DUF4379 - PFAM28P - GREMLIN Contacts

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DUF4379 - Probable Zinc-ribbon domain

PFAM:	PF14311	Sequences: PELAKEWHPTKNGDLTPEDVTPGSNKKVWWKCPKCGHEWEASISNRTRGNGGCPYC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (54)
Sequences:	33270 (29105)
Seq/√Len:	3960.7
META:	0.946

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_E	46_R	2.911	1.00
8_H	38_E	2.296	1.00
16_T	19_D	2.186	1.00
29_W	40_E	2.086	1.00
15_L	20_V	1.908	1.00
8_H	31_K	1.891	1.00
42_S	45_N	1.876	1.00
31_K	38_E	1.827	1.00
37_H	55_Y	1.807	1.00
28_V	43_I	1.772	1.00
27_K	40_E	1.756	1.00
23_G	47_T	1.556	1.00
41_A	45_N	1.496	1.00
11_K	38_E	1.421	1.00
11_K	29_W	1.411	1.00
39_W	46_R	1.378	1.00
25_N	44_S	1.358	1.00
24_S	43_I	1.335	1.00
6_E	33_P	1.319	1.00
27_K	42_S	1.302	1.00
20_V	43_I	1.290	1.00
7_W	28_V	1.229	1.00
29_W	38_E	1.221	1.00
15_L	28_V	1.105	1.00
23_G	44_S	1.072	1.00
41_A	46_R	1.069	1.00
30_W	46_R	1.059	1.00
8_H	29_W	1.049	1.00
53_C	56_C	1.005	1.00
4_A	17_P	0.983	1.00
7_W	17_P	0.972	1.00
39_W	54_P	0.971	1.00
44_S	48_R	0.949	1.00
15_L	26_K	0.949	1.00
25_N	42_S	0.922	1.00
45_N	49_G	0.906	1.00
3_L	47_T	0.904	1.00
45_N	48_R	0.873	1.00
45_N	50_N	0.847	1.00
8_H	11_K	0.834	1.00
9_P	17_P	0.830	1.00
7_W	16_T	0.790	1.00
6_E	39_W	0.790	1.00
20_V	28_V	0.784	1.00
21_T	24_S	0.766	1.00
20_V	26_K	0.745	1.00
4_A	16_T	0.727	1.00
15_L	19_D	0.712	1.00
32_C	56_C	0.710	1.00
22_P	47_T	0.701	1.00
32_C	37_H	0.696	1.00
34_K	55_Y	0.687	1.00
34_K	37_H	0.676	1.00
48_R	51_G	0.671	1.00
33_P	36_G	0.668	1.00
9_P	31_K	0.664	1.00
24_S	28_V	0.654	1.00
5_K	33_P	0.649	1.00
41_A	51_G	0.641	1.00
7_W	12_N	0.631	1.00
46_R	51_G	0.631	1.00
2_E	5_K	0.628	1.00
12_N	29_W	0.627	1.00
41_A	50_N	0.592	1.00
30_W	43_I	0.585	1.00
23_G	48_R	0.579	1.00
30_W	39_W	0.575	1.00
45_N	51_G	0.574	1.00
36_G	55_Y	0.567	1.00
1_P	4_A	0.560	1.00
24_S	42_S	0.549	1.00
7_W	43_I	0.547	1.00
7_W	20_V	0.538	1.00
27_K	41_A	0.536	1.00
4_A	7_W	0.530	1.00
33_P	37_H	0.529	1.00
21_T	25_N	0.524	1.00
27_K	43_I	0.518	1.00
18_E	22_P	0.514	1.00
10_T	29_W	0.505	1.00
8_H	12_N	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
4aybP	1	0.4464	70.5	0.713	Contact Map
4tpuA	3	0.9107	69	0.715	Contact Map
2lcqA	1	0.8393	68.7	0.716	Contact Map
1yuzA	2	0.875	63.6	0.726	Contact Map
3pwfA	4	0.8393	58.4	0.734	Contact Map
1lkoA	3	0.9107	55.9	0.739	Contact Map
5aunA	1	0.9286	54.2	0.741	Contact Map
1s24A	1	0.5536	54.2	0.741	Contact Map
2kdxA	1	0.8393	52.3	0.744	Contact Map
4qiwP	1	0.4107	50.8	0.746	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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