PSP1 - PFAM28P - GREMLIN Contacts

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PSP1 - PSP1 C-terminal conserved region

PFAM:	PF04468	Sequences: KKVLRKATEEDLEKLEENREKEKEALEICREKIRELGLPMKLVDVEYQFDGSKLTFYFTAEGRVDFRELVKDLASEFRTRIELRQI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	86 (85)
Sequences:	24140 (13978)
Seq/√Len:	1516.1
META:	0.939

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_I	76_E	2.910	1.00
36_L	72_D	2.528	1.00
21_K	51_G	2.276	1.00
32_K	35_E	2.272	1.00
32_K	72_D	2.252	1.00
15_L	19_R	2.182	1.00
29_C	42_L	2.033	1.00
28_I	32_K	1.995	1.00
28_I	31_E	1.952	1.00
33_I	42_L	1.895	1.00
29_C	56_F	1.873	1.00
25_A	47_Y	1.872	1.00
47_Y	54_L	1.790	1.00
36_L	68_E	1.611	1.00
9_E	13_E	1.548	1.00
19_R	22_E	1.493	1.00
48_Q	55_T	1.448	1.00
31_E	35_E	1.429	1.00
35_E	72_D	1.423	1.00
26_L	30_R	1.407	1.00
48_Q	52_S	1.405	1.00
14_K	17_E	1.401	1.00
13_E	17_E	1.381	1.00
26_L	42_L	1.369	1.00
28_I	77_F	1.348	1.00
26_L	45_V	1.338	1.00
21_K	24_E	1.316	1.00
18_N	51_G	1.288	1.00
24_E	28_I	1.285	1.00
43_V	86_I	1.278	1.00
13_E	16_E	1.271	1.00
5_R	11_D	1.270	1.00
10_E	13_E	1.261	1.00
27_E	31_E	1.236	1.00
17_E	20_E	1.214	1.00
54_L	79_T	1.177	1.00
17_E	21_K	1.167	1.00
9_E	12_L	1.134	1.00
10_E	14_K	1.113	1.00
32_K	76_E	1.109	1.00
30_R	34_R	1.092	1.00
25_A	56_F	1.088	1.00
14_K	51_G	1.077	1.00
12_L	15_L	1.071	1.00
23_K	27_E	1.063	1.00
68_E	72_D	1.042	1.00
7_A	12_L	1.024	1.00
20_E	24_E	0.997	1.00
12_L	16_E	0.978	1.00
46_E	57_Y	0.977	1.00
54_L	77_F	0.970	1.00
21_K	47_Y	0.963	1.00
27_E	30_R	0.960	1.00
16_E	20_E	0.942	1.00
14_K	18_N	0.930	1.00
43_V	59_T	0.925	1.00
33_I	40_M	0.915	1.00
72_D	75_S	0.882	1.00
24_E	27_E	0.877	1.00
16_E	19_R	0.864	1.00
22_E	25_A	0.864	1.00
31_E	34_R	0.852	1.00
66_F	70_V	0.838	1.00
23_K	26_L	0.835	1.00
70_V	83_L	0.827	1.00
29_C	73_L	0.826	1.00
7_A	15_L	0.823	1.00
29_C	33_I	0.820	1.00
68_E	71_K	0.818	1.00
18_N	49_F	0.817	1.00
48_Q	57_Y	0.807	1.00
74_A	82_E	0.807	1.00
39_P	62_G	0.804	1.00
40_M	66_F	0.802	1.00
47_Y	79_T	0.794	1.00
15_L	18_N	0.791	1.00
26_L	29_C	0.766	1.00
40_M	64_V	0.752	1.00
31_E	76_E	0.749	1.00
25_A	54_L	0.740	1.00
22_E	44_D	0.726	1.00
17_E	51_G	0.720	1.00
45_V	54_L	0.716	1.00
72_D	76_E	0.715	1.00
20_E	23_K	0.712	1.00
33_I	69_L	0.705	1.00
58_F	83_L	0.701	1.00
53_K	82_E	0.700	1.00
5_R	8_T	0.694	1.00
34_R	37_G	0.692	1.00
32_K	36_L	0.676	1.00
24_E	76_E	0.674	1.00
48_Q	53_K	0.674	1.00
60_A	63_R	0.666	1.00
45_V	56_F	0.662	1.00
44_D	57_Y	0.654	1.00
57_Y	84_R	0.632	1.00
40_M	60_A	0.629	1.00
25_A	77_F	0.628	1.00
47_Y	51_G	0.625	1.00
58_F	66_F	0.608	1.00
66_F	83_L	0.607	1.00
18_N	47_Y	0.599	1.00
26_L	44_D	0.575	1.00
18_N	21_K	0.574	1.00
44_D	47_Y	0.569	1.00
58_F	85_Q	0.563	1.00
3_V	6_K	0.555	1.00
4_L	74_A	0.547	1.00
55_T	82_E	0.546	1.00
29_C	45_V	0.542	1.00
38_L	69_L	0.536	1.00
75_S	79_T	0.535	1.00
63_R	85_Q	0.533	1.00
5_R	49_F	0.532	1.00
33_I	36_L	0.523	1.00
57_Y	62_G	0.522	1.00
62_G	74_A	0.521	1.00
22_E	45_V	0.519	1.00
63_R	66_F	0.516	1.00
11_D	48_Q	0.516	1.00
66_F	71_K	0.512	1.00
25_A	45_V	0.508	1.00
39_P	61_E	0.508	1.00
77_F	81_I	0.507	1.00
67_R	85_Q	0.506	1.00
40_M	58_F	0.500	1.00
41_K	59_T	0.500	1.00

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
3af5A	1	0.7093	23.6	0.865	Contact Map
2ycbA	2	0.7326	22.5	0.867	Contact Map
2xr1A	2	0.7558	15.6	0.876	Contact Map
2dyjA	1	0.8256	13.4	0.88	Contact Map
1pa4A	1	0.7907	11.5	0.883	Contact Map
2kzfA	1	0.9186	11	0.884	Contact Map
3cfxA	1	0.4186	10	0.886	Contact Map
3cijA	1	0.407	9.8	0.887	Contact Map
1mh3A	1	0.4535	9.8	0.887	Contact Map
4qq0A	1	0.9651	9.6	0.888	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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