RS17E - HALSA - GREMLIN Contacts

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RS17E - 30S ribosomal protein S17e

UniProt:	Q9HPX1	Sequences: MAIKPDYVKKTGNILMERYQDAFSREDFEHNKDAVTELTNIESKNVRNRIAGYITHKRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	59 (52)
Sequences:	101 (51)
Seq/√Len:	7.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_I	50_I	2.832	0.80
20_Q	38_L	2.300	0.64
11_T	54_I	2.272	0.63
22_A	34_A	2.186	0.59
19_Y	29_E	2.148	0.58
8_V	50_I	1.863	0.47
14_I	18_R	1.849	0.47
24_S	55_T	1.777	0.44
4_K	46_V	1.665	0.40
7_Y	37_E	1.662	0.40
19_Y	38_L	1.478	0.33
6_D	10_K	1.381	0.30
20_Q	41_I	1.324	0.28
4_K	27_D	1.289	0.27
24_S	30_H	1.278	0.27
4_K	10_K	1.246	0.26
34_A	38_L	1.237	0.25
16_M	54_I	1.228	0.25
12_G	40_N	1.217	0.25
12_G	34_A	1.210	0.25
44_K	51_A	1.202	0.24
5_P	46_V	1.191	0.24
24_S	29_E	1.171	0.23
23_F	56_H	1.128	0.22
19_Y	55_T	1.108	0.22
11_T	36_T	1.102	0.22
3_I	24_S	1.096	0.21
19_Y	35_V	1.090	0.21
30_H	45_N	1.064	0.21
36_T	40_N	1.049	0.20
5_P	8_V	1.048	0.20
10_K	30_H	1.048	0.20
20_Q	35_V	1.042	0.20
10_K	14_I	1.030	0.20
38_L	41_I	0.911	0.17
13_N	36_T	0.907	0.17
12_G	49_R	0.898	0.17
11_T	50_I	0.898	0.17
13_N	21_D	0.884	0.16
4_K	16_M	0.880	0.16
4_K	49_R	0.880	0.16
23_F	35_V	0.846	0.16
3_I	6_D	0.792	0.15
7_Y	46_V	0.788	0.15
24_S	33_D	0.778	0.14
29_E	56_H	0.749	0.14
21_D	24_S	0.747	0.14
7_Y	43_S	0.739	0.14
33_D	36_T	0.737	0.14
35_V	38_L	0.706	0.13
16_M	33_D	0.690	0.13
3_I	17_E	0.671	0.12
5_P	36_T	0.650	0.12
22_A	42_E	0.649	0.12
3_I	12_G	0.632	0.12
3_I	9_K	0.609	0.11
17_E	34_A	0.607	0.11
5_P	49_R	0.603	0.11
4_K	11_T	0.591	0.11
43_S	46_V	0.589	0.11
8_V	14_I	0.584	0.11
11_T	16_M	0.578	0.11
13_N	34_A	0.574	0.11
8_V	23_F	0.573	0.11
27_D	36_T	0.564	0.11
3_I	51_A	0.561	0.11
33_D	54_I	0.559	0.11
16_M	30_H	0.549	0.11
21_D	27_D	0.541	0.10
36_T	56_H	0.535	0.10
35_V	39_T	0.535	0.10
15_L	23_F	0.533	0.10
3_I	54_I	0.529	0.10
22_A	33_D	0.527	0.10
14_I	23_F	0.513	0.10
34_A	40_N	0.505	0.10
45_N	50_I	0.502	0.10
27_D	39_T	0.500	0.10

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
3j7aW	1	0.9492	99.9	0.208	Contact Map
3j60R	1	0.9831	99.9	0.209	Contact Map
4bpeV	1	0.9661	99.9	0.211	Contact Map
3j20S	1	0.9831	99.9	0.212	Contact Map
4ujpS	1	0.9661	99.9	0.214	Contact Map
1rq6A	1	0.9831	99.9	0.214	Contact Map
4w23R	1	0.9831	99.9	0.218	Contact Map
3zeyL	1	0.9661	99.9	0.219	Contact Map
1ithA	3	0.7627	12.4	0.905	Contact Map
5ak0A	2	0.9831	10	0.909	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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