Terminase_4 - PFAM28P - GREMLIN Contacts

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Terminase_4 - Phage terminase, small subunit

PFAM:	PF05119	Sequences: AKAEWRRLAPELEALGLLTEADRAALAAYCEAYARWREAEEELAKEGLVVKTPNGNGYPKQNPAVAIANKAAKQMRKLAAEFGLTPSSRSRLAVPKAEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (92)
Sequences:	14446 (12036)
Seq/√Len:	1254.9
META:	0.913

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_E	68_A	2.681	1.00
61_Q	66_A	2.366	1.00
73_K	77_K	2.280	1.00
42_E	64_A	2.133	1.00
42_E	46_E	2.058	1.00
22_D	89_R	1.989	1.00
66_A	70_K	1.932	1.00
81_E	88_S	1.914	1.00
36_W	68_A	1.772	1.00
29_Y	75_M	1.736	1.00
35_R	68_A	1.728	1.00
87_S	91_R	1.717	1.00
4_E	7_R	1.665	1.00
28_A	72_A	1.656	1.00
69_N	73_K	1.652	1.00
4_E	24_A	1.640	1.00
31_E	40_E	1.596	1.00
25_A	82_F	1.580	1.00
32_A	71_A	1.574	1.00
61_Q	70_K	1.563	1.00
29_Y	79_A	1.539	1.00
70_K	73_K	1.536	1.00
33_Y	75_M	1.531	1.00
9_A	26_L	1.468	1.00
69_N	74_Q	1.462	1.00
81_E	85_T	1.462	1.00
32_A	74_Q	1.344	1.00
76_R	81_E	1.339	1.00
28_A	79_A	1.338	1.00
36_W	72_A	1.286	1.00
35_R	71_A	1.282	1.00
52_T	58_Y	1.274	1.00
76_R	80_A	1.260	1.00
39_A	67_I	1.214	1.00
52_T	55_G	1.206	1.00
52_T	60_K	1.204	1.00
35_R	40_E	1.198	1.00
75_M	79_A	1.179	1.00
39_A	64_A	1.162	1.00
61_Q	67_I	1.162	1.00
8_L	26_L	1.151	1.00
4_E	33_Y	1.146	1.00
51_K	59_P	1.141	1.00
71_A	74_Q	1.133	1.00
25_A	78_L	1.130	1.00
2_K	6_R	1.127	1.00
32_A	72_A	1.116	1.00
38_E	48_L	1.087	1.00
33_Y	37_R	1.079	1.00
28_A	78_L	1.036	1.00
68_A	72_A	1.034	1.00
29_Y	78_L	1.030	1.00
42_E	62_N	1.015	1.00
72_A	78_L	1.015	1.00
77_K	80_A	1.013	1.00
34_A	38_E	1.008	1.00
10_P	14_A	1.006	1.00
36_W	75_M	1.006	1.00
28_A	36_W	0.991	1.00
85_T	88_S	0.972	1.00
80_A	88_S	0.969	1.00
40_E	44_A	0.949	1.00
11_E	20_E	0.946	1.00
36_W	40_E	0.944	1.00
46_E	64_A	0.931	1.00
32_A	75_M	0.896	1.00
53_P	58_Y	0.889	1.00
24_A	33_Y	0.873	1.00
8_L	29_Y	0.869	1.00
9_A	13_E	0.868	1.00
46_E	62_N	0.867	1.00
35_R	48_L	0.862	1.00
15_L	21_A	0.854	1.00
54_N	58_Y	0.845	1.00
5_W	30_C	0.843	1.00
39_A	71_A	0.823	1.00
77_K	81_E	0.811	1.00
32_A	35_R	0.804	1.00
27_A	31_E	0.792	1.00
31_E	36_W	0.792	1.00
11_E	21_A	0.781	1.00
4_E	8_L	0.779	1.00
83_G	92_L	0.769	1.00
39_A	68_A	0.762	1.00
66_A	69_N	0.753	1.00
73_K	76_R	0.741	1.00
38_E	42_E	0.734	1.00
24_A	29_Y	0.716	1.00
27_A	37_R	0.716	1.00
37_R	41_E	0.715	1.00
11_E	14_A	0.709	1.00
7_R	11_E	0.708	1.00
32_A	78_L	0.695	1.00
25_A	85_T	0.682	1.00
50_V	60_K	0.679	1.00
43_L	68_A	0.678	1.00
7_R	24_A	0.665	1.00
49_V	64_A	0.658	1.00
42_E	45_K	0.656	1.00
9_A	18_L	0.651	1.00
30_C	34_A	0.646	1.00
70_K	74_Q	0.632	1.00
6_R	10_P	0.632	1.00
61_Q	69_N	0.618	1.00
4_E	29_Y	0.613	1.00
24_A	27_A	0.606	1.00
26_L	82_F	0.606	1.00
23_R	27_A	0.605	1.00
20_E	23_R	0.601	1.00
25_A	79_A	0.600	1.00
11_E	15_L	0.598	1.00
19_T	22_D	0.594	1.00
29_Y	82_F	0.592	1.00
79_A	85_T	0.592	1.00
33_Y	36_W	0.590	1.00
80_A	91_R	0.582	1.00
61_Q	65_V	0.565	1.00
3_A	6_R	0.563	1.00
43_L	47_G	0.562	1.00
48_L	64_A	0.561	1.00
80_A	87_S	0.545	1.00
31_E	35_R	0.545	1.00
65_V	71_A	0.543	1.00
8_L	84_L	0.543	1.00
5_W	9_A	0.542	1.00
27_A	33_Y	0.532	1.00
80_A	85_T	0.527	1.00
31_E	44_A	0.526	1.00
67_I	70_K	0.525	1.00
78_L	82_F	0.523	1.00
67_I	71_A	0.523	1.00
55_G	58_Y	0.522	1.00
74_Q	77_K	0.522	1.00
32_A	36_W	0.519	1.00
7_R	23_R	0.510	1.00
31_E	68_A	0.505	1.00
49_V	59_P	0.504	1.00
40_E	72_A	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
4u0wA	2	0.9899	9.9	0.869	Contact Map
4bm5A	1	0.8586	9.8	0.87	Contact Map
2gf5A	1	0.9697	9.7	0.87	Contact Map
4pt7A	3	0.7879	8.7	0.873	Contact Map
4w9rA	2	0.9798	7.7	0.875	Contact Map
4ufcA	1	0.9495	7.3	0.877	Contact Map
3tqnA	2	0.8586	7	0.878	Contact Map
1rr7A	2	0.8586	6.4	0.88	Contact Map
3f8mA	2	0.9394	5.9	0.882	Contact Map
4zbwA	2	0.5051	5.4	0.884	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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