DUF630 - PFAM28P - GREMLIN Contacts

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DUF630 - Protein of unknown function (DUF630)

PFAM:	PF04783	Sequences: MGCSASKLDDEEAVALCKERKRLIKQAVDARYALAAAHVAYIQSLRNVGAALRRFAEGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (59)
Sequences:	560 (253)
Seq/√Len:	32.9
META:	0.093

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_C	14_V	3.812	1.00
49_G	59_E	2.927	1.00
12_E	28_V	2.278	0.99
21_K	25_K	2.259	0.99
46_R	49_G	2.114	0.98
53_R	57_E	1.905	0.97
8_L	38_H	1.893	0.97
39_V	57_E	1.799	0.96
19_E	27_A	1.763	0.95
24_I	32_Y	1.536	0.91
37_A	49_G	1.522	0.90
2_G	20_R	1.513	0.90
27_A	51_A	1.461	0.88
23_L	35_A	1.405	0.86
47_N	50_A	1.387	0.85
28_V	48_V	1.381	0.85
3_C	6_S	1.365	0.84
23_L	26_Q	1.348	0.84
26_Q	53_R	1.279	0.80
34_L	38_H	1.262	0.79
2_G	6_S	1.216	0.77
20_R	31_R	1.169	0.74
21_K	35_A	1.147	0.72
3_C	9_D	1.127	0.71
54_R	58_G	1.103	0.69
24_I	36_A	1.085	0.68
10_D	19_E	1.025	0.64
10_D	30_A	1.021	0.63
35_A	40_A	1.011	0.63
15_A	39_V	0.997	0.61
28_V	31_R	0.989	0.61
37_A	55_F	0.985	0.60
8_L	14_V	0.972	0.59
22_R	49_G	0.969	0.59
5_A	16_L	0.966	0.59
15_A	25_K	0.927	0.56
16_L	36_A	0.922	0.55
10_D	58_G	0.905	0.54
28_V	45_L	0.866	0.51
35_A	39_V	0.865	0.51
33_A	47_N	0.865	0.51
7_K	53_R	0.854	0.50
35_A	38_H	0.853	0.50
24_I	58_G	0.840	0.49
30_A	48_V	0.825	0.47
18_K	25_K	0.823	0.47
49_G	55_F	0.822	0.47
18_K	55_F	0.794	0.45
40_A	46_R	0.766	0.42
4_S	49_G	0.747	0.41
1_M	7_K	0.746	0.41
29_D	34_L	0.737	0.40
29_D	42_I	0.718	0.39
5_A	39_V	0.716	0.38
34_L	37_A	0.713	0.38
9_D	14_V	0.692	0.37
2_G	35_A	0.686	0.36
7_K	13_A	0.681	0.36
37_A	45_L	0.674	0.35
10_D	15_A	0.672	0.35
29_D	51_A	0.663	0.34
4_S	19_E	0.658	0.34
25_K	51_A	0.656	0.34
48_V	52_L	0.646	0.33
10_D	17_C	0.640	0.33
23_L	38_H	0.626	0.32
39_V	43_Q	0.623	0.31
27_A	56_A	0.617	0.31
8_L	48_V	0.615	0.31
4_S	41_Y	0.614	0.31
2_G	7_K	0.589	0.29
23_L	56_A	0.585	0.29
19_E	41_Y	0.584	0.29
11_E	32_Y	0.579	0.28
25_K	46_R	0.575	0.28
51_A	56_A	0.572	0.28
29_D	32_Y	0.569	0.28
5_A	23_L	0.569	0.28
5_A	21_K	0.568	0.28
13_A	42_I	0.565	0.27
1_M	6_S	0.561	0.27
17_C	44_S	0.556	0.27
13_A	38_H	0.523	0.25
39_V	42_I	0.521	0.25
14_V	50_A	0.517	0.24
4_S	40_A	0.511	0.24
4_S	16_L	0.501	0.23
16_L	24_I	0.500	0.23

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
3uekA	1	1	12.2	0.885	Contact Map
4a0dA	1	0.8814	9.7	0.89	Contact Map
4ijrA	2	0.8644	6.7	0.898	Contact Map
2ehbA	1	0.7797	5.3	0.902	Contact Map
4exbA	2	0.8644	5.1	0.903	Contact Map
1nh1A	1	0.6271	5	0.904	Contact Map
1zgdA	1	0.8644	4.8	0.904	Contact Map
1pz1A	1	0.8814	4.8	0.904	Contact Map
3v0sA	1	0.8136	3.6	0.91	Contact Map
1pyfA	1	0.8814	3.4	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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