YURT - BACSU - GREMLIN Contacts

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YURT - Uncharacterized protein YurT

UniProt:	O32161	Sequences: MKIVVTSIFVQDQDMALEFYTEKLGFIKKEDVPMGKFRWITLVSPDDQDGTELLLEPNEHPAAKEYQKKIFSEGLPATMFGVADIQKEYNRLKEKGVTFTTEPTKMGEVTIAVFDDTCGNLIQIVQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	127 (120)
Sequences:	3549 (1816)
Seq/√Len:	165.8

ECOLI - LGUL YAER
BACSU - YURT YETH YWKD YWBC YRAH YQJC
HALSA - Q9HQK8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_E	22_E	5.832	1.00
90_N	94_E	3.845	1.00
98_T	115_D	3.805	1.00
91_R	95_K	2.943	1.00
84_D	87_K	2.929	1.00
93_K	102_E	2.491	1.00
29_K	43_V	2.278	1.00
13_Q	40_I	2.265	1.00
66_Y	72_S	2.187	1.00
92_L	97_V	2.093	1.00
100_T	121_L	2.001	1.00
11_Q	15_M	1.994	1.00
86_Q	110_T	1.858	1.00
23_K	95_K	1.829	1.00
4_V	81_G	1.759	1.00
17_L	28_K	1.750	1.00
31_D	38_R	1.711	1.00
115_D	121_L	1.663	1.00
65_E	68_K	1.606	1.00
61_P	64_K	1.563	1.00
12_D	15_M	1.540	1.00
34_M	37_F	1.525	1.00
28_K	31_D	1.489	1.00
86_Q	105_K	1.477	1.00
26_F	44_S	1.460	1.00
85_I	103_P	1.458	1.00
29_K	52_E	1.456	1.00
106_M	109_V	1.455	1.00
82_V	88_E	1.432	1.00
18_E	23_K	1.403	1.00
113_V	123_Q	1.393	1.00
11_Q	118_C	1.372	1.00
88_E	91_R	1.369	1.00
21_T	42_L	1.346	1.00
5_V	79_M	1.344	1.00
28_K	40_I	1.338	1.00
44_S	80_F	1.291	1.00
87_K	91_R	1.282	1.00
90_N	93_K	1.259	1.00
33_P	38_R	1.242	1.00
14_D	18_E	1.220	1.00
27_I	45_P	1.211	1.00
5_V	54_L	1.193	1.00
89_Y	112_A	1.185	1.00
101_T	104_T	1.156	1.00
86_Q	90_N	1.151	1.00
58_N	67_Q	1.148	1.00
92_L	99_F	1.146	1.00
100_T	115_D	1.100	1.00
3_I	80_F	1.096	1.00
33_P	59_E	1.087	1.00
23_K	92_L	1.085	1.00
78_T	122_I	1.073	1.00
27_I	46_D	1.057	0.99
27_I	43_V	1.055	0.99
18_E	21_T	1.051	0.99
15_M	118_C	1.049	0.99
89_Y	93_K	1.041	0.99
37_F	58_N	1.035	0.99
10_V	13_Q	1.033	0.99
79_M	125_V	1.023	0.99
112_A	124_I	0.983	0.99
10_V	16_A	0.977	0.99
99_F	103_P	0.962	0.99
38_R	59_E	0.961	0.99
53_L	78_T	0.953	0.99
92_L	124_I	0.939	0.99
35_G	59_E	0.930	0.99
5_V	41_T	0.922	0.98
17_L	40_I	0.917	0.98
101_T	112_A	0.906	0.98
62_A	65_E	0.891	0.98
22_E	95_K	0.891	0.98
99_F	114_F	0.880	0.98
101_T	111_I	0.868	0.98
11_Q	117_T	0.861	0.98
16_A	118_C	0.855	0.98
99_F	112_A	0.845	0.97
111_I	123_Q	0.843	0.97
86_Q	103_P	0.839	0.97
20_Y	24_L	0.835	0.97
60_H	63_A	0.834	0.97
86_Q	89_Y	0.832	0.97
11_Q	64_K	0.824	0.97
5_V	77_A	0.819	0.97
4_V	79_M	0.818	0.97
105_K	110_T	0.814	0.97
75_L	78_T	0.812	0.97
64_K	68_K	0.802	0.96
14_D	31_D	0.792	0.96
41_T	52_E	0.789	0.96
8_I	20_Y	0.780	0.96
39_W	56_E	0.780	0.96
16_A	20_Y	0.772	0.95
85_I	125_V	0.765	0.95
30_E	52_E	0.737	0.94
56_E	77_A	0.732	0.94
20_Y	116_D	0.725	0.94
92_L	114_F	0.722	0.94
10_V	40_I	0.715	0.93
60_H	73_E	0.713	0.93
41_T	54_L	0.710	0.93
97_V	114_F	0.709	0.93
88_E	92_L	0.706	0.93
20_Y	122_I	0.704	0.93
19_F	117_T	0.703	0.93
10_V	18_E	0.700	0.92
24_L	114_F	0.697	0.92
82_V	87_K	0.697	0.92
54_L	58_N	0.694	0.92
15_M	18_E	0.691	0.92
111_I	125_V	0.687	0.92
63_A	67_Q	0.684	0.92
85_I	126_Q	0.682	0.91
76_P	123_Q	0.674	0.91
56_E	75_L	0.674	0.91
68_K	72_S	0.660	0.90
86_Q	104_T	0.649	0.89
24_L	53_L	0.643	0.89
33_P	36_K	0.641	0.89
66_Y	77_A	0.640	0.89
42_L	52_E	0.633	0.88
89_Y	102_E	0.631	0.88
65_E	72_S	0.628	0.88
9_F	58_N	0.627	0.88
64_K	67_Q	0.625	0.88
62_A	66_Y	0.619	0.87
77_A	123_Q	0.619	0.87
23_K	97_V	0.615	0.87
85_I	111_I	0.614	0.87
77_A	113_V	0.611	0.86
11_Q	16_A	0.609	0.86
76_P	79_M	0.608	0.86
43_V	52_E	0.604	0.86
106_M	111_I	0.601	0.85
115_D	119_G	0.601	0.85
22_E	91_R	0.595	0.85
37_F	106_M	0.592	0.85
61_P	65_E	0.590	0.84
116_D	119_G	0.588	0.84
81_G	125_V	0.587	0.84
45_P	48_Q	0.586	0.84
54_L	77_A	0.581	0.84
68_K	74_G	0.578	0.83
54_L	79_M	0.578	0.83
9_F	75_L	0.576	0.83
44_S	47_D	0.572	0.83
7_S	54_L	0.569	0.82
29_K	41_T	0.569	0.82
104_T	111_I	0.565	0.82
37_F	56_E	0.561	0.81
9_F	72_S	0.553	0.80
60_H	64_K	0.551	0.80
26_F	80_F	0.551	0.80
32_V	35_G	0.550	0.80
56_E	60_H	0.549	0.80
67_Q	119_G	0.547	0.80
13_Q	57_P	0.545	0.79
14_D	38_R	0.544	0.79
17_L	21_T	0.539	0.79
87_K	90_N	0.538	0.79
21_T	28_K	0.536	0.78
17_L	42_L	0.535	0.78
6_T	77_A	0.529	0.77
116_D	120_N	0.528	0.77
23_K	114_F	0.527	0.77
47_D	51_T	0.523	0.77
5_V	52_E	0.523	0.77
113_V	125_V	0.521	0.76
85_I	88_E	0.521	0.76
8_I	75_L	0.515	0.76
89_Y	99_F	0.515	0.76
31_D	39_W	0.511	0.75
6_T	41_T	0.505	0.74
42_L	53_L	0.503	0.74
31_D	40_I	0.502	0.74
63_A	119_G	0.501	0.74
88_E	124_I	0.501	0.74
8_I	39_W	0.500	0.73
34_M	39_W	0.500	0.73

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
4g6xA	2	1	99.9	0.397	Contact Map
3w0tA	2	1	99.9	0.399	Contact Map
4mtsA	2	0.9606	99.9	0.412	Contact Map
1f9zA	2	0.9606	99.9	0.417	Contact Map
1ss4A	4	0.9764	99.9	0.424	Contact Map
3kolA	2	0.9685	99.8	0.442	Contact Map
3l7tA	2	0.9449	99.8	0.444	Contact Map
3hdpA	2	0.9606	99.8	0.444	Contact Map
2c21A	2	0.937	99.8	0.447	Contact Map
2p25A	2	0.9449	99.8	0.451	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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