ETC_C1_NDUFA5 - PFAM28P - GREMLIN Contacts

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ETC_C1_NDUFA5 - ETC complex I subunit conserved region

PFAM:	PF04716	Sequences: NPRETLIKLYTKTLDKLKKIPEDSVYRQSTEALTKHRLKIVEEEEDIEKIEKKIG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (54)
Sequences:	901 (674)
Seq/√Len:	91.7
META:	0.499

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_K	43_E	3.258	1.00
27_R	31_E	2.569	1.00
44_E	49_K	2.031	1.00
15_D	18_K	1.982	1.00
18_K	22_E	1.939	1.00
46_D	49_K	1.934	1.00
40_I	50_I	1.928	1.00
11_T	42_E	1.917	1.00
7_I	38_L	1.831	1.00
31_E	35_K	1.829	1.00
43_E	53_K	1.759	1.00
13_T	34_T	1.520	1.00
11_T	38_L	1.429	0.99
25_V	28_Q	1.373	0.99
17_L	30_T	1.347	0.99
3_R	45_E	1.299	0.99
6_L	10_Y	1.220	0.98
3_R	7_I	1.184	0.98
25_V	29_S	1.168	0.98
10_Y	13_T	1.139	0.97
20_I	24_S	1.105	0.97
37_R	54_I	1.100	0.97
10_Y	34_T	1.097	0.97
29_S	32_A	1.090	0.96
46_D	51_E	1.082	0.96
10_Y	41_V	1.074	0.96
18_K	31_E	1.054	0.96
48_E	52_K	1.031	0.95
47_I	51_E	1.006	0.94
23_D	28_Q	0.981	0.94
10_Y	37_R	0.965	0.93
40_I	53_K	0.963	0.93
1_N	4_E	0.940	0.92
28_Q	32_A	0.926	0.92
7_I	41_V	0.920	0.91
44_E	50_I	0.901	0.90
26_Y	30_T	0.885	0.90
22_E	27_R	0.878	0.89
30_T	34_T	0.846	0.87
5_T	9_L	0.831	0.86
12_K	16_K	0.803	0.84
50_I	54_I	0.802	0.84
44_E	53_K	0.798	0.84
49_K	52_K	0.794	0.84
33_L	37_R	0.772	0.82
36_H	40_I	0.756	0.81
9_L	12_K	0.755	0.81
35_K	39_K	0.745	0.80
7_I	42_E	0.739	0.79
35_K	38_L	0.739	0.79
5_T	8_K	0.734	0.79
17_L	27_R	0.726	0.78
4_E	8_K	0.723	0.78
22_E	31_E	0.711	0.77
7_I	11_T	0.702	0.76
39_K	42_E	0.692	0.75
49_K	53_K	0.685	0.74
8_K	11_T	0.681	0.73
3_R	50_I	0.649	0.70
6_L	13_T	0.645	0.69
10_Y	33_L	0.644	0.69
40_I	54_I	0.643	0.69
2_P	41_V	0.628	0.67
4_E	7_I	0.627	0.67
4_E	12_K	0.623	0.67
45_E	49_K	0.610	0.65
6_L	41_V	0.603	0.64
41_V	47_I	0.599	0.64
20_I	37_R	0.588	0.62
2_P	30_T	0.583	0.62
38_L	42_E	0.580	0.61
36_H	54_I	0.558	0.58
16_K	20_I	0.555	0.58
14_L	34_T	0.553	0.58
20_I	30_T	0.538	0.56
7_I	35_K	0.530	0.54
45_E	51_E	0.522	0.53
24_S	29_S	0.518	0.53
41_V	50_I	0.510	0.52
29_S	33_L	0.502	0.51
28_Q	39_K	0.500	0.50

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
3uv5A	1	1	29.7	0.806	Contact Map
3aadA	1	1	24.3	0.814	Contact Map
1s94A	1	0.6545	19.1	0.823	Contact Map
4xy8A	1	0.9455	13.2	0.835	Contact Map
1e6iA	1	0.9636	12	0.838	Contact Map
4uitA	1	0.9636	11.1	0.841	Contact Map
2i7kA	1	1	10.3	0.843	Contact Map
2dkwA	1	0.9273	8.1	0.85	Contact Map
4algA	2	0.9455	7.7	0.852	Contact Map
4i3hA	2	1	7.4	0.853	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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