YCBL - ECOLI - GREMLIN Contacts

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YCBL - Uncharacterized protein YcbL

UniProt:	P75849	Sequences: MNYRIIPVTAFSQNCSLIWCEQTRLAALVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLDHVGAAAELAQHYGVPVFGPEKEDEFWLQGLPAQSRMFGLEECQPLTPDRWLNEGDTISIGNVTLQVLHCPGHTPGHVVFFDDRAKLLISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLGDDVIFIPGHGPLSTLGYERLHNPFLQDEMPVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13704
Length:	215 (179)
Sequences:	17739 (12652)
Seq/√Len:	945.7

ECOLI - YCBL GLO2
BACSU - YQGX PKSB YYBB YOBT YQJP YFLN YRKH YTNP
HALSA - Q9HQ50 Q9HNJ2 Q9HRG5 Q9HNJ9 O54647 Q9HSD1 Q9HSH2 O54661 Q9HS22 Q9HQ42
SULSO - Q97U88 Q7LYK3 Q97YZ2 Q97VU4 Q97VU0 Q97XZ1 Q97UV2 Q97UR2 Q97WC2 Q97Y13 Q97YH8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_L	50_M	3.770	1.00
129_C	138_V	3.712	1.00
54_L	65_A	2.981	1.00
116_T	123_T	2.733	1.00
51_Q	77_F	2.624	1.00
118_S	123_T	2.607	1.00
116_T	125_Q	2.411	1.00
124_L	141_D	2.399	1.00
125_Q	142_D	2.358	1.00
53_L	139_F	2.286	1.00
126_V	137_V	2.282	1.00
27_A	51_Q	2.248	1.00
39_K	71_H	2.236	1.00
113_E	178_K	2.201	1.00
77_F	109_R	2.199	1.00
146_L	189_I	2.145	1.00
80_E	112_N	2.099	1.00
184_D	202_R	2.086	1.00
75_P	109_R	2.020	1.00
126_V	139_F	1.884	1.00
141_D	144_A	1.837	1.00
82_E	135_G	1.834	1.00
16_S	189_I	1.794	1.00
51_Q	75_P	1.788	1.00
26_A	47_L	1.761	1.00
167_D	170_Q	1.755	1.00
25_L	48_T	1.737	1.00
79_P	128_H	1.734	1.00
145_K	185_D	1.719	1.00
41_E	45_S	1.641	1.00
69_A	108_D	1.623	1.00
19_W	47_L	1.616	1.00
77_F	111_L	1.600	1.00
29_V	148_I	1.571	1.00
19_W	26_A	1.568	1.00
184_D	199_G	1.526	1.00
112_N	115_D	1.523	1.00
39_K	43_D	1.516	1.00
67_E	71_H	1.491	1.00
29_V	55_T	1.480	1.00
27_A	53_L	1.472	1.00
200_Y	204_H	1.464	1.00
172_I	176_K	1.461	1.00
41_E	44_D	1.438	1.00
125_Q	140_F	1.436	1.00
16_S	148_I	1.417	1.00
79_P	137_V	1.417	1.00
39_K	72_Y	1.416	1.00
65_A	76_V	1.403	1.00
122_V	141_D	1.389	1.00
35_A	67_E	1.383	1.00
127_L	140_F	1.369	1.00
80_E	110_W	1.316	1.00
138_V	147_L	1.303	1.00
42_V	49_L	1.290	1.00
140_F	147_L	1.277	1.00
127_L	178_K	1.259	1.00
187_I	195_L	1.238	1.00
49_L	74_V	1.217	1.00
66_A	70_Q	1.212	1.00
111_L	137_V	1.211	1.00
140_F	186_V	1.210	1.00
40_Q	44_D	1.206	1.00
146_L	187_I	1.202	1.00
129_C	174_S	1.198	1.00
109_R	115_D	1.179	1.00
83_D	110_W	1.174	1.00
36_E	40_Q	1.163	1.00
49_L	72_Y	1.152	1.00
134_P	170_Q	1.151	1.00
35_A	39_K	1.143	1.00
138_V	179_L	1.141	1.00
170_Q	173_S	1.140	1.00
22_Q	121_N	1.115	1.00
66_A	69_A	1.113	1.00
188_F	196_S	1.106	1.00
81_K	128_H	1.104	1.00
31_P	52_I	1.093	1.00
178_K	181_P	1.091	1.00
35_A	64_A	1.087	1.00
26_A	49_L	1.085	1.00
69_A	76_V	1.066	1.00
28_L	49_L	1.049	1.00
114_G	125_Q	1.038	1.00
136_H	150_G	1.034	1.00
176_K	180_L	1.032	1.00
168_H	172_I	1.030	1.00
118_S	121_N	1.028	1.00
131_G	174_S	1.025	1.00
147_L	182_L	1.016	1.00
43_D	71_H	1.004	1.00
133_T	136_H	0.995	1.00
113_E	128_H	0.982	1.00
164_P	167_D	0.975	1.00
40_Q	43_D	0.958	1.00
152_V	179_L	0.947	1.00
149_S	188_F	0.934	1.00
122_V	144_A	0.927	1.00
25_L	51_Q	0.927	1.00
198_L	201_E	0.922	1.00
199_G	203_L	0.921	1.00
155_K	194_P	0.920	1.00
67_E	70_Q	0.916	1.00
17_L	26_A	0.916	1.00
138_V	152_V	0.915	1.00
17_L	41_E	0.913	1.00
55_T	150_G	0.904	1.00
59_L	63_G	0.904	1.00
52_I	74_V	0.903	1.00
34_D	37_K	0.900	1.00
15_C	38_I	0.899	1.00
27_A	124_L	0.894	1.00
78_G	82_E	0.894	1.00
57_G	78_G	0.891	1.00
81_K	84_E	0.888	1.00
152_V	171_L	0.880	1.00
78_G	107_P	0.880	1.00
54_L	76_V	0.867	1.00
180_L	204_H	0.864	1.00
196_S	201_E	0.862	1.00
161_S	168_H	0.857	1.00
129_C	152_V	0.857	1.00
53_L	124_L	0.852	1.00
168_H	171_L	0.850	1.00
158_V	161_S	0.850	1.00
140_F	182_L	0.845	1.00
169_N	173_S	0.845	1.00
119_I	122_V	0.844	1.00
75_P	108_D	0.835	1.00
27_A	119_I	0.832	1.00
18_I	29_V	0.825	1.00
161_S	171_L	0.818	1.00
80_E	83_D	0.812	1.00
197_T	200_Y	0.806	1.00
31_P	65_A	0.802	1.00
123_T	142_D	0.799	1.00
15_C	32_G	0.798	1.00
57_G	82_E	0.794	1.00
156_G	200_Y	0.792	1.00
189_I	195_L	0.789	1.00
152_V	174_S	0.780	1.00
37_K	41_E	0.776	1.00
156_G	204_H	0.771	1.00
28_L	31_P	0.767	1.00
160_R	163_F	0.758	1.00
52_I	65_A	0.758	1.00
187_I	197_T	0.757	1.00
147_L	188_F	0.756	1.00
125_Q	182_L	0.753	1.00
129_C	136_H	0.752	1.00
26_A	50_M	0.749	1.00
176_K	181_P	0.748	1.00
37_K	40_Q	0.747	1.00
111_L	139_F	0.744	1.00
19_W	41_E	0.736	1.00
180_L	202_R	0.735	1.00
107_P	110_W	0.735	1.00
124_L	139_F	0.734	1.00
188_F	198_L	0.733	1.00
23_T	121_N	0.729	1.00
136_H	152_V	0.729	1.00
82_E	133_T	0.725	1.00
111_L	126_V	0.725	1.00
179_L	198_L	0.723	1.00
116_T	142_D	0.715	1.00
155_K	204_H	0.714	1.00
13_Q	32_G	0.712	1.00
127_L	138_V	0.710	1.00
19_W	24_R	0.709	1.00
149_S	190_P	0.708	1.00
141_D	146_L	0.706	1.00
22_Q	25_L	0.706	1.00
34_D	38_I	0.705	1.00
134_P	165_R	0.703	1.00
65_A	69_A	0.703	1.00
57_G	135_G	0.699	1.00
51_Q	109_R	0.696	1.00
140_F	145_K	0.693	1.00
148_I	189_I	0.687	1.00
128_H	137_V	0.686	1.00
140_F	184_D	0.685	1.00
156_G	159_G	0.682	1.00
154_F	159_G	0.680	1.00
19_W	23_T	0.678	1.00
52_I	76_V	0.675	1.00
29_V	139_F	0.671	1.00
19_W	45_S	0.670	1.00
105_L	108_D	0.669	1.00
145_K	183_G	0.667	1.00
17_L	28_L	0.667	1.00
54_L	62_V	0.664	1.00
16_S	191_G	0.663	1.00
13_Q	191_G	0.662	1.00
8_V	15_C	0.652	1.00
66_A	105_L	0.646	1.00
28_L	42_V	0.646	1.00
14_N	191_G	0.645	1.00
142_D	145_K	0.644	1.00
111_L	115_D	0.644	1.00
58_H	61_H	0.638	1.00
112_N	128_H	0.638	1.00
28_L	68_L	0.636	1.00
50_M	75_P	0.633	1.00
82_E	85_F	0.629	1.00
36_E	39_K	0.627	1.00
68_L	72_Y	0.626	1.00
38_I	41_E	0.625	1.00
38_I	42_V	0.625	1.00
11_F	59_L	0.624	1.00
64_A	67_E	0.620	1.00
127_L	182_L	0.620	1.00
25_L	120_G	0.620	1.00
19_W	22_Q	0.616	1.00
8_V	34_D	0.609	1.00
29_V	53_L	0.608	1.00
184_D	188_F	0.604	1.00
79_P	82_E	0.603	1.00
130_P	174_S	0.602	1.00
128_H	178_K	0.595	1.00
8_V	13_Q	0.595	1.00
18_I	141_D	0.594	1.00
36_E	67_E	0.594	1.00
78_G	83_D	0.591	1.00
175_I	180_L	0.589	1.00
69_A	73_G	0.585	1.00
18_I	27_A	0.577	1.00
117_I	126_V	0.575	1.00
151_D	192_H	0.573	1.00
53_L	137_V	0.572	1.00
171_L	175_I	0.569	1.00
183_G	186_V	0.566	1.00
123_T	143_R	0.566	1.00
33_G	38_I	0.565	1.00
173_S	176_K	0.564	1.00
9_T	13_Q	0.560	1.00
77_F	115_D	0.560	1.00
114_G	178_K	0.557	1.00
155_K	196_S	0.553	1.00
24_R	46_G	0.553	1.00
35_A	38_I	0.552	1.00
43_D	46_G	0.551	1.00
200_Y	203_L	0.551	1.00
52_I	68_L	0.551	1.00
196_S	200_Y	0.549	1.00
165_R	168_H	0.547	1.00
131_G	161_S	0.546	1.00
62_V	65_A	0.546	1.00
77_F	108_D	0.545	1.00
26_A	42_V	0.543	1.00
172_I	180_L	0.542	1.00
66_A	103_Q	0.542	1.00
55_T	139_F	0.538	1.00
17_L	42_V	0.537	1.00
24_R	47_L	0.535	1.00
165_R	171_L	0.535	1.00
173_S	178_K	0.527	1.00
153_I	188_F	0.526	1.00
120_G	123_T	0.522	1.00
14_N	193_G	0.520	1.00
53_L	117_I	0.519	1.00
28_L	38_I	0.517	1.00
155_K	200_Y	0.517	1.00
35_A	71_H	0.516	1.00
157_G	160_R	0.513	1.00
154_F	158_V	0.509	1.00
115_D	126_V	0.508	1.00
198_L	202_R	0.504	1.00
42_V	72_Y	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
2xf4A	2	0.9767	100	0.244	Contact Map
3tp9A	2	0.9395	100	0.245	Contact Map
3r2uA	4	0.9349	100	0.246	Contact Map
4yslA	2	0.9907	100	0.257	Contact Map
4efzA	2	0.9767	100	0.261	Contact Map
1qh5A	1	0.8791	100	0.264	Contact Map
1xm8A	1	0.8884	100	0.273	Contact Map
2zwrA	1	0.9535	100	0.273	Contact Map
2p18A	1	0.8884	100	0.275	Contact Map
2qedA	1	0.8651	100	0.289	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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