CSPD - BACSU - GREMLIN Contacts

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CSPD - Cold shock protein CspD

UniProt:	P51777	Sequences: MQNGKVKWFNNEKGFGFIEVEGGDDVFVHFTAIEGDGYKSLEEGQEVSFEIVEGNRGPQASNVVKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	66 (62)
Sequences:	4500 (1688)
Seq/√Len:	214.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_V	63_V	3.504	1.00
52_V	61_S	3.434	1.00
50_E	62_N	2.626	1.00
21_E	46_E	2.141	1.00
48_S	64_V	2.134	1.00
3_N	48_S	2.049	1.00
5_K	46_E	2.014	1.00
11_N	42_E	1.871	1.00
3_N	46_E	1.830	1.00
34_E	64_V	1.814	1.00
42_E	45_Q	1.708	1.00
28_V	41_L	1.682	1.00
20_V	24_D	1.653	1.00
54_G	59_Q	1.538	1.00
34_E	62_N	1.523	1.00
20_V	23_G	1.491	1.00
11_N	38_Y	1.485	1.00
32_A	61_S	1.483	1.00
53_E	58_P	1.470	1.00
9_F	30_F	1.365	1.00
54_G	58_P	1.320	1.00
20_V	49_F	1.305	1.00
26_V	51_I	1.262	1.00
33_I	38_Y	1.255	1.00
11_N	40_S	1.234	1.00
5_K	19_E	1.212	1.00
51_I	58_P	1.195	1.00
54_G	57_G	1.154	1.00
3_N	21_E	1.130	1.00
30_F	39_K	1.095	1.00
18_I	49_F	1.094	1.00
52_V	59_Q	1.078	1.00
24_D	58_P	1.050	1.00
33_I	39_K	0.930	0.99
4_G	60_A	0.920	0.99
41_L	47_V	0.912	0.99
33_I	36_D	0.891	0.99
32_A	62_N	0.891	0.99
4_G	18_I	0.854	0.99
32_A	52_V	0.833	0.99
18_I	60_A	0.806	0.98
49_F	60_A	0.796	0.98
7_K	25_D	0.770	0.98
33_I	41_L	0.766	0.98
8_W	28_V	0.756	0.98
5_K	21_E	0.748	0.97
7_K	13_K	0.744	0.97
35_G	39_K	0.719	0.97
30_F	33_I	0.714	0.97
18_I	28_V	0.712	0.97
30_F	56_R	0.711	0.97
33_I	63_V	0.702	0.96
19_E	44_G	0.699	0.96
30_F	38_Y	0.690	0.96
36_D	64_V	0.677	0.95
20_V	51_I	0.675	0.95
10_N	27_F	0.675	0.95
35_G	38_Y	0.659	0.95
8_W	43_E	0.651	0.94
26_V	60_A	0.629	0.93
4_G	49_F	0.619	0.93
14_G	25_D	0.616	0.93
53_E	56_R	0.598	0.92
51_I	61_S	0.594	0.91
13_K	25_D	0.594	0.91
50_E	61_S	0.592	0.91
41_L	45_Q	0.586	0.91
34_E	39_K	0.584	0.91
18_I	47_V	0.564	0.89
55_N	58_P	0.563	0.89
17_F	27_F	0.563	0.89
40_S	45_Q	0.559	0.89
32_A	59_Q	0.557	0.88
14_G	33_I	0.556	0.88
55_N	59_Q	0.552	0.88
36_D	39_K	0.551	0.88
4_G	47_V	0.549	0.88
18_I	31_T	0.549	0.88
8_W	13_K	0.547	0.88
38_Y	42_E	0.544	0.87
26_V	52_V	0.540	0.87
11_N	36_D	0.540	0.87
15_F	41_L	0.535	0.86
17_F	44_G	0.531	0.86
31_T	56_R	0.531	0.86
12_E	45_Q	0.530	0.86
36_D	47_V	0.527	0.86
16_G	28_V	0.526	0.85
13_K	37_G	0.526	0.85
38_Y	63_V	0.523	0.85
24_D	53_E	0.515	0.84
53_E	59_Q	0.512	0.84
3_N	42_E	0.500	0.82

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
2lxjA	1	1	99.8	0.128	Contact Map
1c9oA	2	1	99.8	0.139	Contact Map
3camA	2	1	99.8	0.139	Contact Map
3a0jA	1	1	99.8	0.154	Contact Map
1g6pA	1	0.9848	99.8	0.164	Contact Map
3i2zB	2	1	99.8	0.165	Contact Map
3uljA	3	1	99.7	0.176	Contact Map
2mqhA	1	0.9697	99.7	0.182	Contact Map
2lssA	1	1	99.7	0.189	Contact Map
3ts2A	1	1	99.7	0.19	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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