PDGLE - PFAM28P - GREMLIN Contacts

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PDGLE - PDGLE domain

PFAM:	PF13190	Sequences: VAALLLAGVLSPFASSSPDGLEWVAEDLTGTEELEAEGGFHAAAAALQEKTAPLPDYAFPGIGNEALGTILAGVVGVLLVFGLALGLGF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (81)
Sequences:	8377 (6080)
Seq/√Len:	675.6
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_W	27_D	5.197	1.00
22_E	56_D	2.551	1.00
8_G	12_P	2.040	1.00
41_H	44_A	2.023	1.00
59_F	68_G	1.974	1.00
40_F	44_A	1.933	1.00
9_V	12_P	1.928	1.00
40_F	43_A	1.807	1.00
77_V	81_F	1.771	1.00
41_H	45_A	1.743	1.00
80_V	84_A	1.654	1.00
38_G	41_H	1.631	1.00
7_A	70_I	1.607	1.00
42_A	45_A	1.569	1.00
47_L	50_K	1.535	1.00
84_A	88_G	1.518	1.00
6_L	10_L	1.513	1.00
22_E	69_T	1.512	1.00
46_A	49_E	1.475	1.00
8_G	70_I	1.459	1.00
42_A	46_A	1.411	1.00
43_A	48_Q	1.401	1.00
25_A	29_T	1.347	1.00
39_G	42_A	1.331	1.00
5_L	9_V	1.308	1.00
58_A	68_G	1.296	1.00
54_L	72_A	1.294	1.00
39_G	43_A	1.269	1.00
44_A	50_K	1.230	1.00
43_A	46_A	1.230	1.00
54_L	59_F	1.226	1.00
59_F	62_I	1.216	1.00
12_P	69_T	1.201	1.00
82_G	85_L	1.175	1.00
7_A	11_S	1.111	1.00
59_F	71_L	1.111	1.00
78_L	82_G	1.107	1.00
46_A	50_K	1.076	1.00
69_T	72_A	1.071	1.00
23_W	26_E	1.065	1.00
62_I	65_E	1.058	1.00
44_A	48_Q	1.046	1.00
8_G	74_V	1.025	1.00
77_V	80_V	1.022	1.00
63_G	66_A	1.005	1.00
54_L	68_G	0.992	1.00
52_A	55_P	0.991	1.00
39_G	44_A	0.987	1.00
8_G	11_S	0.979	1.00
12_P	70_I	0.955	1.00
59_F	75_V	0.954	1.00
4_L	74_V	0.952	1.00
81_F	85_L	0.947	1.00
6_L	9_V	0.947	1.00
11_S	70_I	0.924	1.00
41_H	47_L	0.914	1.00
69_T	73_G	0.911	1.00
45_A	49_E	0.907	1.00
81_F	84_A	0.905	1.00
38_G	42_A	0.900	1.00
44_A	47_L	0.890	1.00
40_F	48_Q	0.880	1.00
9_V	13_F	0.855	1.00
25_A	28_L	0.838	1.00
82_G	86_G	0.836	1.00
15_S	19_D	0.833	1.00
43_A	47_L	0.813	1.00
20_G	24_V	0.811	1.00
45_A	48_Q	0.802	1.00
25_A	31_T	0.779	1.00
41_H	48_Q	0.763	1.00
10_L	24_V	0.759	1.00
54_L	58_A	0.751	1.00
41_H	46_A	0.741	1.00
13_F	66_A	0.740	1.00
11_S	69_T	0.718	1.00
54_L	75_V	0.714	1.00
62_I	68_G	0.692	1.00
53_P	79_L	0.671	1.00
4_L	8_G	0.665	1.00
7_A	77_V	0.661	1.00
59_F	63_G	0.654	1.00
40_F	46_A	0.649	1.00
40_F	47_L	0.648	1.00
43_A	50_K	0.647	1.00
81_F	88_G	0.640	1.00
24_V	27_D	0.636	1.00
24_V	28_L	0.631	1.00
44_A	49_E	0.627	1.00
3_A	7_A	0.624	1.00
26_E	56_D	0.624	1.00
2_A	6_L	0.622	1.00
62_I	71_L	0.620	1.00
58_A	69_T	0.611	1.00
67_L	71_L	0.589	1.00
21_L	24_V	0.588	1.00
6_L	16_S	0.588	1.00
11_S	73_G	0.585	1.00
26_E	31_T	0.584	1.00
3_A	77_V	0.583	1.00
38_G	43_A	0.581	1.00
61_G	86_G	0.578	1.00
73_G	77_V	0.574	1.00
77_V	84_A	0.567	1.00
51_T	55_P	0.564	1.00
16_S	23_W	0.555	1.00
8_G	73_G	0.545	1.00
16_S	22_E	0.543	1.00
80_V	85_L	0.538	1.00
31_T	38_G	0.535	1.00
78_L	81_F	0.535	1.00
26_E	30_G	0.531	1.00
40_F	45_A	0.527	1.00
12_P	81_F	0.527	1.00
70_I	74_V	0.525	1.00
67_L	70_I	0.520	0.99
43_A	49_E	0.517	0.99
70_I	73_G	0.515	0.99
3_A	81_F	0.514	0.99
58_A	62_I	0.507	0.99
5_L	8_G	0.500	0.99
48_Q	51_T	0.500	0.99

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
1iijA	1	0.3258	16.3	0.874	Contact Map
2m20A	2	0.2697	15.8	0.874	Contact Map
2l2tA	2	0.3483	12.7	0.88	Contact Map
2kluA	1	0.3146	10	0.885	Contact Map
2jwaA	2	0.3596	9.7	0.886	Contact Map
2kncB	1	0.3596	8.6	0.889	Contact Map
2l9uA	2	0.2921	6.8	0.894	Contact Map
2ks1B	1	0.3596	6.7	0.894	Contact Map
2z6oA	1	0.3708	3.7	0.907	Contact Map
1fftA	1	0.382	3.2	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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