R	0.584	1.00
94_M	121_G	0.584	1.00
39_Y	99_M	0.582	1.00
154_K	157_R	0.581	1.00
24_T	70_E	0.580	1.00
16_C	56_Q	0.571	1.00
52_V	56_Q	0.570	1.00
109_Y	112_E	0.567	1.00
129_K	159_W	0.566	1.00
33_P	37_T	0.565	1.00
142_I	145_A	0.565	1.00
77_F	80_Q	0.565	1.00
83_I	94_M	0.564	1.00
35_V	99_M	0.562	1.00
58_N	62_Y	0.560	1.00
96_I	130_M	0.547	1.00
12_I	112_E	0.546	1.00
32_D	103_R	0.543	1.00
94_M	130_M	0.534	1.00
130_M	150_M	0.527	1.00
35_V	38_Y	0.527	1.00
98_Y	132_A	0.526	1.00
133_L	159_W	0.526	1.00
85_P	94_M	0.525	1.00
144_V	147_K	0.523	1.00
56_Q	60_K	0.522	1.00
82_G	97_G	0.521	1.00
92_T	126_Q	0.519	1.00
114_A	150_M	0.517	1.00
35_V	39_Y	0.511	1.00
138_N	141_S	0.509	1.00
17_M	77_F	0.507	1.00
153_S	156_I	0.503	1.00
10_D	13_R	0.503	1.00
25_L	52_V	0.501	1.00
122_F	130_M	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
2fckA	2	0.9767	100	0.318	Contact Map
3pzjA	2	0.9709	100	0.344	Contact Map
3r9fA	1	0.9651	100	0.344	Contact Map
1yreA	2	0.9419	100	0.346	Contact Map
2vzyA	3	0.8895	100	0.351	Contact Map
1s7kA	2	0.8663	99.9	0.365	Contact Map
3fbuA	2	0.9302	99.9	0.373	Contact Map
3igrA	2	0.9767	99.9	0.382	Contact Map
1nslA	3	0.9651	99.9	0.383	Contact Map
2z10A	2	0.9477	99.9	0.385	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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