Germane - PFAM28P - GREMLIN Contacts

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Germane - Sporulation and spore germination

PFAM:	PF10646	Sequences: TLYFLDPDGTYVPVRLVPETTEALARAALEALLAGPTPGLRSAIPAGTKLLSVTVEDGVATVDLSGEFLGSASERLAVAQIVNTLTQFPGVKRVQILVDGKPVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	104 (102)
Sequences:	24795 (19454)
Seq/√Len:	1926.3
META:	0.884

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_V	93_R	3.084	1.00
61_T	97_L	2.383	1.00
95_Q	102_P	2.358	1.00
63_D	97_L	2.287	1.00
51_L	63_D	2.223	1.00
42_S	80_Q	2.204	1.00
26_R	30_E	2.079	1.00
79_A	83_N	2.074	1.00
66_G	99_D	2.027	1.00
31_A	34_A	2.003	1.00
43_A	80_Q	1.879	1.00
59_V	95_Q	1.876	1.00
82_V	86_T	1.788	1.00
61_T	95_Q	1.773	1.00
28_A	84_T	1.769	1.00
55_V	60_A	1.739	1.00
29_L	85_L	1.696	1.00
60_A	91_V	1.664	1.00
27_A	31_A	1.624	1.00
54_T	61_T	1.618	1.00
49_K	65_S	1.603	1.00
25_A	85_L	1.541	1.00
25_A	53_V	1.486	1.00
15_R	18_P	1.480	1.00
28_A	88_F	1.420	1.00
16_L	19_E	1.412	1.00
71_S	74_E	1.406	1.00
5_L	43_A	1.400	1.00
51_L	99_D	1.360	1.00
83_N	86_T	1.313	1.00
58_G	92_K	1.299	1.00
73_S	76_L	1.298	1.00
21_T	24_L	1.282	1.00
56_E	61_T	1.257	1.00
71_S	75_R	1.244	1.00
63_D	100_G	1.241	1.00
11_Y	14_V	1.233	1.00
29_L	33_L	1.231	1.00
72_A	75_R	1.226	1.00
70_G	74_E	1.204	1.00
97_L	102_P	1.203	1.00
52_S	63_D	1.199	1.00
17_V	20_T	1.183	1.00
29_L	81_I	1.179	1.00
68_F	77_A	1.168	1.00
27_A	30_E	1.098	1.00
10_T	13_P	1.097	1.00
62_V	85_L	1.094	1.00
23_A	26_R	1.087	1.00
32_L	84_T	1.085	1.00
64_L	68_F	1.084	1.00
6_D	9_G	1.048	1.00
25_A	90_G	1.048	1.00
33_L	64_L	1.032	1.00
66_G	69_L	1.029	1.00
44_I	77_A	1.016	1.00
16_L	20_T	0.998	1.00
15_R	19_E	0.993	1.00
60_A	85_L	0.983	1.00
70_G	73_S	0.975	1.00
72_A	76_L	0.943	1.00
50_L	53_V	0.938	1.00
70_G	75_R	0.937	1.00
4_F	35_G	0.936	1.00
26_R	50_L	0.929	1.00
45_P	48_T	0.928	1.00
78_V	96_I	0.928	1.00
71_S	76_L	0.891	1.00
48_T	68_F	0.889	1.00
73_S	77_A	0.885	1.00
25_A	60_A	0.883	1.00
78_V	82_V	0.871	1.00
64_L	81_I	0.870	1.00
5_L	76_L	0.854	1.00
98_V	103_V	0.846	1.00
74_E	77_A	0.838	1.00
33_L	50_L	0.831	1.00
81_I	96_I	0.830	1.00
29_L	50_L	0.827	1.00
68_F	78_V	0.826	1.00
55_V	91_V	0.801	1.00
79_A	82_V	0.788	1.00
26_R	53_V	0.782	1.00
25_A	88_F	0.771	1.00
5_L	9_G	0.769	1.00
82_V	94_V	0.766	1.00
30_E	34_A	0.764	1.00
80_Q	83_N	0.758	1.00
32_L	44_I	0.757	1.00
86_T	94_V	0.750	1.00
75_R	79_A	0.749	1.00
10_T	14_V	0.749	1.00
51_L	65_S	0.744	1.00
24_L	28_A	0.735	1.00
53_V	60_A	0.731	1.00
6_D	10_T	0.730	1.00
53_V	85_L	0.720	1.00
54_T	57_D	0.715	1.00
24_L	90_G	0.710	1.00
80_Q	84_T	0.702	1.00
55_V	58_G	0.699	1.00
64_L	96_I	0.699	1.00
69_L	103_V	0.697	1.00
82_V	96_I	0.688	1.00
23_A	27_A	0.687	1.00
74_E	78_V	0.685	1.00
88_F	91_V	0.684	1.00
32_L	80_Q	0.683	1.00
50_L	62_V	0.682	1.00
5_L	80_Q	0.677	1.00
83_N	87_Q	0.676	1.00
4_F	36_P	0.671	1.00
69_L	98_V	0.665	1.00
44_I	81_I	0.660	1.00
15_R	20_T	0.658	1.00
70_G	76_L	0.653	1.00
77_A	80_Q	0.652	1.00
30_E	33_L	0.650	1.00
86_T	93_R	0.627	1.00
2_L	31_A	0.618	1.00
62_V	94_V	0.611	1.00
48_T	64_L	0.609	1.00
81_I	94_V	0.603	1.00
25_A	28_A	0.601	1.00
86_T	91_V	0.599	1.00
55_V	90_G	0.597	1.00
78_V	83_N	0.594	1.00
29_L	32_L	0.587	1.00
36_P	40_L	0.587	1.00
47_G	67_E	0.575	1.00
14_V	17_V	0.568	1.00
25_A	55_V	0.566	1.00
24_L	27_A	0.559	1.00
44_I	68_F	0.557	1.00
22_E	26_R	0.555	1.00
53_V	62_V	0.553	1.00
54_T	97_L	0.550	1.00
33_L	44_I	0.548	1.00
49_K	67_E	0.540	1.00
28_A	87_Q	0.540	1.00
60_A	94_V	0.533	1.00
58_G	93_R	0.533	1.00
84_T	87_Q	0.532	1.00
14_V	40_L	0.532	1.00
29_L	62_V	0.529	1.00
50_L	65_S	0.524	1.00
42_S	46_A	0.514	1.00
77_A	81_I	0.512	1.00
6_D	11_Y	0.510	1.00
63_D	99_D	0.507	1.00
65_S	68_F	0.505	1.00
37_T	40_L	0.501	1.00
68_F	98_V	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
3cq1A	2	0.8173	50.7	0.827	Contact Map
1uwdA	1	0.8269	49.7	0.828	Contact Map
3lnoA	1	0.8558	47	0.831	Contact Map
4b0mA	1	0.4135	22.2	0.857	Contact Map
2e0gA	1	0.7692	16.1	0.866	Contact Map
1jfuA	1	0.3173	15.5	0.867	Contact Map
3lorA	3	0.3365	14.6	0.869	Contact Map
3eytA	4	0.3654	14	0.869	Contact Map
3cmiA	1	0.3365	13.3	0.871	Contact Map
3ny5A	2	0.7308	12.9	0.872	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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