FER - HALSA - GREMLIN Contacts

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FER - Ferredoxin

UniProt:	P00216	Sequences: MPTVEYLNYETLDDQGWDMDDDDLFEKAADAGLDGEDYGTMEVAEGEYILEAAEAQGYDWPFSCRAGACANCASIVKEGEIDMDMQQILSDEEVEEKDVRLTCIGSPAADEVKIVYNAKHLDYLQNRVI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	129 (111)
Sequences:	1673 (1048)
Seq/√Len:	99.5

ECOLI - PAAE YEAX HCR
HALSA - FER Q9HMG3 Q9HS23

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_E	108_A	5.560	1.00
74_S	102_T	4.798	1.00
91_D	96_E	4.506	1.00
80_E	109_A	3.840	1.00
78_E	111_E	3.432	1.00
47_E	55_A	3.279	1.00
81_I	105_G	2.897	1.00
84_D	106_S	2.762	1.00
53_A	60_W	2.453	1.00
76_V	100_R	2.297	1.00
78_E	113_K	2.145	1.00
39_G	58_Y	2.083	1.00
54_E	65_R	2.003	1.00
29_A	40_T	1.937	1.00
48_Y	51_E	1.772	1.00
30_D	34_D	1.686	1.00
114_I	117_N	1.648	1.00
31_A	34_D	1.638	1.00
49_I	112_V	1.613	1.00
83_M	94_V	1.605	1.00
81_I	112_V	1.596	1.00
77_K	115_V	1.370	0.99
75_I	99_V	1.338	0.99
86_Q	94_V	1.328	0.99
28_A	31_A	1.248	0.99
62_F	65_R	1.246	0.99
44_A	47_E	1.244	0.99
51_E	65_R	1.210	0.99
43_V	49_I	1.207	0.99
87_Q	91_D	1.124	0.98
8_N	12_L	1.113	0.98
82_D	106_S	1.099	0.97
41_M	56_Q	1.061	0.97
41_M	52_A	1.059	0.97
77_K	113_K	1.053	0.97
47_E	52_A	1.050	0.96
49_I	53_A	1.045	0.96
63_S	66_A	1.044	0.96
85_M	88_I	1.043	0.96
17_W	20_D	1.024	0.96
100_R	105_G	1.014	0.96
10_E	14_D	1.007	0.96
54_E	62_F	1.000	0.95
50_L	54_E	0.991	0.95
29_A	111_E	0.988	0.95
88_I	93_E	0.983	0.95
73_A	99_V	0.975	0.95
54_E	60_W	0.961	0.94
9_Y	13_D	0.957	0.94
45_E	110_D	0.952	0.94
15_Q	20_D	0.943	0.94
73_A	93_E	0.938	0.94
28_A	32_G	0.925	0.93
26_E	110_D	0.919	0.93
102_T	116_Y	0.914	0.93
71_N	87_Q	0.911	0.92
22_D	26_E	0.909	0.92
50_L	60_W	0.903	0.92
29_A	32_G	0.892	0.92
20_D	24_L	0.889	0.92
32_G	53_A	0.882	0.91
90_S	104_I	0.879	0.91
29_A	42_E	0.864	0.90
111_E	114_I	0.861	0.90
33_L	38_Y	0.855	0.90
9_Y	21_D	0.845	0.89
33_L	113_K	0.844	0.89
19_M	22_D	0.839	0.89
82_D	105_G	0.837	0.89
52_A	55_A	0.837	0.89
6_Y	21_D	0.836	0.89
68_A	73_A	0.828	0.88
78_E	112_V	0.824	0.88
70_A	88_I	0.814	0.88
65_R	70_A	0.810	0.87
92_E	96_E	0.808	0.87
86_Q	104_I	0.806	0.87
83_M	93_E	0.805	0.87
59_D	90_S	0.802	0.87
19_M	23_D	0.802	0.87
83_M	100_R	0.798	0.87
48_Y	65_R	0.794	0.86
18_D	22_D	0.785	0.86
105_G	109_A	0.784	0.86
24_L	28_A	0.780	0.85
85_M	94_V	0.777	0.85
73_A	87_Q	0.773	0.85
54_E	66_A	0.764	0.84
62_F	89_L	0.746	0.83
71_N	74_S	0.744	0.82
13_D	17_W	0.743	0.82
75_I	98_D	0.734	0.82
65_R	68_A	0.722	0.81
21_D	25_F	0.720	0.80
21_D	24_L	0.703	0.79
50_L	62_F	0.702	0.79
6_Y	87_Q	0.691	0.78
65_R	71_N	0.689	0.77
59_D	62_F	0.688	0.77
71_N	88_I	0.685	0.77
82_D	108_A	0.683	0.77
27_K	30_D	0.676	0.76
31_A	40_T	0.676	0.76
83_M	86_Q	0.675	0.76
50_L	68_A	0.670	0.75
71_N	83_M	0.670	0.75
53_A	66_A	0.666	0.75
6_Y	9_Y	0.665	0.75
8_N	13_D	0.661	0.74
27_K	42_E	0.658	0.74
8_N	11_T	0.655	0.74
68_A	88_I	0.651	0.73
29_A	33_L	0.642	0.72
22_D	42_E	0.642	0.72
76_V	81_I	0.640	0.72
60_W	102_T	0.639	0.72
51_E	89_L	0.628	0.71
52_A	65_R	0.625	0.70
43_V	52_A	0.618	0.69
46_G	106_S	0.610	0.68
15_Q	18_D	0.607	0.68
35_G	74_S	0.607	0.68
57_G	63_S	0.607	0.68
70_A	74_S	0.602	0.67
39_G	56_Q	0.596	0.67
91_D	97_K	0.596	0.67
23_D	27_K	0.592	0.66
48_Y	106_S	0.592	0.66
88_I	99_V	0.581	0.65
9_Y	17_W	0.580	0.64
19_M	97_K	0.575	0.64
27_K	31_A	0.568	0.63
65_R	89_L	0.566	0.63
75_I	117_N	0.561	0.62
99_V	117_N	0.560	0.62
37_D	58_Y	0.558	0.62
36_E	90_S	0.553	0.61
61_P	74_S	0.553	0.61
44_A	106_S	0.551	0.61
68_A	90_S	0.542	0.59
71_N	115_V	0.541	0.59
48_Y	53_A	0.538	0.59
93_E	100_R	0.537	0.59
24_L	45_E	0.533	0.58
9_Y	14_D	0.532	0.58
62_F	84_D	0.527	0.57
30_D	45_E	0.526	0.57
48_Y	84_D	0.525	0.57
37_D	60_W	0.524	0.57
107_P	112_V	0.524	0.57
52_A	56_Q	0.521	0.56
18_D	23_D	0.520	0.56
87_Q	94_V	0.518	0.56
50_L	86_Q	0.518	0.56
19_M	24_L	0.516	0.56
23_D	45_E	0.515	0.55
7_L	11_T	0.512	0.55
13_D	16_G	0.511	0.55
43_V	107_P	0.510	0.55
88_I	104_I	0.506	0.54
18_D	24_L	0.506	0.54
52_A	62_F	0.505	0.54
49_I	111_E	0.505	0.54
73_A	88_I	0.504	0.54
6_Y	18_D	0.503	0.54
58_Y	63_S	0.500	0.53

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
1doiA	5	0.9767	99.9	0.422	Contact Map
2piaA	1	0.8372	99.9	0.449	Contact Map
3zyyX	2	0.7752	99.9	0.501	Contact Map
1qoaA	1	0.7442	99.9	0.501	Contact Map
1iueA	1	0.7597	99.9	0.504	Contact Map
1frrA	1	0.7364	99.9	0.505	Contact Map
3wcqA	1	0.7364	99.9	0.509	Contact Map
4itkA	1	0.7829	99.9	0.509	Contact Map
1frdA	1	0.7442	99.9	0.512	Contact Map
1awdA	2	0.7209	99.9	0.512	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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