OPENSEQ.org - NAPF - ECOLI GREMLIN

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NAPF - Ferredoxin-type protein NapF

UniProt:	P0AAL0	Sequence MKIDASRRGILTGRWRKASNGIRPPWSGDESHFLTHCTRCDACINACENNILQRGAGGYPSVNFKNNECSFCYACAQACPESLFSPRHTRAWDLQFTIGDACLAYQSVECRRCQDSCEPMAIIFRPTLSGIYQPQLNSQLCNGCGACAASCPVSAITAEYLHAH	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12068
Length:	164 (160)
Sequences:	495
Seq/Len:	3.09

NAPF
Paralog alert: 0.67 [within 20: 0.30] - ratio of genomes with paralogs
Cluster includes: NAPF NAPG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
23_R	30_E	2.914	1.00
52_L	62_V	2.812	1.00
51_I	67_N	2.631	1.00
42_A	80_P	2.573	1.00
74_A	77_Q	2.455	1.00
123_I	137_N	1.97	1.00
7_R	10_I	1.905	0.99
44_I	52_L	1.855	0.99
39_R	58_G	1.826	0.99
41_D	54_R	1.781	0.99
23_R	27_S	1.771	0.99
30_E	34_L	1.756	0.99
46_A	74_A	1.699	0.98
51_I	62_V	1.668	0.98
39_R	59_Y	1.66	0.98
44_I	54_R	1.65	0.98
24_P	27_S	1.63	0.98
28_G	36_H	1.615	0.98
42_A	45_N	1.505	0.96
93_D	96_F	1.477	0.95
39_R	136_L	1.438	0.94
111_R	132_Y	1.417	0.94
23_R	59_Y	1.401	0.93
68_E	84_F	1.384	0.93
111_R	115_D	1.383	0.93
71_F	142_N	1.353	0.92
109_E	132_Y	1.346	0.92
125_R	136_L	1.338	0.91
8_R	11_L	1.32	0.90
120_M	140_L	1.312	0.90
44_I	136_L	1.311	0.90
105_Y	133_Q	1.303	0.90
51_I	70_S	1.288	0.89
73_Y	76_A	1.261	0.88
46_A	83_L	1.251	0.87
63_N	66_N	1.242	0.86
76_A	84_F	1.241	0.86
27_S	83_L	1.239	0.86
9_G	96_F	1.204	0.84
11_L	24_P	1.198	0.84
26_W	76_A	1.191	0.83
10_I	15_W	1.178	0.82
115_D	152_P	1.171	0.82
68_E	149_A	1.164	0.81
46_A	142_N	1.16	0.81
123_I	140_L	1.145	0.80
92_W	95_Q	1.143	0.80
39_R	57_G	1.141	0.79
100_D	137_N	1.139	0.79
68_E	71_F	1.132	0.79
51_I	64_F	1.124	0.78
53_Q	63_N	1.116	0.77
60_P	155_A	1.115	0.77
7_R	11_L	1.112	0.77
41_D	44_I	1.11	0.77
126_P	129_S	1.106	0.76
100_D	138_S	1.099	0.76
124_F	148_A	1.095	0.75
49_N	70_S	1.09	0.75
111_R	114_Q	1.066	0.73
55_G	58_G	1.06	0.72
119_P	142_N	1.059	0.72
56_A	127_T	1.058	0.72
38_T	81_E	1.055	0.71
116_S	150_S	1.052	0.71
136_L	148_A	1.042	0.70
114_Q	119_P	1.04	0.70
99_G	125_R	1.036	0.69
29_D	32_H	1.033	0.69
128_L	150_S	1.031	0.69
67_N	149_A	1.031	0.69
122_I	152_P	1.03	0.69
34_L	59_Y	1.026	0.68
6_S	15_W	1.008	0.66
82_S	96_F	1.002	0.66
22_I	62_V	1.002	0.66

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
1kqfB	1	0.8841	99.7	0.652	Contact Map	0.205
1h0hB	2	0.7561	99.7	0.676	Contact Map	0.135
2ivfB	1	0.8415	99.7	0.679	Contact Map	0.208
1ti6B	6	0.75	99.6	0.685	Contact Map	0.181
2vpzB	2	0.7439	99.6	0.695	Contact Map	0.15
1q16B	1	0.8232	98.9	0.779	Contact Map	0.225
1jnrB	2	0.3902	98.8	0.787	Contact Map	0.061
2c42A	2	0.8659	98.8	0.788	Contact Map	0.119
3gyxB	6	0.3841	98.8	0.79	Contact Map	0.063
2v2kA	2	0.372	98.8	0.793	Contact Map	0.335

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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