RALF - PFAM28P - GREMLIN Contacts

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RALF - Rapid ALkalinization Factor (RALF)

PFAM:	PF05498	Sequences: EEFEMDSEISRRILAGTRRYISYGALRRNRVPCSRRGASYYNCRPGAPANPYSRGCSAITRCRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (62)
Sequences:	511 (310)
Seq/√Len:	39.3
META:	0.088

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_D	10_S	4.422	1.00
33_C	43_C	2.656	1.00
27_R	30_R	2.305	1.00
5_M	8_E	2.283	1.00
38_A	45_P	1.962	0.99
41_Y	60_T	1.833	0.98
5_M	10_S	1.778	0.97
24_G	27_R	1.675	0.96
28_R	45_P	1.674	0.96
8_E	11_R	1.618	0.95
37_G	40_Y	1.594	0.95
38_A	46_G	1.429	0.91
30_R	36_R	1.410	0.91
54_R	59_I	1.382	0.90
11_R	14_L	1.370	0.90
35_R	59_I	1.352	0.89
7_S	10_S	1.331	0.88
25_A	57_S	1.329	0.88
53_S	63_R	1.278	0.86
26_L	29_N	1.277	0.86
49_A	55_G	1.257	0.85
29_N	39_S	1.230	0.84
32_P	41_Y	1.222	0.83
40_Y	43_C	1.200	0.82
9_I	15_A	1.182	0.81
15_A	35_R	1.175	0.81
10_S	49_A	1.120	0.78
60_T	64_R	1.066	0.74
33_C	40_Y	1.065	0.74
57_S	64_R	1.052	0.73
19_R	23_Y	1.025	0.71
22_S	57_S	1.010	0.70
12_R	43_C	1.002	0.69
21_I	29_N	0.985	0.68
23_Y	26_L	0.967	0.66
24_G	30_R	0.963	0.66
4_E	61_R	0.936	0.64
51_P	54_R	0.894	0.60
22_S	28_R	0.893	0.60
17_T	21_I	0.886	0.60
17_T	48_P	0.884	0.59
10_S	18_R	0.862	0.57
18_R	44_R	0.862	0.57
32_P	60_T	0.861	0.57
41_Y	52_Y	0.843	0.56
17_T	30_R	0.829	0.54
25_A	41_Y	0.822	0.54
33_C	56_C	0.805	0.52
32_P	42_N	0.804	0.52
43_C	56_C	0.788	0.51
21_I	26_L	0.771	0.49
23_Y	32_P	0.767	0.49
42_N	57_S	0.753	0.48
24_G	34_S	0.744	0.47
23_Y	40_Y	0.743	0.47
32_P	52_Y	0.734	0.46
26_L	37_G	0.733	0.46
4_E	7_S	0.731	0.46
38_A	47_A	0.724	0.45
22_S	51_P	0.722	0.45
34_S	42_N	0.718	0.44
50_N	63_R	0.705	0.43
49_A	64_R	0.695	0.42
10_S	15_A	0.692	0.42
3_F	47_A	0.674	0.40
13_I	59_I	0.668	0.40
18_R	58_A	0.662	0.39
48_P	61_R	0.660	0.39
52_Y	55_G	0.656	0.39
6_D	9_I	0.645	0.38
37_G	41_Y	0.644	0.38
31_V	41_Y	0.640	0.38
15_A	27_R	0.625	0.36
30_R	38_A	0.625	0.36
41_Y	59_I	0.624	0.36
32_P	39_S	0.624	0.36
56_C	62_C	0.621	0.36
50_N	55_G	0.615	0.35
20_Y	32_P	0.603	0.34
21_I	58_A	0.583	0.33
23_Y	31_V	0.582	0.33
19_R	58_A	0.579	0.33
24_G	36_R	0.575	0.32
22_S	43_C	0.574	0.32
28_R	52_Y	0.572	0.32
20_Y	63_R	0.557	0.31
23_Y	28_R	0.557	0.31
57_S	60_T	0.555	0.31
19_R	36_R	0.542	0.30
30_R	44_R	0.527	0.28
30_R	58_A	0.518	0.28
39_S	43_C	0.508	0.27
39_S	42_N	0.500	0.27

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
2dunA	1	0.7344	3	0.913	Contact Map
3sqgC	1	0.8594	2	0.922	Contact Map
2e1zA	2	0.2656	1.8	0.923	Contact Map
2y9yB	1	0.2969	1.8	0.923	Contact Map
1e6yC	1	0.8594	1.7	0.924	Contact Map
1hbnC	1	0.8594	1.7	0.924	Contact Map
1e6vC	1	0.8594	1.7	0.925	Contact Map
1d8hA	2	0.3594	1.6	0.925	Contact Map
3u3zA	1	0.3438	1.4	0.928	Contact Map
3ef1A	1	0.3438	1.3	0.929	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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