Phage_term_smal - PFAM28P - GREMLIN Contacts

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Phage_term_smal - Phage small terminase subunit

PFAM:	PF05944	Sequences: LAQLAEDRRRLKQIQSIERKAELKRELLPKYLPWVEGVLAAGKGAQDDVLMTVMVWLIDAGDFEGALDIAEYALRHGLAMPDRFKRTTATLVAEEVADAALKALKAGESVDLPYLSRVEELTADWDMPDQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (129)
Sequences:	1112 (829)
Seq/√Len:	73.0
META:	0.517

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_L	65_G	3.050	1.00
73_A	88_T	2.923	1.00
44_G	72_Y	2.763	1.00
71_E	117_R	2.746	1.00
23_L	27_L	2.714	1.00
7_D	31_Y	2.608	1.00
50_L	69_I	2.419	1.00
70_A	92_V	2.336	1.00
3_Q	7_D	2.267	1.00
51_M	73_A	2.166	1.00
62_D	65_G	2.114	1.00
87_T	90_T	2.056	1.00
17_I	21_A	2.018	1.00
55_V	84_F	1.995	1.00
46_Q	79_A	1.964	1.00
14_I	23_L	1.929	1.00
3_Q	30_K	1.918	1.00
10_R	26_E	1.887	1.00
7_D	27_L	1.881	1.00
7_D	30_K	1.868	1.00
15_Q	87_T	1.866	1.00
80_M	91_L	1.823	1.00
12_K	20_K	1.751	1.00
90_T	128_P	1.725	1.00
68_D	117_R	1.684	1.00
36_E	40_A	1.651	1.00
51_M	88_T	1.608	0.99
35_V	69_I	1.588	0.99
35_V	53_V	1.574	0.99
58_I	66_A	1.565	0.99
22_E	25_R	1.555	0.99
57_L	62_D	1.530	0.99
42_G	75_R	1.511	0.99
77_G	125_W	1.479	0.99
63_F	99_A	1.463	0.99
23_L	26_E	1.459	0.99
50_L	73_A	1.448	0.99
8_R	83_R	1.445	0.99
10_R	23_L	1.421	0.99
28_L	60_A	1.409	0.99
67_L	118_V	1.408	0.99
21_A	60_A	1.391	0.98
111_D	116_S	1.380	0.98
33_P	36_E	1.373	0.98
65_G	68_D	1.370	0.98
7_D	10_R	1.363	0.98
55_V	80_M	1.342	0.98
32_L	65_G	1.332	0.98
52_T	84_F	1.303	0.98
28_L	53_V	1.239	0.97
55_V	91_L	1.208	0.96
94_E	97_A	1.207	0.96
94_E	127_M	1.199	0.96
17_I	20_K	1.185	0.96
19_R	22_E	1.177	0.95
36_E	65_G	1.170	0.95
42_G	45_A	1.158	0.95
93_A	127_M	1.154	0.95
63_F	114_Y	1.144	0.95
96_V	118_V	1.121	0.94
15_Q	90_T	1.120	0.94
103_A	110_V	1.097	0.93
126_D	129_D	1.089	0.93
42_G	76_H	1.083	0.93
5_A	9_R	1.073	0.93
54_M	80_M	1.029	0.91
119_E	123_A	1.006	0.90
103_A	108_E	0.971	0.88
9_R	12_K	0.967	0.88
6_E	9_R	0.963	0.88
58_I	96_V	0.943	0.87
15_Q	128_P	0.914	0.85
5_A	8_R	0.911	0.85
120_E	123_A	0.909	0.85
53_V	57_L	0.868	0.82
63_F	110_V	0.868	0.82
38_V	47_D	0.867	0.82
32_L	57_L	0.861	0.81
100_A	110_V	0.860	0.81
72_Y	78_L	0.849	0.81
58_I	63_F	0.846	0.80
51_M	54_M	0.832	0.79
86_R	94_E	0.829	0.79
17_I	84_F	0.828	0.79
10_R	13_Q	0.817	0.78
3_Q	6_E	0.802	0.77
71_E	75_R	0.795	0.76
36_E	68_D	0.792	0.76
44_G	78_L	0.788	0.75
64_E	68_D	0.786	0.75
113_P	116_S	0.785	0.75
19_R	23_L	0.782	0.75
111_D	114_Y	0.775	0.74
3_Q	31_Y	0.775	0.74
34_W	37_G	0.766	0.73
32_L	53_V	0.764	0.73
27_L	30_K	0.759	0.73
8_R	52_T	0.750	0.72
122_T	126_D	0.745	0.71
34_W	128_P	0.745	0.71
64_E	117_R	0.742	0.71
38_V	45_A	0.724	0.69
52_T	83_R	0.722	0.69
54_M	88_T	0.720	0.69
3_Q	23_L	0.720	0.69
2_A	6_E	0.720	0.69
58_I	92_V	0.719	0.69
38_V	50_L	0.718	0.68
57_L	68_D	0.715	0.68
19_R	27_L	0.713	0.68
71_E	120_E	0.711	0.68
72_Y	76_H	0.709	0.67
109_S	121_L	0.708	0.67
80_M	88_T	0.699	0.66
35_V	57_L	0.698	0.66
4_L	49_V	0.697	0.66
37_G	66_A	0.696	0.66
14_I	21_A	0.694	0.66
54_M	73_A	0.683	0.65
4_L	52_T	0.682	0.64
63_F	96_V	0.680	0.64
100_A	115_L	0.677	0.64
113_P	117_R	0.670	0.63
22_E	26_E	0.663	0.62
74_L	125_W	0.661	0.62
112_L	116_S	0.660	0.62
42_G	50_L	0.656	0.61
16_S	129_D	0.655	0.61
86_R	95_E	0.653	0.61
85_K	130_Q	0.648	0.61
46_Q	51_M	0.646	0.60
35_V	124_D	0.641	0.60
58_I	91_L	0.641	0.60
51_M	55_V	0.635	0.59
99_A	103_A	0.632	0.59
47_D	78_L	0.632	0.59
82_D	85_K	0.629	0.58
102_K	106_A	0.622	0.57
44_G	76_H	0.621	0.57
74_L	89_A	0.619	0.57
125_W	128_P	0.617	0.57
100_A	107_G	0.614	0.56
20_K	23_L	0.613	0.56
64_E	111_D	0.609	0.56
33_P	37_G	0.602	0.55
14_I	82_D	0.592	0.54
47_D	72_Y	0.583	0.53
42_G	90_T	0.580	0.52
30_K	130_Q	0.579	0.52
32_L	36_E	0.573	0.51
104_L	107_G	0.571	0.51
11_L	20_K	0.570	0.51
39_L	78_L	0.564	0.50
114_Y	130_Q	0.560	0.50
122_T	129_D	0.558	0.50
11_L	56_W	0.557	0.49
118_V	122_T	0.554	0.49
16_S	128_P	0.554	0.49
98_D	101_L	0.553	0.49
39_L	67_L	0.553	0.49
99_A	113_P	0.552	0.49
101_L	105_K	0.552	0.49
16_S	97_A	0.551	0.49
34_W	84_F	0.550	0.49
99_A	114_Y	0.550	0.49
79_A	88_T	0.548	0.48
30_K	49_V	0.548	0.48
119_E	122_T	0.540	0.47
69_I	79_A	0.538	0.47
24_K	81_P	0.537	0.47
64_E	107_G	0.537	0.47
19_R	77_G	0.535	0.47
58_I	99_A	0.535	0.47
122_T	127_M	0.532	0.46
78_L	82_D	0.531	0.46
63_F	111_D	0.529	0.46
34_W	58_I	0.524	0.45
110_V	118_V	0.524	0.45
9_R	19_R	0.524	0.45
116_S	120_E	0.523	0.45
32_L	62_D	0.521	0.45
26_E	64_E	0.519	0.45
83_R	90_T	0.517	0.44
117_R	120_E	0.517	0.44
38_V	76_H	0.515	0.44
114_Y	117_R	0.515	0.44
56_W	59_D	0.506	0.43
54_M	72_Y	0.506	0.43
53_V	65_G	0.506	0.43
72_Y	82_D	0.504	0.43
5_A	13_Q	0.503	0.43
57_L	69_I	0.503	0.43
88_T	92_V	0.503	0.43
107_G	110_V	0.500	0.42

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
3o0yA	3	0.9154	17.4	0.931	Contact Map
3gnlA	1	0.3231	6.6	0.943	Contact Map
1x4qA	1	0.6538	4.6	0.947	Contact Map
2x5hA	2	0.3231	4.5	0.947	Contact Map
1mwqA	2	0.6615	4.3	0.948	Contact Map
3pvzA	2	0.3154	4.3	0.948	Contact Map
1hdhA	1	0.3	4.2	0.948	Contact Map
1z8uA	1	0.1923	3.1	0.952	Contact Map
3qwpA	1	0.9077	3	0.952	Contact Map
1xngA	2	0.3154	3	0.952	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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