YRKL - BACSU - GREMLIN Contacts

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YRKL - Uncharacterized NAD(P)H oxidoreductase YrkL

UniProt:	P54439	Sequences: MKTLVIVIHPNLETSVVNKTWMNRLKQEKDITVHDLYGEYPNFIIDVEKEQQLLLDHERIVFQFPMYWYSSPALLKQWEDDVLTHGWAYGTGGTKLHGKELLLAISLGAQESDYQAGGEYNITISELIRPFQVTANYIGMRFLPAFTQYGTLHLSKEDVKNSAERLVDYLKAEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	174 (165)
Sequences:	3729 (2713)
Seq/√Len:	211.2

ECOLI - KEFG KEFF YCAK MDAB AZOR
BACSU - YRKL GS14 YDEQ AZOR2 AZOR1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_T	56_D	3.661	1.00
77_Q	81_D	2.419	1.00
34_H	53_L	2.407	1.00
8_I	74_L	2.390	1.00
35_D	38_G	2.352	1.00
2_K	30_D	2.270	1.00
51_Q	87_W	2.135	1.00
32_T	53_L	2.084	1.00
101_L	135_A	2.050	1.00
66_M	105_I	2.029	1.00
59_R	100_E	2.003	1.00
7_V	18_N	1.972	1.00
52_Q	56_D	1.962	1.00
155_S	158_D	1.911	1.00
48_E	52_Q	1.910	1.00
34_H	39_E	1.908	1.00
43_F	77_Q	1.895	1.00
100_E	141_R	1.877	1.00
60_I	140_M	1.871	1.00
3_T	59_R	1.847	1.00
123_T	126_E	1.812	1.00
22_M	26_K	1.809	1.00
156_K	160_K	1.788	1.00
52_Q	55_L	1.779	1.00
76_K	80_D	1.772	1.00
19_K	23_N	1.759	1.00
55_L	87_W	1.756	1.00
4_L	53_L	1.731	1.00
49_K	53_L	1.730	1.00
39_E	53_L	1.670	1.00
164_E	167_V	1.639	1.00
32_T	57_H	1.631	1.00
8_I	37_Y	1.612	1.00
2_K	56_D	1.595	1.00
73_A	77_Q	1.591	1.00
5_V	22_M	1.563	1.00
50_E	78_W	1.543	1.00
23_N	26_K	1.519	1.00
24_R	167_V	1.468	1.00
63_Q	166_L	1.454	1.00
79_E	83_L	1.438	1.00
104_A	166_L	1.427	1.00
17_V	106_S	1.419	1.00
24_R	27_Q	1.414	1.00
101_L	140_M	1.405	1.00
4_L	57_H	1.377	1.00
34_H	50_E	1.377	1.00
158_D	161_N	1.375	1.00
160_K	164_E	1.367	1.00
20_T	24_R	1.359	1.00
51_Q	88_A	1.349	1.00
23_N	27_Q	1.349	1.00
162_S	165_R	1.331	1.00
3_T	29_K	1.322	1.00
18_N	33_V	1.316	1.00
97_H	139_G	1.313	1.00
154_L	159_V	1.300	1.00
47_V	51_Q	1.275	1.00
90_G	93_G	1.268	1.00
94_T	97_H	1.267	1.00
39_E	49_K	1.264	1.00
49_K	52_Q	1.262	1.00
63_Q	104_A	1.228	1.00
161_N	165_R	1.210	1.00
66_M	124_I	1.205	1.00
135_A	140_M	1.197	1.00
124_I	147_T	1.194	1.00
14_T	106_S	1.186	1.00
46_D	49_K	1.185	1.00
146_F	165_R	1.178	1.00
37_Y	74_L	1.174	1.00
8_I	75_L	1.161	1.00
148_Q	154_L	1.160	1.00
39_E	50_E	1.150	1.00
164_E	168_D	1.118	1.00
126_E	129_R	1.117	1.00
21_W	25_L	1.110	1.00
71_S	75_L	1.103	1.00
104_A	146_F	1.100	1.00
20_T	23_N	1.100	1.00
14_T	63_Q	1.099	1.00
111_E	115_Q	1.088	1.00
20_T	167_V	1.075	1.00
133_V	136_N	1.071	1.00
24_R	28_E	1.065	1.00
57_H	60_I	1.065	1.00
61_V	102_L	1.060	1.00
98_G	141_R	1.057	1.00
90_G	95_K	1.056	1.00
96_L	140_M	1.043	1.00
111_E	149_Y	1.035	1.00
22_M	33_V	1.028	1.00
107_L	149_Y	1.020	1.00
6_I	34_H	1.010	1.00
53_L	56_D	1.002	1.00
48_E	51_Q	1.001	1.00
58_E	99_K	0.997	1.00
83_L	138_I	0.996	1.00
41_P	44_I	0.982	1.00
64_F	103_L	0.964	1.00
51_Q	84_T	0.951	1.00
148_Q	162_S	0.943	0.99
7_V	15_S	0.941	0.99
27_Q	167_V	0.928	0.99
129_R	132_Q	0.923	0.99
55_L	95_K	0.922	0.99
110_Q	113_D	0.921	0.99
8_I	36_L	0.920	0.99
26_K	30_D	0.915	0.99
166_L	169_Y	0.908	0.99
30_D	56_D	0.907	0.99
15_S	18_N	0.905	0.99
154_L	158_D	0.899	0.99
68_W	80_D	0.895	0.99
159_V	163_A	0.893	0.99
41_P	77_Q	0.892	0.99
16_V	163_A	0.890	0.99
41_P	45_I	0.867	0.99
109_A	120_Y	0.859	0.99
10_P	67_Y	0.852	0.99
69_Y	137_Y	0.848	0.99
105_I	147_T	0.847	0.99
104_A	148_Q	0.820	0.99
16_V	156_K	0.816	0.98
105_I	128_I	0.809	0.98
107_L	147_T	0.806	0.98
134_T	138_I	0.804	0.98
102_L	169_Y	0.803	0.98
59_R	102_L	0.803	0.98
54_L	60_I	0.797	0.98
69_Y	133_V	0.796	0.98
85_H	91_T	0.795	0.98
34_H	78_W	0.793	0.98
100_E	143_L	0.790	0.98
79_E	134_T	0.789	0.98
64_F	124_I	0.787	0.98
62_F	135_A	0.787	0.98
102_L	146_F	0.786	0.98
2_K	58_E	0.785	0.98
23_N	167_V	0.778	0.98
25_L	166_L	0.776	0.98
18_N	63_Q	0.769	0.98
107_L	124_I	0.769	0.98
66_M	127_L	0.768	0.98
12_L	38_G	0.759	0.98
16_V	159_V	0.748	0.97
20_T	160_K	0.746	0.97
155_S	159_V	0.745	0.97
21_W	104_A	0.745	0.97
73_A	81_D	0.745	0.97
46_D	50_E	0.735	0.97
54_L	78_W	0.730	0.97
135_A	142_F	0.728	0.97
66_M	114_Y	0.727	0.97
68_W	89_Y	0.725	0.97
161_N	164_E	0.724	0.97
101_L	142_F	0.723	0.97
127_L	133_V	0.721	0.97
64_F	105_I	0.721	0.97
159_V	162_S	0.715	0.97
54_L	62_F	0.711	0.96
5_V	61_V	0.708	0.96
144_P	169_Y	0.697	0.96
64_F	128_I	0.693	0.96
85_H	89_Y	0.692	0.96
21_W	166_L	0.692	0.96
165_R	168_D	0.690	0.96
11_N	14_T	0.690	0.96
100_E	139_G	0.683	0.96
50_E	53_L	0.675	0.95
8_I	35_D	0.667	0.95
16_V	20_T	0.662	0.95
40_Y	45_I	0.660	0.95
113_D	119_E	0.658	0.95
5_V	21_W	0.654	0.94
109_A	150_G	0.651	0.94
107_L	114_Y	0.650	0.94
43_F	81_D	0.648	0.94
17_V	104_A	0.641	0.94
4_L	34_H	0.640	0.94
20_T	163_A	0.638	0.94
21_W	148_Q	0.636	0.93
94_T	139_G	0.633	0.93
114_Y	118_G	0.632	0.93
48_E	161_N	0.631	0.93
126_E	132_Q	0.626	0.93
41_P	81_D	0.625	0.93
2_K	35_D	0.625	0.93
64_F	75_L	0.624	0.93
64_F	71_S	0.624	0.93
72_P	80_D	0.624	0.93
15_S	19_K	0.619	0.93
151_T	159_V	0.613	0.92
51_Q	82_V	0.613	0.92
71_S	79_E	0.613	0.92
5_V	31_I	0.612	0.92
88_A	96_L	0.612	0.92
93_G	97_H	0.606	0.92
6_I	62_F	0.600	0.91
7_V	12_L	0.596	0.91
6_I	78_W	0.591	0.91
54_L	83_L	0.590	0.91
44_I	77_Q	0.588	0.91
86_G	90_G	0.579	0.90
119_E	137_Y	0.577	0.90
74_L	78_W	0.575	0.90
51_Q	85_H	0.567	0.89
108_G	152_L	0.565	0.89
64_F	72_P	0.564	0.89
125_S	145_A	0.562	0.88
43_F	74_L	0.560	0.88
75_L	79_E	0.557	0.88
7_V	22_M	0.556	0.88
132_Q	142_F	0.554	0.88
61_V	166_L	0.551	0.88
154_L	162_S	0.550	0.87
20_T	164_E	0.549	0.87
116_A	126_E	0.547	0.87
17_V	162_S	0.546	0.87
102_L	144_P	0.544	0.87
21_W	162_S	0.543	0.87
48_E	84_T	0.538	0.86
69_Y	109_A	0.536	0.86
81_D	84_T	0.532	0.86
125_S	147_T	0.532	0.86
29_K	59_R	0.530	0.85
70_S	76_K	0.530	0.85
146_F	166_L	0.528	0.85
13_E	19_K	0.527	0.85
120_Y	133_V	0.526	0.85
68_W	133_V	0.523	0.85
156_K	159_V	0.522	0.85
11_N	81_D	0.522	0.85
146_F	169_Y	0.517	0.84
52_Q	168_D	0.516	0.84
25_L	28_E	0.516	0.84
43_F	73_A	0.513	0.84
31_I	36_L	0.512	0.83
7_V	33_V	0.512	0.83
10_P	37_Y	0.512	0.83
79_E	101_L	0.511	0.83
91_T	138_I	0.510	0.83
121_N	126_E	0.509	0.83
69_Y	120_Y	0.508	0.83
14_T	77_Q	0.506	0.83
6_I	79_E	0.505	0.83
157_E	161_N	0.502	0.82
50_E	82_V	0.500	0.82

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
1d4aA	2	0.9943	100	0.365	Contact Map
4gi5A	2	0.9943	100	0.386	Contact Map
2amjA	2	0.9425	100	0.423	Contact Map
3l9wA	2	0.9885	100	0.431	Contact Map
4fglA	2	0.9943	100	0.435	Contact Map
3f2vA	2	0.977	100	0.444	Contact Map
3ha2A	2	0.9483	100	0.448	Contact Map
3rpeA	2	0.9598	100	0.454	Contact Map
3lcmA	2	0.9655	100	0.461	Contact Map
4r81A	4	0.977	100	0.47	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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