YBAJ - BACSU - GREMLIN Contacts

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YBAJ - Uncharacterized methyltransferase YbaJ

UniProt:	P70976	Sequences: MNALVAHNSKAWDKKVETGNEWTVAVEQQVIEQAKKGNWDIRVTPMKDVPKDWFPPIKGLKVLCLASGGGQQGPVLAAAGADVTVLDNSEKQLNQDRMIAERDGLTIHTVKGSMDDLSVFNDESFDVIVHPVANVFVENVLPVWKEAYRVLKRNGILISGFVNPVVFLFDTELEQQGVLKVKHSIPYADPEDLPKHKVKKLIENNEALEFGHSLEDQIKGQIDAGFIVTGFYEDKGGFVLDQYIHTYSATRSVKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (211)
Sequences:	12662 (9618)
Seq/√Len:	662.2

ECOLI - UBIE UBIG CMOA SMTA BIOC YJHP TAM TEHB YAFE CMOB RLMA
BACSU - YBAJ MENG YQEM YRRT YXBB YCGJ YODH YDAC YRHH YXJB
HALSA - Q9HR81 Q9HMT2 Q9HND6 Q9HRX3 Q9HR63 ARSM Q9HQ85 Q9HSK6
SULSO - Q97WN4 Q7LXN7 Q97ZU8 Q97WT7 Q97XD7 Q97X57 Q97YX4 Q97WH3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_K	82_D	3.663	1.00
90_E	111_K	3.228	1.00
141_L	223_D	3.016	1.00
67_S	85_V	2.876	1.00
84_T	125_F	2.777	1.00
126_D	152_K	2.777	1.00
86_L	112_G	2.654	1.00
148_Y	226_F	2.648	1.00
93_L	111_K	2.641	1.00
66_A	133_A	2.616	1.00
147_A	157_L	2.598	1.00
95_Q	98_M	2.553	1.00
73_G	83_V	2.501	1.00
65_L	147_A	2.431	1.00
78_A	103_D	2.348	1.00
63_L	125_F	2.330	1.00
96_D	109_T	2.297	1.00
82_D	108_H	2.282	1.00
90_E	94_N	2.262	1.00
62_V	76_L	2.253	1.00
146_E	149_R	2.224	1.00
213_S	216_D	2.192	1.00
140_V	220_G	2.181	1.00
128_I	147_A	2.165	1.00
84_T	110_V	2.008	1.00
120_F	125_F	1.952	1.00
67_S	73_G	1.936	1.00
93_L	109_T	1.930	1.00
141_L	220_G	1.820	1.00
74_P	100_A	1.811	1.00
61_K	152_K	1.793	1.00
141_L	145_K	1.776	1.00
218_I	222_I	1.764	1.00
73_G	85_V	1.705	1.00
151_L	157_L	1.691	1.00
146_E	150_V	1.677	1.00
137_V	143_V	1.676	1.00
151_L	155_G	1.664	1.00
128_I	151_L	1.658	1.00
139_N	142_P	1.645	1.00
100_A	109_T	1.644	1.00
57_I	60_L	1.614	1.00
62_V	127_V	1.602	1.00
66_A	130_H	1.602	1.00
65_L	114_M	1.580	1.00
74_P	99_I	1.564	1.00
113_S	116_D	1.555	1.00
23_T	89_S	1.553	1.00
61_K	126_D	1.544	1.00
142_P	145_K	1.518	1.00
19_G	23_T	1.502	1.00
75_V	78_A	1.500	1.00
23_T	91_K	1.471	1.00
84_T	108_H	1.452	1.00
61_K	84_T	1.393	1.00
219_K	223_D	1.390	1.00
91_K	94_N	1.377	1.00
88_N	113_S	1.370	1.00
112_G	119_V	1.351	1.00
51_K	79_A	1.331	1.00
63_L	128_I	1.315	1.00
87_D	93_L	1.310	1.00
85_V	109_T	1.309	1.00
114_M	133_A	1.298	1.00
94_N	97_R	1.295	1.00
60_L	127_V	1.293	1.00
219_K	222_I	1.282	1.00
77_A	106_T	1.261	1.00
117_L	146_E	1.252	1.00
73_G	107_I	1.225	1.00
141_L	224_A	1.224	1.00
122_D	149_R	1.220	1.00
78_A	105_L	1.212	1.00
100_A	107_I	1.207	1.00
86_L	117_L	1.195	1.00
98_M	102_R	1.187	1.00
121_N	124_S	1.172	1.00
218_I	231_F	1.171	1.00
61_K	125_F	1.165	1.00
130_H	133_A	1.154	1.00
73_G	109_T	1.151	1.00
93_L	97_R	1.150	1.00
143_V	147_A	1.142	1.00
32_E	69_G	1.136	1.00
124_S	152_K	1.133	1.00
67_S	96_D	1.130	1.00
74_P	78_A	1.125	1.00
132_V	135_V	1.123	1.00
120_F	150_V	1.121	1.00
151_L	226_F	1.117	1.00
115_D	139_N	1.112	1.00
61_K	123_E	1.112	1.00
49_V	52_D	1.107	1.00
61_K	124_S	1.091	1.00
214_L	233_E	1.086	1.00
75_V	79_A	1.077	1.00
128_I	150_V	1.071	1.00
216_D	219_K	1.050	1.00
117_L	120_F	1.041	1.00
97_R	101_E	1.041	1.00
35_K	39_W	1.040	1.00
198_V	201_L	1.035	1.00
69_G	92_Q	1.030	1.00
48_D	52_D	1.030	1.00
144_W	221_Q	1.022	1.00
183_H	187_Y	1.020	1.00
157_L	221_Q	1.014	1.00
185_I	188_A	1.004	1.00
161_F	217_Q	0.996	1.00
77_A	105_L	0.992	1.00
50_P	158_I	0.992	1.00
85_V	96_D	0.992	1.00
134_N	137_V	0.991	1.00
86_L	110_V	0.986	1.00
147_A	151_L	0.977	1.00
132_V	136_F	0.959	1.00
70_G	109_T	0.959	1.00
49_V	232_Y	0.958	1.00
119_V	146_E	0.958	1.00
71_Q	99_I	0.949	1.00
22_W	25_A	0.946	1.00
70_G	96_D	0.940	1.00
100_A	105_L	0.935	1.00
65_L	128_I	0.933	1.00
198_V	202_I	0.928	1.00
134_N	217_Q	0.922	1.00
65_L	86_L	0.920	1.00
117_L	150_V	0.899	1.00
46_M	50_P	0.898	1.00
89_S	92_Q	0.897	1.00
62_V	83_V	0.893	1.00
94_N	98_M	0.879	1.00
140_V	144_W	0.879	1.00
148_Y	224_A	0.871	1.00
62_V	81_A	0.868	1.00
54_F	127_V	0.863	1.00
135_V	161_F	0.849	1.00
76_L	129_V	0.834	1.00
53_W	232_Y	0.829	1.00
222_I	228_V	0.823	1.00
145_K	149_R	0.819	1.00
132_V	160_G	0.805	1.00
163_N	233_E	0.799	1.00
60_L	126_D	0.797	1.00
145_K	224_A	0.797	1.00
74_P	109_T	0.791	1.00
71_Q	75_V	0.790	1.00
63_L	150_V	0.783	1.00
74_P	103_D	0.780	1.00
60_L	81_A	0.780	1.00
181_V	185_I	0.777	1.00
72_Q	129_V	0.768	1.00
189_D	192_D	0.764	1.00
30_V	33_Q	0.763	1.00
176_Q	179_L	0.763	1.00
77_A	107_I	0.761	1.00
200_K	203_E	0.760	1.00
174_E	178_V	0.760	1.00
133_A	137_V	0.752	1.00
59_G	81_A	0.746	1.00
32_E	99_I	0.741	1.00
168_L	172_E	0.739	1.00
133_A	136_F	0.737	1.00
65_L	143_V	0.737	1.00
39_W	42_R	0.733	1.00
49_V	53_W	0.733	1.00
144_W	217_Q	0.732	1.00
183_H	186_P	0.732	1.00
46_M	49_V	0.731	1.00
114_M	137_V	0.728	1.00
84_T	120_F	0.725	1.00
112_G	117_L	0.725	1.00
174_E	179_L	0.724	1.00
214_L	218_I	0.723	1.00
53_W	56_P	0.718	1.00
142_P	146_E	0.717	1.00
53_W	230_G	0.713	1.00
47_K	51_K	0.712	1.00
69_G	99_I	0.712	1.00
48_D	79_A	0.708	1.00
101_E	105_L	0.702	1.00
116_D	142_P	0.700	1.00
136_F	207_A	0.699	1.00
74_P	105_L	0.697	1.00
29_Q	32_E	0.694	1.00
119_V	149_R	0.694	1.00
134_N	143_V	0.689	1.00
220_G	224_A	0.687	1.00
184_S	188_A	0.686	1.00
99_I	102_R	0.685	1.00
40_D	44_T	0.685	1.00
67_S	87_D	0.684	1.00
100_A	104_G	0.684	1.00
215_E	219_K	0.683	1.00
90_E	97_R	0.683	1.00
38_N	41_I	0.683	1.00
64_C	85_V	0.680	1.00
66_A	114_M	0.680	1.00
39_W	43_V	0.679	1.00
197_K	200_K	0.678	1.00
145_K	223_D	0.677	1.00
72_Q	76_L	0.677	1.00
56_P	60_L	0.677	1.00
98_M	101_E	0.677	1.00
131_P	160_G	0.674	1.00
135_V	162_V	0.674	1.00
43_V	46_M	0.672	1.00
199_K	203_E	0.671	1.00
42_R	45_P	0.671	1.00
215_E	218_I	0.668	1.00
95_Q	99_I	0.666	1.00
173_L	177_G	0.661	1.00
59_G	80_G	0.661	1.00
130_H	137_V	0.657	1.00
167_F	170_D	0.656	1.00
214_L	231_F	0.653	1.00
26_V	29_Q	0.653	1.00
110_V	120_F	0.652	1.00
29_Q	95_Q	0.651	1.00
122_D	150_V	0.650	1.00
64_C	68_G	0.650	1.00
177_G	181_V	0.646	1.00
173_L	179_L	0.645	1.00
37_G	40_D	0.640	1.00
181_V	188_A	0.639	1.00
46_M	54_F	0.638	1.00
41_I	45_P	0.636	1.00
36_K	40_D	0.635	1.00
64_C	72_Q	0.630	1.00
199_K	202_I	0.630	1.00
130_H	159_S	0.628	1.00
23_T	26_V	0.627	1.00
220_G	223_D	0.623	1.00
167_F	172_E	0.622	1.00
35_K	38_N	0.622	1.00
120_F	124_S	0.622	1.00
22_W	136_F	0.618	1.00
93_L	96_D	0.616	1.00
124_S	149_R	0.615	1.00
22_W	135_V	0.610	1.00
91_K	95_Q	0.608	1.00
205_N	208_L	0.606	1.00
216_D	220_G	0.605	1.00
67_S	93_L	0.604	1.00
125_F	150_V	0.603	1.00
127_V	156_I	0.603	1.00
192_D	198_V	0.598	1.00
211_G	217_Q	0.598	1.00
31_I	35_K	0.598	1.00
100_A	106_T	0.591	1.00
22_W	32_E	0.588	1.00
148_Y	151_L	0.586	1.00
101_E	104_G	0.585	1.00
41_I	44_T	0.585	1.00
85_V	107_I	0.585	1.00
127_V	155_G	0.583	1.00
140_V	212_H	0.582	1.00
124_S	150_V	0.580	1.00
53_W	158_I	0.580	1.00
97_R	109_T	0.580	1.00
206_E	209_E	0.577	1.00
122_D	146_E	0.577	1.00
19_G	111_K	0.572	1.00
74_P	77_A	0.571	1.00
174_E	177_G	0.570	1.00
134_N	159_S	0.565	1.00
184_S	187_Y	0.564	1.00
92_Q	132_V	0.564	1.00
170_D	173_L	0.560	1.00
87_D	92_Q	0.560	1.00
134_N	144_W	0.559	1.00
62_V	129_V	0.559	1.00
60_L	156_I	0.558	1.00
134_N	161_F	0.556	1.00
181_V	184_S	0.554	1.00
165_V	168_L	0.553	1.00
188_A	191_E	0.553	1.00
21_E	25_A	0.550	1.00
175_Q	178_V	0.546	1.00
191_E	194_P	0.545	1.00
32_E	35_K	0.545	1.00
167_F	171_T	0.541	1.00
222_I	227_I	0.541	1.00
190_P	194_P	0.540	1.00
115_D	137_V	0.540	1.00
157_L	226_F	0.536	1.00
164_P	213_S	0.535	1.00
192_D	196_H	0.534	1.00
22_W	26_V	0.533	1.00
159_S	221_Q	0.531	1.00
31_I	36_K	0.529	0.99
115_D	143_V	0.529	0.99
187_Y	192_D	0.528	0.99
35_K	40_D	0.526	0.99
201_L	204_N	0.526	0.99
204_N	207_A	0.522	0.99
198_V	203_E	0.519	0.99
97_R	108_H	0.519	0.99
42_R	46_M	0.517	0.99
20_N	24_V	0.517	0.99
190_P	193_L	0.515	0.99
213_S	217_Q	0.515	0.99
48_D	75_V	0.515	0.99
40_D	43_V	0.514	0.99
149_R	152_K	0.511	0.99
119_V	150_V	0.508	0.99
114_M	146_E	0.507	0.99
47_K	71_Q	0.504	0.99
131_P	135_V	0.504	0.99
50_P	72_Q	0.504	0.99
22_W	31_I	0.504	0.99
196_H	200_K	0.504	0.99
65_L	117_L	0.502	0.99
69_G	95_Q	0.501	0.99
64_C	129_V	0.501	0.99
123_E	152_K	0.500	0.99

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
1y8cA	1	0.898	100	0.41	Contact Map
1wznA	4	0.8784	100	0.425	Contact Map
4obxA	2	0.8392	100	0.425	Contact Map
3g5lA	3	0.8275	100	0.435	Contact Map
4kdcA	1	0.8157	100	0.437	Contact Map
3bkwA	2	0.8157	100	0.438	Contact Map
4hgzA	4	0.8588	100	0.442	Contact Map
3d2lA	1	0.8824	100	0.443	Contact Map
3thrA	3	0.9882	100	0.446	Contact Map
4kdrA	1	0.7804	100	0.446	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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