YUTI - BACSU - GREMLIN Contacts

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YUTI - Putative nitrogen fixation protein YutI

UniProt:	O32119	Sequences: MCYNRESNFANQTIDFYCYTEYNGFMTTKGANVMTEVEMKEQVQEVLDKLRPFLLRDGGDCELVDVDEGIVKLRLLGACGSCPSSTITLKAGIERALLEEVPGVVEVEQVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	111 (88)
Sequences:	706 (358)
Seq/√Len:	38.2

ECOLI - NFUA
BACSU - YUTI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_E	98_L	3.757	1.00
71_V	97_L	3.612	1.00
54_L	80_G	2.868	1.00
54_L	83_P	2.764	1.00
40_K	44_Q	2.496	1.00
70_I	106_E	2.455	1.00
53_F	61_C	2.064	0.99
47_L	93_I	2.058	0.99
36_E	44_Q	1.925	0.98
73_L	108_E	1.875	0.98
96_A	100_E	1.841	0.98
60_D	100_E	1.839	0.98
55_L	60_D	1.831	0.98
64_V	74_R	1.756	0.97
36_E	40_K	1.725	0.97
49_K	100_E	1.723	0.97
43_V	66_V	1.722	0.97
61_C	93_I	1.711	0.96
80_G	83_P	1.707	0.96
78_A	81_S	1.631	0.95
53_F	78_A	1.602	0.95
73_L	109_Q	1.595	0.95
76_L	80_G	1.583	0.94
87_I	91_A	1.537	0.94
86_T	93_I	1.392	0.90
36_E	46_V	1.346	0.88
54_L	102_P	1.313	0.87
49_K	99_E	1.309	0.86
54_L	61_C	1.303	0.86
47_L	72_K	1.301	0.86
55_L	81_S	1.272	0.85
83_P	102_P	1.243	0.83
72_K	108_E	1.195	0.81
53_F	94_E	1.178	0.80
46_V	49_K	1.119	0.76
49_K	73_L	1.073	0.73
23_N	67_D	1.064	0.73
30_G	64_V	1.049	0.72
93_I	107_V	1.047	0.71
25_F	28_T	1.044	0.71
76_L	81_S	1.036	0.71
37_V	40_K	1.027	0.70
25_F	29_K	1.016	0.69
54_L	95_R	1.008	0.68
69_G	104_V	1.007	0.68
84_S	87_I	0.977	0.66
45_E	96_A	0.977	0.66
23_N	27_T	0.955	0.64
95_R	102_P	0.928	0.62
27_T	31_A	0.903	0.60
79_C	82_C	0.892	0.59
105_V	108_E	0.888	0.59
70_I	105_V	0.882	0.58
44_Q	63_L	0.879	0.58
37_V	47_L	0.871	0.57
42_Q	50_L	0.859	0.56
32_N	36_E	0.855	0.56
26_M	33_V	0.846	0.55
61_C	80_G	0.846	0.55
24_G	27_T	0.830	0.53
89_L	93_I	0.822	0.53
55_L	74_R	0.810	0.52
26_M	29_K	0.792	0.50
50_L	86_T	0.786	0.49
37_V	60_D	0.757	0.47
101_V	105_V	0.756	0.47
62_E	106_E	0.741	0.45
42_Q	56_R	0.735	0.45
48_D	76_L	0.731	0.45
25_F	35_T	0.727	0.44
49_K	60_D	0.726	0.44
83_P	86_T	0.713	0.43
62_E	74_R	0.707	0.42
63_L	95_R	0.696	0.41
62_E	75_L	0.693	0.41
79_C	88_T	0.685	0.41
34_M	50_L	0.683	0.40
66_V	103_G	0.673	0.39
48_D	86_T	0.658	0.38
31_A	39_M	0.658	0.38
98_L	105_V	0.657	0.38
90_K	94_E	0.651	0.38
32_N	41_E	0.646	0.37
35_T	46_V	0.643	0.37
28_T	33_V	0.642	0.37
50_L	64_V	0.636	0.36
32_N	47_L	0.633	0.36
65_D	72_K	0.627	0.36
42_Q	49_K	0.621	0.35
62_E	95_R	0.619	0.35
23_N	26_M	0.619	0.35
30_G	109_Q	0.618	0.35
25_F	30_G	0.617	0.35
55_L	99_E	0.616	0.35
33_V	36_E	0.608	0.34
31_A	35_T	0.608	0.34
54_L	81_S	0.608	0.34
57_D	79_C	0.607	0.34
36_E	69_G	0.595	0.33
76_L	109_Q	0.594	0.33
40_K	66_V	0.591	0.33
62_E	76_L	0.590	0.33
84_S	90_K	0.590	0.33
54_L	62_E	0.590	0.33
34_M	40_K	0.589	0.33
34_M	63_L	0.587	0.32
66_V	104_V	0.581	0.32
29_K	33_V	0.578	0.32
82_C	88_T	0.574	0.31
23_N	31_A	0.569	0.31
60_D	76_L	0.565	0.31
29_K	32_N	0.560	0.30
40_K	60_D	0.559	0.30
37_V	41_E	0.557	0.30
39_M	103_G	0.553	0.30
45_E	48_D	0.548	0.29
25_F	68_E	0.546	0.29
38_E	43_V	0.541	0.29
30_G	34_M	0.541	0.29
87_I	98_L	0.534	0.28
56_R	103_G	0.534	0.28
74_R	103_G	0.533	0.28
23_N	28_T	0.532	0.28
84_S	92_G	0.527	0.28
105_V	110_V	0.524	0.28
85_S	89_L	0.517	0.27
81_S	86_T	0.517	0.27
45_E	49_K	0.517	0.27
40_K	63_L	0.514	0.27
80_G	98_L	0.512	0.27
24_G	29_K	0.510	0.27
70_I	102_P	0.500	0.26

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
1vehA	1	0.7748	100	0.369	Contact Map
1xhjA	1	0.7207	100	0.374	Contact Map
2m5oA	1	0.8198	100	0.383	Contact Map
2z51A	2	0.6937	99.9	0.402	Contact Map
1th5A	1	0.6577	99.9	0.497	Contact Map
3lnoA	1	0.7207	98.1	0.792	Contact Map
1uwdA	1	0.6847	97.5	0.816	Contact Map
3cq1A	2	0.6757	97.4	0.82	Contact Map
3ux2A	2	0.7568	68.7	0.904	Contact Map
4q2lA	1	0.3423	33.5	0.923	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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