PTH - HALSA - GREMLIN Contacts

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PTH - Peptidyl-tRNA hydrolase

UniProt:	P61414	Sequences: MKQVIAARTDIGMGQGKLAAQVAHASLNAYEYTDDRAVRRWKDEGQTKVVVKVGSERELYERSEEAKRAGLPTGLISDAGRTQLEPGTPTALAIGPAPDADVDQITGDLSLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	112 (110)
Sequences:	657 (436)
Seq/√Len:	41.5

HALSA - PTH
SULSO - PTH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_G	83_Q	4.072	1.00
71_L	94_I	3.289	1.00
31_E	42_K	2.759	1.00
28_N	76_I	2.711	1.00
94_I	102_V	2.616	1.00
55_S	58_E	2.501	1.00
29_A	93_A	2.489	1.00
23_A	26_S	2.286	1.00
54_G	58_E	2.154	0.99
5_I	22_V	2.091	0.99
27_L	30_Y	1.987	0.99
30_Y	38_V	1.972	0.99
69_A	104_Q	1.852	0.98
47_T	81_R	1.781	0.98
3_Q	29_A	1.729	0.97
63_S	73_T	1.704	0.97
4_V	51_V	1.605	0.96
34_D	72_P	1.587	0.96
3_Q	26_S	1.562	0.95
19_A	22_V	1.542	0.95
64_E	68_R	1.523	0.95
53_V	58_E	1.521	0.95
34_D	37_A	1.520	0.95
71_L	102_V	1.497	0.94
28_N	74_G	1.489	0.94
47_T	99_D	1.478	0.94
62_R	92_L	1.458	0.93
22_V	91_A	1.424	0.92
63_S	67_K	1.409	0.92
75_L	92_L	1.401	0.92
15_Q	83_Q	1.400	0.92
61_E	65_E	1.351	0.90
7_A	22_V	1.340	0.90
77_S	89_P	1.335	0.90
98_P	101_D	1.311	0.89
7_A	18_L	1.303	0.88
69_A	105_I	1.299	0.88
84_L	88_T	1.263	0.87
71_L	105_I	1.244	0.86
56_E	89_P	1.243	0.86
99_D	103_D	1.213	0.85
8_R	56_E	1.194	0.84
6_A	53_V	1.175	0.83
5_I	91_A	1.173	0.83
13_M	18_L	1.170	0.82
11_I	88_T	1.142	0.81
14_G	50_V	1.138	0.81
38_V	42_K	1.124	0.80
97_A	101_D	1.101	0.78
8_R	88_T	1.099	0.78
13_M	20_A	1.079	0.77
20_A	81_R	1.068	0.76
9_T	12_G	1.064	0.76
77_S	87_G	1.047	0.75
50_V	100_A	1.026	0.73
9_T	54_G	1.005	0.72
8_R	53_V	0.988	0.70
15_Q	110_S	0.959	0.68
31_E	38_V	0.950	0.67
6_A	92_L	0.942	0.67
37_A	98_P	0.939	0.66
56_E	60_Y	0.939	0.66
61_E	67_K	0.933	0.66
53_V	59_L	0.927	0.65
71_L	97_A	0.897	0.63
9_T	55_S	0.893	0.62
3_Q	74_G	0.890	0.62
44_E	99_D	0.881	0.61
4_V	94_I	0.877	0.61
51_V	62_R	0.875	0.61
32_Y	76_I	0.870	0.60
65_E	69_A	0.865	0.60
39_R	68_R	0.852	0.59
30_Y	42_K	0.841	0.58
7_A	91_A	0.833	0.57
81_R	86_P	0.831	0.57
65_E	68_R	0.825	0.56
7_A	81_R	0.813	0.55
23_A	35_D	0.811	0.55
18_L	22_V	0.807	0.55
17_K	82_T	0.802	0.54
83_Q	110_S	0.802	0.54
37_A	72_P	0.799	0.54
49_V	81_R	0.788	0.53
9_T	52_K	0.787	0.53
52_K	84_L	0.782	0.52
17_K	80_G	0.776	0.52
10_D	95_G	0.776	0.52
13_M	84_L	0.773	0.51
33_T	72_P	0.766	0.51
6_A	51_V	0.756	0.50
62_R	108_D	0.748	0.49
60_Y	89_P	0.743	0.49
50_V	97_A	0.741	0.48
84_L	87_G	0.740	0.48
71_L	101_D	0.740	0.48
38_V	91_A	0.738	0.48
69_A	103_D	0.736	0.48
47_T	97_A	0.735	0.48
100_A	104_Q	0.733	0.48
4_V	7_A	0.730	0.47
12_G	86_P	0.729	0.47
67_K	73_T	0.728	0.47
27_L	73_T	0.723	0.47
29_A	72_P	0.700	0.45
3_Q	72_P	0.700	0.45
32_Y	74_G	0.698	0.44
13_M	16_G	0.694	0.44
34_D	101_D	0.678	0.43
66_A	94_I	0.669	0.42
39_R	100_A	0.667	0.42
94_I	106_T	0.651	0.40
95_G	102_V	0.648	0.40
63_S	92_L	0.644	0.40
63_S	75_L	0.637	0.39
3_Q	91_A	0.633	0.39
51_V	109_L	0.632	0.38
58_E	93_A	0.632	0.38
6_A	106_T	0.626	0.38
52_K	99_D	0.623	0.38
20_A	23_A	0.622	0.38
40_R	44_E	0.617	0.37
55_S	65_E	0.616	0.37
79_A	82_T	0.606	0.36
81_R	91_A	0.605	0.36
9_T	76_I	0.604	0.36
50_V	59_L	0.603	0.36
49_V	65_E	0.602	0.36
68_R	73_T	0.601	0.36
10_D	56_E	0.599	0.36
79_A	87_G	0.594	0.35
56_E	77_S	0.591	0.35
83_Q	88_T	0.586	0.34
80_G	83_Q	0.583	0.34
8_R	95_G	0.580	0.34
33_T	38_V	0.576	0.34
10_D	55_S	0.574	0.33
61_E	68_R	0.571	0.33
66_A	73_T	0.567	0.33
7_A	50_V	0.564	0.33
102_V	105_I	0.564	0.33
13_M	56_E	0.563	0.33
62_R	109_L	0.556	0.32
56_E	84_L	0.553	0.32
47_T	50_V	0.550	0.32
9_T	84_L	0.548	0.31
69_A	101_D	0.547	0.31
29_A	33_T	0.542	0.31
5_I	50_V	0.541	0.31
11_I	84_L	0.540	0.31
45_G	79_A	0.536	0.30
52_K	83_Q	0.534	0.30
62_R	103_D	0.532	0.30
37_A	101_D	0.527	0.30
50_V	87_G	0.525	0.30
62_R	101_D	0.523	0.29
25_A	91_A	0.522	0.29
36_R	44_E	0.518	0.29
36_R	43_D	0.517	0.29
40_R	70_G	0.514	0.29
96_P	102_V	0.512	0.29
57_R	61_E	0.511	0.28
46_Q	75_L	0.505	0.28
51_V	94_I	0.504	0.28
52_K	65_E	0.500	0.28

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
2zv3A	2	1	100	0.132	Contact Map
1rzwA	1	1	100	0.135	Contact Map
1xtyA	2	1	100	0.137	Contact Map
1q7sA	2	1	100	0.137	Contact Map
1wn2A	2	1	100	0.145	Contact Map
1rlkA	2	1	100	0.145	Contact Map
2gaxA	2	0.9643	99.8	0.574	Contact Map
2uz1A	4	0.7857	36	0.93	Contact Map
1hh2P	2	0.5268	31.4	0.932	Contact Map
2mt4A	1	0.5268	30.3	0.932	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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