YYBB - BACSU - GREMLIN Contacts

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YYBB - Probable metallo-hydrolase YybB

UniProt:	P37502	Sequences: MNLRQLSEHVFQCEFELDVPLRIPVHTWFIKDGDDVYIVDTGIERFADAQIRAALAIGNPKAILLTHGHSDHIGGASKWLERFDIPIFAHQKELKYINGEEPYPNKNEVENTGVAHIVQPLTEQTLAHLPLKYYLTPGHSPGHVVYYHKIDRTLLTGDLFITSKEDLHPPIRRFSVDINENIDSGSIIDQIKPTLICSSHGEEILYNEELYKNYVVRYRD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	220 (181)
Sequences:	19616 (13984)
Seq/√Len:	1039.4

ECOLI - YCBL GLO2 YJCS
BACSU - YYBB YOBT YFLN YQJP YQGX PKSB YRKH YTNP
HALSA - Q9HRG5 Q9HNJ9 Q9HSH2 Q9HQ50 Q9HSD1 Q9HNJ2 O54647 O54661 Q9HS22 Q9HQ42
SULSO - Q97VU4 Q97VU0 Q97U88 Q97XZ1 Q97YZ2 Q7LYK3 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
136_T	145_V	4.345	1.00
35_D	61_K	3.975	1.00
65_L	76_A	3.533	1.00
121_L	124_Q	3.253	1.00
62_A	88_F	3.092	1.00
132_K	149_K	2.911	1.00
131_L	148_H	2.628	1.00
64_L	146_Y	2.501	1.00
37_Y	62_A	2.370	1.00
133_Y	144_V	2.367	1.00
125_T	130_P	2.351	1.00
51_I	82_R	2.335	1.00
153_T	197_C	2.089	1.00
148_H	151_D	2.068	1.00
62_A	86_P	2.061	1.00
93_E	142_G	2.060	1.00
28_W	197_C	2.053	1.00
133_Y	146_Y	1.990	1.00
120_P	124_Q	1.985	1.00
118_V	121_L	1.950	1.00
35_D	59_N	1.924	1.00
152_R	194_T	1.923	1.00
177_D	180_E	1.892	1.00
39_V	66_T	1.877	1.00
53_A	57_I	1.813	1.00
90_H	135_L	1.804	1.00
132_K	147_Y	1.681	1.00
90_H	144_V	1.677	1.00
53_A	56_A	1.667	1.00
39_V	155_L	1.623	1.00
28_W	155_L	1.582	1.00
91_Q	122_T	1.579	1.00
37_Y	64_L	1.494	1.00
78_K	82_R	1.492	1.00
94_L	98_N	1.480	1.00
76_A	87_I	1.479	1.00
145_V	154_L	1.447	1.00
51_I	55_L	1.435	1.00
183_D	186_S	1.430	1.00
134_Y	147_Y	1.408	1.00
60_P	85_I	1.400	1.00
88_F	119_Q	1.394	1.00
147_Y	152_R	1.380	1.00
35_D	62_A	1.352	1.00
36_V	60_P	1.352	1.00
147_Y	154_L	1.344	1.00
134_Y	187_I	1.301	1.00
86_P	119_Q	1.293	1.00
77_S	81_E	1.284	1.00
129_L	148_H	1.276	1.00
138_G	184_S	1.271	1.00
143_H	157_G	1.271	1.00
187_I	190_Q	1.268	1.00
31_K	36_V	1.265	1.00
48_D	52_R	1.254	1.00
180_E	183_D	1.248	1.00
51_I	83_F	1.238	1.00
52_R	56_A	1.234	1.00
55_L	82_R	1.232	1.00
60_P	83_F	1.205	1.00
80_L	118_V	1.191	1.00
126_L	129_L	1.190	1.00
32_D	128_H	1.166	1.00
118_V	124_Q	1.137	1.00
38_I	60_P	1.137	1.00
92_K	135_L	1.135	1.00
206_Y	209_E	1.135	1.00
145_V	188_I	1.133	1.00
77_S	80_L	1.132	1.00
54_A	60_P	1.129	1.00
127_A	130_P	1.123	1.00
66_T	157_G	1.119	1.00
153_T	195_L	1.099	1.00
80_L	87_I	1.098	1.00
39_V	146_Y	1.096	1.00
52_R	55_L	1.089	1.00
88_F	121_L	1.086	1.00
195_L	203_E	1.085	1.00
140_S	143_H	1.073	1.00
41_T	63_I	1.069	1.00
136_T	184_S	1.062	1.00
196_I	204_I	1.048	1.00
89_A	93_E	1.043	1.00
129_L	151_D	1.030	1.00
36_V	61_K	1.020	1.00
123_E	132_K	1.020	1.00
120_P	123_E	1.017	1.00
123_E	187_I	1.006	1.00
186_S	190_Q	0.998	1.00
27_T	50_Q	0.997	1.00
63_I	85_I	0.987	1.00
178_I	182_I	0.986	1.00
121_L	144_V	0.984	1.00
179_N	183_D	0.973	1.00
37_Y	131_L	0.972	1.00
145_V	159_L	0.959	1.00
167_L	170_P	0.951	1.00
91_Q	120_P	0.947	1.00
30_I	39_V	0.943	1.00
182_I	186_S	0.941	1.00
68_G	89_A	0.939	1.00
147_Y	191_I	0.931	1.00
49_A	53_A	0.931	1.00
159_L	188_I	0.927	1.00
47_A	75_G	0.926	1.00
149_K	152_R	0.923	1.00
66_T	146_Y	0.923	1.00
186_S	189_D	0.917	1.00
141_P	180_E	0.904	1.00
65_L	87_I	0.903	1.00
49_A	52_R	0.901	1.00
178_I	181_N	0.901	1.00
70_S	74_G	0.898	1.00
119_Q	124_Q	0.895	1.00
41_T	76_A	0.893	1.00
125_T	128_H	0.893	1.00
29_F	36_V	0.886	1.00
120_P	187_I	0.883	1.00
156_T	196_I	0.883	1.00
123_E	130_P	0.880	1.00
93_E	140_S	0.872	1.00
132_K	191_I	0.869	1.00
27_T	42_G	0.865	1.00
91_Q	94_L	0.862	1.00
47_A	78_K	0.856	1.00
63_I	76_A	0.855	1.00
94_L	120_P	0.850	1.00
29_F	53_A	0.850	1.00
92_K	95_K	0.849	1.00
36_V	59_N	0.847	1.00
136_T	143_H	0.842	1.00
154_L	191_I	0.834	1.00
26_H	201_G	0.833	1.00
64_L	131_L	0.828	1.00
134_Y	145_V	0.827	1.00
37_Y	126_L	0.825	1.00
168_H	181_N	0.822	1.00
136_T	159_L	0.822	1.00
95_K	99_G	0.821	1.00
38_I	41_T	0.819	1.00
72_H	158_D	0.804	1.00
147_Y	193_P	0.798	1.00
39_V	64_L	0.792	1.00
162_T	202_E	0.787	1.00
154_L	196_I	0.785	1.00
99_G	102_P	0.778	1.00
32_D	35_D	0.776	1.00
152_R	192_K	0.773	1.00
137_P	184_S	0.772	1.00
78_K	81_E	0.770	1.00
159_L	181_N	0.768	1.00
25_V	42_G	0.767	1.00
174_F	177_D	0.758	1.00
195_L	205_L	0.758	1.00
68_G	93_E	0.752	1.00
159_L	184_S	0.748	1.00
63_I	87_I	0.746	1.00
131_L	146_Y	0.739	1.00
181_N	185_G	0.736	1.00
75_G	78_K	0.734	1.00
161_I	164_K	0.731	1.00
48_D	51_I	0.730	1.00
161_I	166_D	0.729	1.00
193_P	207_N	0.729	1.00
29_F	38_I	0.725	1.00
90_H	93_E	0.723	1.00
185_G	189_D	0.720	1.00
95_K	98_N	0.720	1.00
168_H	178_I	0.718	1.00
130_P	150_I	0.718	1.00
25_V	199_S	0.718	1.00
110_E	117_I	0.716	1.00
129_L	150_I	0.715	1.00
93_E	96_Y	0.705	1.00
69_H	72_H	0.694	1.00
193_P	210_L	0.693	1.00
124_Q	132_K	0.692	1.00
117_I	120_P	0.691	1.00
61_K	86_P	0.686	1.00
88_F	118_V	0.685	1.00
197_C	203_E	0.683	1.00
188_I	206_Y	0.682	1.00
102_P	105_N	0.681	1.00
100_E	103_Y	0.678	1.00
134_Y	191_I	0.676	1.00
183_D	187_I	0.675	1.00
89_A	97_I	0.675	1.00
156_T	198_S	0.675	1.00
79_W	83_F	0.673	1.00
163_S	207_N	0.673	1.00
117_I	121_L	0.668	1.00
64_L	144_V	0.666	1.00
101_E	104_P	0.664	1.00
143_H	159_L	0.663	1.00
47_A	51_I	0.663	1.00
104_P	108_E	0.662	1.00
28_W	199_S	0.659	1.00
33_G	128_H	0.659	1.00
36_V	54_A	0.650	1.00
30_I	148_H	0.650	1.00
163_S	208_E	0.649	1.00
89_A	94_L	0.644	1.00
38_I	54_A	0.643	1.00
76_A	80_L	0.642	1.00
65_L	73_I	0.642	1.00
29_F	54_A	0.638	1.00
48_D	78_K	0.637	1.00
119_Q	122_T	0.636	1.00
141_P	175_S	0.633	1.00
103_Y	106_K	0.633	1.00
71_D	200_H	0.630	1.00
67_H	158_D	0.618	1.00
54_A	58_G	0.614	1.00
35_D	127_A	0.614	1.00
106_K	109_V	0.610	1.00
40_D	67_H	0.610	1.00
105_N	108_E	0.606	1.00
134_Y	154_L	0.605	1.00
148_H	155_L	0.605	1.00
80_L	84_D	0.603	1.00
148_H	153_T	0.603	1.00
91_Q	95_K	0.602	1.00
198_S	201_G	0.602	1.00
118_V	123_E	0.601	1.00
96_Y	141_P	0.599	1.00
135_L	144_V	0.599	1.00
103_Y	107_N	0.597	1.00
155_L	197_C	0.589	1.00
159_L	166_D	0.589	1.00
147_Y	192_K	0.587	1.00
38_I	50_Q	0.585	1.00
44_E	75_G	0.584	1.00
68_G	142_G	0.583	1.00
193_P	196_I	0.580	1.00
130_P	149_K	0.580	1.00
38_I	79_W	0.577	1.00
196_I	206_Y	0.570	1.00
21_L	27_T	0.569	1.00
67_H	71_D	0.566	1.00
138_G	168_H	0.566	1.00
55_L	58_G	0.563	1.00
34_D	58_G	0.563	1.00
26_H	199_S	0.555	1.00
182_I	189_D	0.554	1.00
148_H	152_R	0.553	1.00
73_I	76_A	0.552	1.00
161_I	165_E	0.549	1.00
46_F	49_A	0.547	1.00
63_I	79_W	0.546	1.00
86_P	118_V	0.542	1.00
118_V	122_T	0.539	1.00
96_Y	101_E	0.538	1.00
41_T	65_L	0.536	1.00
96_Y	99_G	0.536	1.00
31_K	34_D	0.536	1.00
53_A	58_G	0.533	1.00
119_Q	123_E	0.532	1.00
165_E	168_H	0.531	1.00
60_P	79_W	0.529	1.00
103_Y	109_V	0.528	1.00
66_T	69_H	0.526	1.00
179_N	182_I	0.521	1.00
123_E	135_L	0.521	1.00
105_N	109_V	0.520	1.00
90_H	94_L	0.517	1.00
69_H	140_S	0.517	1.00
67_H	72_H	0.514	1.00
92_K	141_P	0.513	1.00
207_N	210_L	0.510	1.00
40_D	158_D	0.508	1.00
135_L	187_I	0.503	1.00
175_S	181_N	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
2zo4A	1	0.9727	100	0.263	Contact Map
2yheA	3	0.9682	100	0.298	Contact Map
2cfuA	2	0.9545	100	0.311	Contact Map
4nurA	2	0.9682	100	0.313	Contact Map
4pdxA	2	0.95	100	0.319	Contact Map
4ad9A	4	0.9318	100	0.33	Contact Map
2fhxA	2	0.9409	100	0.335	Contact Map
3iogA	1	0.9455	100	0.346	Contact Map
3vpeA	1	0.9636	100	0.347	Contact Map
4fekA	1	0.9636	100	0.351	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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