zf-RVT - PFAM28P - GREMLIN Contacts

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zf-RVT - zinc-binding in reverse transcriptase

PFAM:	PF13966	Sequences: FSVKSAYKLLRGGSPSVPWWKLIWKLKAPPKIKFFLWLALHNRLPTKDNLARRGIQLDDLCPLCGEEEETIDHLFFECPFAREVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (85)
Sequences:	10614 (9176)
Seq/√Len:	995.3
META:	0.637

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
1_F	6_A	3.157	1.00
47_K	62_P	2.978	1.00
51_A	59_D	2.775	1.00
49_N	53_R	2.681	1.00
42_N	71_I	2.555	1.00
72_D	77_E	2.347	1.00
48_D	70_T	2.152	1.00
59_D	68_E	2.094	1.00
48_D	68_E	2.037	1.00
72_D	76_F	2.034	1.00
50_L	55_I	1.995	1.00
39_A	75_F	1.799	1.00
45_P	49_N	1.791	1.00
29_P	32_I	1.773	1.00
49_N	52_R	1.771	1.00
66_E	79_P	1.629	1.00
69_E	74_L	1.502	1.00
46_T	74_L	1.490	1.00
51_A	68_E	1.358	1.00
34_F	38_L	1.349	1.00
4_K	8_K	1.345	1.00
34_F	43_R	1.337	1.00
7_Y	11_R	1.326	1.00
2_S	5_S	1.320	1.00
47_K	50_L	1.318	1.00
8_K	11_R	1.317	1.00
30_P	33_K	1.312	1.00
79_P	82_R	1.297	1.00
11_R	14_S	1.297	1.00
60_L	65_G	1.286	1.00
47_K	58_D	1.257	1.00
51_A	57_L	1.187	1.00
60_L	67_E	1.156	1.00
26_L	33_K	1.125	1.00
35_F	44_L	1.120	1.00
6_A	9_L	1.111	1.00
48_D	52_R	1.072	1.00
30_P	34_F	1.050	1.00
31_K	37_W	1.048	1.00
32_I	35_F	1.035	1.00
38_L	45_P	1.023	1.00
38_L	43_R	1.017	1.00
74_L	81_A	1.010	1.00
63_L	80_F	1.006	1.00
60_L	68_E	0.996	1.00
51_A	58_D	0.996	1.00
20_W	23_I	0.992	1.00
5_S	8_K	0.977	1.00
28_A	32_I	0.965	1.00
61_C	64_C	0.949	1.00
42_N	49_N	0.948	1.00
7_Y	10_L	0.946	1.00
80_F	83_E	0.925	1.00
51_A	56_Q	0.914	1.00
8_K	12_G	0.885	1.00
20_W	40_L	0.883	1.00
70_T	77_E	0.875	1.00
38_L	41_H	0.870	1.00
46_T	71_I	0.863	1.00
1_F	7_Y	0.863	1.00
37_W	41_H	0.857	1.00
45_P	55_I	0.832	1.00
13_G	16_S	0.825	1.00
28_A	33_K	0.820	1.00
47_K	51_A	0.812	1.00
63_L	81_A	0.789	1.00
34_F	37_W	0.788	1.00
9_L	12_G	0.775	1.00
38_L	42_N	0.771	1.00
36_L	43_R	0.765	1.00
82_R	85_W	0.764	1.00
60_L	66_E	0.763	1.00
10_L	13_G	0.758	1.00
45_P	53_R	0.751	1.00
46_T	75_F	0.746	1.00
16_S	19_W	0.745	1.00
11_R	15_P	0.738	1.00
46_T	69_E	0.733	1.00
39_A	44_L	0.733	1.00
39_A	71_I	0.720	1.00
43_R	46_T	0.703	1.00
35_F	39_A	0.703	1.00
48_D	51_A	0.699	1.00
20_W	24_W	0.698	1.00
18_P	22_L	0.696	1.00
51_A	54_G	0.696	1.00
36_L	40_L	0.683	1.00
23_I	36_L	0.671	1.00
47_K	59_D	0.669	1.00
42_N	48_D	0.662	1.00
25_K	28_A	0.643	1.00
62_P	80_F	0.637	1.00
31_K	34_F	0.631	1.00
15_P	18_P	0.619	1.00
17_V	20_W	0.617	1.00
47_K	57_L	0.614	1.00
62_P	65_G	0.604	1.00
47_K	69_E	0.601	1.00
9_L	13_G	0.594	1.00
38_L	44_L	0.590	1.00
23_I	29_P	0.588	1.00
8_K	13_G	0.583	1.00
7_Y	25_K	0.582	1.00
74_L	80_F	0.576	1.00
57_L	60_L	0.574	1.00
43_R	49_N	0.562	1.00
29_P	36_L	0.555	1.00
42_N	45_P	0.551	1.00
39_A	46_T	0.549	1.00
4_K	13_G	0.548	1.00
27_K	32_I	0.548	1.00
1_F	63_L	0.543	1.00
49_N	71_I	0.539	1.00
5_S	9_L	0.534	1.00
50_L	56_Q	0.533	1.00
3_V	11_R	0.530	1.00
22_L	26_L	0.524	1.00
14_S	18_P	0.520	1.00
4_K	12_G	0.516	1.00
9_L	14_S	0.514	1.00
7_Y	12_G	0.514	1.00
30_P	43_R	0.506	1.00
35_F	75_F	0.504	1.00
27_K	30_P	0.503	1.00
21_K	25_K	0.502	1.00
35_F	38_L	0.501	1.00
6_A	14_S	0.501	1.00
77_E	80_F	0.500	1.00

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
2aklA	1	0.3765	3.6	0.894	Contact Map
3rj2X	1	0.3294	3.4	0.896	Contact Map
3bvoA	1	0.3176	2.7	0.901	Contact Map
3zpvA	2	0.3647	2.4	0.903	Contact Map
4nn2A	1	0.3294	2.2	0.905	Contact Map
3kv4A	1	0.3176	2	0.907	Contact Map
4rv9A	1	0.3765	1.9	0.909	Contact Map
2wx4A	3	0.3765	1.8	0.91	Contact Map
4nxiA	2	0.4235	1.7	0.911	Contact Map
2wx3A	3	0.4	1.7	0.911	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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