NADH_dehy_S2_C - PFAM28P - GREMLIN Contacts

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NADH_dehy_S2_C - NADH dehydrogenase subunit 2 C-terminus

PFAM:	PF06444	Sequences: LFFYLRLAYATTLTLPPNTTNSMKKWRLKKTQTTLLLAILTTLSILLLPLTPMIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (54)
Sequences:	6912 (2700)
Seq/√Len:	367.4
META:	0.001

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_T	46_L	3.360	1.00
33_T	36_L	2.811	1.00
9_Y	14_T	2.052	1.00
38_A	41_T	2.021	1.00
36_L	39_I	1.918	1.00
20_T	23_M	1.794	1.00
42_T	45_I	1.747	1.00
38_A	42_T	1.741	1.00
2_F	21_N	1.668	1.00
22_S	25_K	1.657	1.00
39_I	42_T	1.647	1.00
10_A	16_P	1.558	1.00
5_L	8_A	1.525	1.00
20_T	24_K	1.434	1.00
17_P	26_W	1.301	1.00
3_F	6_R	1.298	1.00
40_L	43_L	1.289	1.00
43_L	47_L	1.255	1.00
24_K	28_L	1.220	1.00
21_N	30_K	1.218	1.00
5_L	23_M	1.199	1.00
11_T	25_K	1.195	1.00
41_T	45_I	1.193	1.00
20_T	33_T	1.187	1.00
8_A	15_L	1.175	1.00
20_T	30_K	1.165	1.00
7_L	19_T	1.163	1.00
40_L	45_I	1.054	1.00
18_N	22_S	1.039	1.00
15_L	18_N	1.037	1.00
26_W	49_P	0.980	1.00
48_L	54_I	0.944	1.00
7_L	37_L	0.907	1.00
39_I	43_L	0.902	1.00
11_T	22_S	0.894	1.00
7_L	10_A	0.894	1.00
36_L	40_L	0.888	1.00
8_A	19_T	0.872	1.00
11_T	15_L	0.866	1.00
8_A	24_K	0.835	1.00
22_S	27_R	0.831	1.00
13_L	42_T	0.823	1.00
3_F	21_N	0.822	1.00
7_L	18_N	0.815	1.00
14_T	41_T	0.809	1.00
10_A	13_L	0.808	1.00
19_T	26_W	0.796	1.00
19_T	22_S	0.754	1.00
8_A	27_R	0.751	1.00
13_L	18_N	0.744	1.00
9_Y	49_P	0.742	1.00
48_L	51_T	0.736	1.00
20_T	40_L	0.711	0.99
23_M	53_M	0.663	0.99
7_L	43_L	0.658	0.99
15_L	21_N	0.657	0.99
42_T	47_L	0.641	0.99
32_Q	35_L	0.634	0.99
37_L	52_P	0.631	0.99
8_A	20_T	0.630	0.99
18_N	23_M	0.606	0.98
9_Y	28_L	0.598	0.98
3_F	13_L	0.594	0.98
15_L	35_L	0.585	0.98
10_A	15_L	0.583	0.98
40_L	46_L	0.579	0.98
9_Y	21_N	0.571	0.98
10_A	33_T	0.562	0.97
16_P	27_R	0.551	0.97
12_T	17_P	0.545	0.97
13_L	16_P	0.540	0.97
32_Q	39_I	0.528	0.96
34_T	40_L	0.526	0.96
44_S	50_L	0.523	0.96
12_T	52_P	0.523	0.96
25_K	28_L	0.510	0.95
5_L	12_T	0.505	0.95
23_M	54_I	0.504	0.95
12_T	18_N	0.504	0.95
35_L	39_I	0.502	0.95
38_A	46_L	0.500	0.95

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
4he8N	1	0.8727	3.6	0.861	Contact Map
3rkoN	1	0.8727	3.2	0.865	Contact Map
3rkoL	1	0.9091	2.5	0.873	Contact Map
2l2tA	2	0.2727	1.7	0.884	Contact Map
3wu2J	1	0.2545	1.4	0.889	Contact Map
4he8L	1	0.9273	1.3	0.891	Contact Map
4he8M	1	0.8727	1.2	0.893	Contact Map
4zwjA	1	0.9818	0.9	0.901	Contact Map
2wn4A	1	0	0.9	0.902	Contact Map
4c68A	1	0.4182	0.7	0.907	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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