YYAR - BACSU - GREMLIN Contacts

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YYAR - Uncharacterized protein YyaR

UniProt:	P37506	Sequences: MIMKMTHLNMKDFNKPNEPFVVFGRMIPAFENGVWTYTEERFSKPYFKQYEDDDMDVSYVEEEGKAAFLYYLENNCIGRIKIRSNWNGYALIEDIAVAKDYRKKGVGTALLHKAIEWAKENHFCGLMLETQDINISACHFYAKHHFIIGAVDTMLYSNFPTANEIAIFWYYKF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	173 (137)
Sequences:	3545 (2885)
Seq/√Len:	246.4

ECOLI - RIMI YJGM MNAT YEDL PHNO YPEA YIAC YAFP
BACSU - YYAR RIMI YWNH YQJY PAIA YHFO YTMI YBFA YSNE YHDJ YUAI YVBK YESJ SPSD
HALSA - Q9HMF0 Q9HSL3 Q9HMI8 Q9HQD2
SULSO - Y209 Q7LXZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_Y	106_V	3.478	1.00
108_T	143_K	3.428	1.00
115_I	146_F	2.925	1.00
69_L	76_C	2.526	1.00
108_T	144_H	2.509	1.00
113_K	116_E	2.431	1.00
80_I	114_A	2.367	1.00
115_I	171_Y	2.336	1.00
115_I	126_L	2.229	1.00
133_I	164_E	2.197	1.00
125_G	170_Y	2.139	1.00
132_D	165_I	2.135	1.00
148_I	167_I	2.125	1.00
142_A	148_I	2.081	1.00
77_I	101_Y	2.019	1.00
67_A	81_K	1.996	1.00
102_R	136_S	1.930	1.00
112_H	144_H	1.907	1.00
149_G	170_Y	1.894	1.00
36_T	54_D	1.855	1.00
139_H	142_A	1.828	1.00
111_L	144_H	1.816	1.00
71_Y	76_C	1.754	1.00
148_I	151_V	1.753	1.00
103_K	136_S	1.751	1.00
78_G	97_V	1.723	1.00
97_V	106_V	1.713	1.00
117_W	120_E	1.662	1.00
149_G	168_F	1.627	1.00
80_I	92_I	1.625	1.00
138_C	142_A	1.565	1.00
117_W	121_N	1.519	1.00
132_D	167_I	1.498	1.00
38_T	41_R	1.490	1.00
68_F	113_K	1.489	1.00
72_L	77_I	1.478	1.00
159_F	164_E	1.473	1.00
72_L	101_Y	1.433	1.00
71_Y	74_N	1.408	1.00
151_V	165_I	1.367	1.00
82_I	114_A	1.363	1.00
135_I	138_C	1.362	1.00
129_E	166_A	1.309	1.00
90_A	118_A	1.290	1.00
156_Y	166_A	1.275	1.00
127_M	170_Y	1.251	1.00
119_K	171_Y	1.234	1.00
101_Y	104_K	1.213	1.00
75_N	98_A	1.193	1.00
66_A	117_W	1.129	1.00
129_E	156_Y	1.119	1.00
128_L	141_Y	1.081	1.00
75_N	100_D	1.068	1.00
70_Y	78_G	1.051	1.00
83_R	91_L	1.051	1.00
127_M	149_G	1.045	1.00
53_D	56_D	1.037	1.00
105_G	108_T	1.032	1.00
118_A	126_L	1.031	1.00
108_T	112_H	1.027	1.00
34_V	38_T	1.018	1.00
155_L	166_A	1.018	1.00
88_G	124_C	1.004	1.00
42_F	46_Y	1.000	1.00
81_K	93_E	0.997	1.00
46_Y	99_K	0.996	1.00
91_L	127_M	0.987	1.00
80_I	110_L	0.986	1.00
137_A	141_Y	0.981	1.00
72_L	104_K	0.980	1.00
82_I	118_A	0.979	1.00
132_D	151_V	0.967	1.00
66_A	121_N	0.957	1.00
113_K	117_W	0.956	1.00
130_T	134_N	0.955	1.00
77_I	106_V	0.953	1.00
138_C	148_I	0.936	1.00
126_L	146_F	0.930	1.00
148_I	169_W	0.917	1.00
79_R	94_D	0.909	1.00
152_D	168_F	0.905	1.00
109_A	112_H	0.904	1.00
38_T	42_F	0.904	1.00
72_L	75_N	0.900	1.00
89_Y	127_M	0.899	1.00
37_Y	40_E	0.899	1.00
89_Y	152_D	0.895	1.00
68_F	117_W	0.893	1.00
111_L	146_F	0.889	1.00
34_V	37_Y	0.887	1.00
140_F	144_H	0.884	1.00
135_I	139_H	0.871	0.99
39_E	42_F	0.861	0.99
142_A	169_W	0.858	0.99
59_Y	81_K	0.857	0.99
115_I	144_H	0.850	0.99
79_R	96_A	0.844	0.99
82_I	90_A	0.827	0.99
97_V	107_G	0.824	0.99
83_R	93_E	0.816	0.99
103_K	107_G	0.815	0.99
57_V	79_R	0.800	0.99
130_T	137_A	0.794	0.99
70_Y	77_I	0.788	0.99
75_N	101_Y	0.785	0.99
47_F	96_A	0.783	0.99
118_A	123_F	0.781	0.99
130_T	141_Y	0.774	0.99
89_Y	125_G	0.773	0.99
129_E	155_L	0.766	0.99
116_E	120_E	0.765	0.99
142_A	147_I	0.764	0.99
47_F	102_R	0.762	0.99
131_Q	164_E	0.761	0.99
151_V	167_I	0.759	0.99
85_N	88_G	0.750	0.98
40_E	45_P	0.743	0.98
99_K	102_R	0.740	0.98
59_Y	65_K	0.734	0.98
109_A	113_K	0.731	0.98
154_M	160_P	0.727	0.98
81_K	94_D	0.727	0.98
46_Y	98_A	0.726	0.98
102_R	107_G	0.722	0.98
91_L	94_D	0.721	0.98
34_V	71_Y	0.717	0.98
138_C	167_I	0.716	0.98
147_I	170_Y	0.715	0.98
130_T	169_W	0.712	0.98
46_Y	50_Y	0.710	0.98
129_E	152_D	0.709	0.98
70_Y	110_L	0.704	0.98
68_F	80_I	0.702	0.98
50_Y	157_S	0.700	0.98
70_Y	109_A	0.697	0.97
44_K	47_F	0.695	0.97
37_Y	76_C	0.690	0.97
138_C	169_W	0.688	0.97
125_G	149_G	0.688	0.97
67_A	93_E	0.681	0.97
43_S	47_F	0.670	0.97
135_I	142_A	0.669	0.97
44_K	48_K	0.669	0.97
95_I	111_L	0.665	0.97
103_K	139_H	0.665	0.97
32_N	61_E	0.654	0.96
153_T	165_I	0.649	0.96
31_E	34_V	0.648	0.96
140_F	143_K	0.636	0.96
157_S	160_P	0.634	0.96
45_P	99_K	0.633	0.96
153_T	156_Y	0.624	0.95
112_H	116_E	0.622	0.95
131_Q	156_Y	0.622	0.95
103_K	108_T	0.620	0.95
70_Y	97_V	0.619	0.95
91_L	152_D	0.616	0.95
134_N	137_A	0.615	0.95
40_E	43_S	0.615	0.95
65_K	83_R	0.614	0.95
107_G	115_I	0.610	0.95
110_L	114_A	0.605	0.94
132_D	138_C	0.601	0.94
85_N	121_N	0.601	0.94
128_L	137_A	0.592	0.94
85_N	123_F	0.587	0.93
116_E	119_K	0.582	0.93
90_A	123_F	0.581	0.93
34_V	39_E	0.578	0.93
79_R	130_T	0.578	0.93
39_E	43_S	0.578	0.93
101_Y	106_V	0.571	0.93
47_F	51_E	0.570	0.92
129_E	164_E	0.569	0.92
80_I	118_A	0.568	0.92
56_D	93_E	0.567	0.92
88_G	150_A	0.566	0.92
115_I	140_F	0.564	0.92
168_F	171_Y	0.561	0.92
90_A	126_L	0.557	0.92
68_F	71_Y	0.557	0.92
86_W	168_F	0.554	0.91
154_M	165_I	0.552	0.91
51_E	57_V	0.551	0.91
35_W	39_E	0.548	0.91
82_I	126_L	0.543	0.91
98_A	101_Y	0.537	0.90
57_V	81_K	0.537	0.90
57_V	62_E	0.534	0.90
152_D	166_A	0.525	0.89
45_P	48_K	0.524	0.89
127_M	168_F	0.522	0.89
59_Y	67_A	0.519	0.89
77_I	98_A	0.518	0.88
81_K	92_I	0.514	0.88
45_P	50_Y	0.513	0.88
158_N	164_E	0.513	0.88
160_P	164_E	0.513	0.88
152_D	156_Y	0.510	0.88
131_Q	158_N	0.507	0.87
71_Y	75_N	0.506	0.87
116_E	124_C	0.505	0.87
80_I	111_L	0.505	0.87
136_S	139_H	0.501	0.87
50_Y	159_F	0.501	0.87
34_V	42_F	0.500	0.87

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
2reeA	1	0.8728	99.9	0.388	Contact Map
3dr6A	2	0.8613	99.9	0.406	Contact Map
2ob0A	1	0.8671	99.9	0.407	Contact Map
2cntA	1	0.8439	99.9	0.408	Contact Map
4kvxA	1	0.8266	99.9	0.409	Contact Map
4h89A	2	0.8844	99.9	0.41	Contact Map
4pv6C	3	0.8555	99.9	0.411	Contact Map
2j8mA	2	0.8613	99.9	0.413	Contact Map
4l8aA	1	0.8613	99.9	0.421	Contact Map
4ua3A	1	0.9769	99.9	0.424	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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