CSPF - ECOLI - GREMLIN Contacts

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CSPF - Cold shock-like protein CspF

UniProt:	P0A976	Sequences: MSRKMTGIVKTFDGKSGKGLITPSDGRIDVQLHVSALNLRDAEEITTGLRVEFCRINGLRGPSAANVYLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12205
Length:	70 (63)
Sequences:	2393 (976)
Seq/√Len:	122.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_L	67_V	5.111	1.00
56_I	65_A	3.533	1.00
54_C	66_N	2.762	1.00
24_S	50_R	2.496	1.00
14_G	46_T	2.394	1.00
52_E	68_Y	2.227	1.00
6_T	52_E	2.148	1.00
58_G	63_S	1.818	1.00
38_N	68_Y	1.754	1.00
6_T	50_R	1.626	1.00
14_G	44_E	1.591	1.00
23_P	27_R	1.588	1.00
46_T	49_L	1.585	1.00
8_I	50_R	1.507	1.00
57_N	62_P	1.471	1.00
28_I	62_P	1.448	1.00
23_P	26_G	1.377	1.00
23_P	28_I	1.309	1.00
7_G	21_I	1.281	1.00
38_N	66_N	1.229	0.99
36_A	56_I	1.127	0.99
20_L	33_H	1.094	0.99
58_G	62_P	1.091	0.99
10_K	29_D	1.080	0.99
21_I	51_V	1.074	0.98
32_L	45_I	1.069	0.98
21_I	53_F	1.031	0.98
11_T	16_S	1.023	0.98
20_L	31_Q	1.006	0.98
7_G	64_A	0.998	0.98
45_I	51_V	0.987	0.97
8_I	22_T	0.941	0.96
13_D	31_Q	0.936	0.96
36_A	65_A	0.936	0.96
23_P	53_F	0.881	0.95
53_F	64_A	0.864	0.94
39_L	44_E	0.864	0.94
55_R	62_P	0.851	0.94
10_K	16_S	0.834	0.93
34_V	43_E	0.831	0.93
35_S	54_C	0.817	0.92
47_T	63_S	0.815	0.92
12_F	34_V	0.813	0.92
9_V	45_I	0.806	0.92
14_G	42_A	0.800	0.92
37_L	40_R	0.795	0.91
18_K	33_H	0.792	0.91
22_T	28_I	0.779	0.91
28_I	57_N	0.772	0.90
37_L	42_A	0.762	0.90
16_S	29_D	0.751	0.89
7_G	51_V	0.746	0.89
6_T	24_S	0.704	0.86
36_A	66_N	0.692	0.85
37_L	43_E	0.691	0.85
7_G	34_V	0.685	0.84
58_G	61_G	0.685	0.84
48_G	59_L	0.677	0.83
40_R	68_Y	0.668	0.83
28_I	59_L	0.646	0.80
21_I	32_L	0.645	0.80
11_T	29_D	0.643	0.80
39_L	43_E	0.637	0.79
30_V	64_A	0.636	0.79
16_S	61_G	0.634	0.79
36_A	53_F	0.620	0.78
15_K	46_T	0.614	0.77
34_V	37_L	0.609	0.76
11_T	17_G	0.605	0.76
20_L	29_D	0.595	0.75
37_L	41_D	0.589	0.74
19_G	32_L	0.586	0.74
22_T	30_V	0.586	0.74
11_T	41_D	0.580	0.73
18_K	45_I	0.575	0.72
28_I	63_S	0.575	0.72
30_V	36_A	0.564	0.71
10_K	17_G	0.558	0.70
17_G	37_L	0.553	0.69
31_Q	49_L	0.552	0.69
34_V	38_N	0.550	0.69
18_K	31_Q	0.547	0.68
34_V	67_V	0.537	0.67
23_P	30_V	0.537	0.67
30_V	59_L	0.536	0.67
22_T	58_G	0.531	0.66
41_D	45_I	0.527	0.66
8_I	26_G	0.524	0.65
35_S	53_F	0.522	0.65
18_K	30_V	0.520	0.65
15_K	62_P	0.520	0.65
13_D	65_A	0.513	0.64
11_T	61_G	0.512	0.63
56_I	63_S	0.500	0.62

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
2lssA	1	1	99.7	0.166	Contact Map
1h95A	1	1	99.6	0.206	Contact Map
3i2zB	2	1	99.6	0.208	Contact Map
2mqhA	1	0.9714	99.6	0.21	Contact Map
3camA	2	0.9571	99.6	0.228	Contact Map
1wfqA	1	0.9571	99.6	0.228	Contact Map
2ytyA	1	0.9571	99.6	0.23	Contact Map
1x65A	1	0.9429	99.6	0.237	Contact Map
4qqbX	1	0.9571	99.6	0.242	Contact Map
1g6pA	1	0.9286	99.6	0.243	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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