NYD-SP28 - PFAM28P - GREMLIN Contacts

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NYD-SP28 - Sperm tail

PFAM:	PF14772	Sequences: AADAREEQRRKKEEELRRERKEKLEEEAKSSAKNNAKINMKWREILRKAKPQELRKEIEIQSQNCERIIDRKDALIQELQQELKEADEQYVKALRKHLEDI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	101 (99)
Sequences:	633 (499)
Seq/√Len:	50.2
META:	0.427

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_E	9_R	3.386	1.00
90_Y	94_L	3.023	1.00
36_A	40_M	2.612	1.00
70_D	74_A	2.431	1.00
27_E	42_W	2.224	1.00
57_E	60_I	2.219	1.00
29_K	33_K	2.168	1.00
55_R	59_E	2.122	1.00
51_P	55_R	1.995	1.00
3_D	10_R	1.985	1.00
62_S	66_E	1.952	0.99
22_E	26_E	1.773	0.99
15_E	19_E	1.752	0.99
34_N	37_K	1.707	0.99
38_I	72_K	1.622	0.98
27_E	31_S	1.559	0.97
71_R	74_A	1.557	0.97
43_R	47_R	1.554	0.97
37_K	40_M	1.511	0.97
33_K	40_M	1.448	0.96
63_Q	70_D	1.444	0.96
25_E	29_K	1.444	0.96
4_A	8_Q	1.443	0.96
60_I	67_R	1.410	0.95
20_R	79_L	1.408	0.95
91_V	95_R	1.402	0.95
60_I	63_Q	1.382	0.95
14_E	17_R	1.355	0.94
88_E	92_K	1.328	0.93
45_I	68_I	1.319	0.93
73_D	100_D	1.313	0.93
45_I	54_L	1.302	0.93
8_Q	12_K	1.263	0.91
34_N	67_R	1.260	0.91
26_E	30_S	1.237	0.91
73_D	76_I	1.204	0.89
88_E	95_R	1.181	0.88
65_C	78_E	1.142	0.87
10_R	13_E	1.130	0.86
12_K	58_I	1.116	0.85
21_K	88_E	1.115	0.85
61_Q	65_C	1.094	0.84
27_E	73_D	1.086	0.84
86_A	89_Q	1.069	0.83
6_E	13_E	1.067	0.83
15_E	20_R	1.041	0.81
67_R	70_D	1.029	0.80
63_Q	67_R	1.027	0.80
59_E	62_S	1.015	0.79
38_I	65_C	1.011	0.79
7_E	14_E	1.005	0.79
5_R	19_E	1.005	0.79
46_L	50_K	1.000	0.78
38_I	68_I	0.996	0.78
60_I	70_D	0.996	0.78
79_L	97_H	0.982	0.77
68_I	87_D	0.979	0.77
61_Q	75_L	0.976	0.77
6_E	14_E	0.957	0.75
19_E	23_K	0.955	0.75
73_D	84_K	0.947	0.75
74_A	78_E	0.944	0.74
6_E	10_R	0.942	0.74
28_A	32_A	0.939	0.74
72_K	76_I	0.938	0.74
95_R	98_L	0.930	0.73
42_W	82_E	0.925	0.73
87_D	95_R	0.899	0.71
16_L	20_R	0.892	0.70
60_I	64_N	0.889	0.70
89_Q	95_R	0.887	0.70
20_R	25_E	0.883	0.69
7_E	11_K	0.869	0.68
8_Q	14_E	0.869	0.68
33_K	58_I	0.860	0.67
66_E	69_I	0.838	0.65
4_A	12_K	0.838	0.65
48_K	84_K	0.837	0.65
88_E	94_L	0.835	0.65
51_P	83_L	0.820	0.63
8_Q	11_K	0.811	0.63
23_K	26_E	0.807	0.62
3_D	7_E	0.807	0.62
21_K	24_L	0.779	0.59
10_R	68_I	0.777	0.59
86_A	91_V	0.773	0.59
38_I	41_K	0.773	0.59
61_Q	68_I	0.770	0.59
68_I	78_E	0.768	0.58
4_A	19_E	0.761	0.58
59_E	88_E	0.758	0.57
30_S	36_A	0.758	0.57
42_W	97_H	0.739	0.55
89_Q	97_H	0.738	0.55
55_R	66_E	0.735	0.55
82_E	92_K	0.720	0.54
67_R	89_Q	0.718	0.53
24_L	57_E	0.710	0.53
29_K	38_I	0.707	0.52
25_E	39_N	0.704	0.52
13_E	86_A	0.701	0.52
82_E	85_E	0.679	0.49
48_K	52_Q	0.677	0.49
44_E	68_I	0.673	0.49
52_Q	56_K	0.668	0.48
48_K	90_Y	0.659	0.47
41_K	59_E	0.659	0.47
74_A	77_Q	0.655	0.47
19_E	101_I	0.655	0.47
12_K	59_E	0.652	0.47
29_K	32_A	0.639	0.45
30_S	34_N	0.632	0.45
66_E	77_Q	0.625	0.44
55_R	87_D	0.616	0.43
12_K	88_E	0.615	0.43
69_I	79_L	0.607	0.42
88_E	93_A	0.598	0.41
36_A	39_N	0.596	0.41
51_P	58_I	0.596	0.41
32_A	36_A	0.595	0.41
37_K	94_L	0.585	0.40
81_Q	85_E	0.576	0.39
18_R	25_E	0.576	0.39
31_S	45_I	0.573	0.39
29_K	58_I	0.573	0.39
3_D	9_R	0.571	0.38
35_N	45_I	0.565	0.38
28_A	31_S	0.564	0.38
56_K	60_I	0.563	0.38
65_C	68_I	0.561	0.37
8_Q	101_I	0.555	0.37
95_R	99_E	0.553	0.37
84_K	87_D	0.552	0.37
32_A	60_I	0.547	0.36
64_N	77_Q	0.545	0.36
93_A	97_H	0.543	0.36
68_I	72_K	0.538	0.35
15_E	26_E	0.531	0.35
45_I	79_L	0.531	0.35
56_K	74_A	0.528	0.34
7_E	85_E	0.526	0.34
49_A	85_E	0.517	0.33
68_I	71_R	0.516	0.33
17_R	99_E	0.512	0.33
59_E	77_Q	0.511	0.33
28_A	43_R	0.508	0.33
21_K	29_K	0.500	0.32
21_K	25_E	0.500	0.32

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
2dfsA	2	0.7624	6.9	0.88	Contact Map
3mq9A	4	0.9109	5.4	0.885	Contact Map
3ghgA	2	0.6535	3.9	0.893	Contact Map
1zxaA	1	0.3465	2.9	0.9	Contact Map
4hpqC	2	0.7129	2.8	0.9	Contact Map
4noxA	1	0	2	0.908	Contact Map
4ll8E	2	0.9307	1.9	0.909	Contact Map
4emcA	2	0.3465	1.9	0.909	Contact Map
3nmdA	2	0.4851	1.9	0.909	Contact Map
4jkvA	2	0.7129	1.7	0.911	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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