TPX - ECOLI - GREMLIN Contacts

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TPX - Thiol peroxidase

UniProt:	P0A862	Sequences: MSQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12672
Length:	168 (142)
Sequences:	12495 (7570)
Seq/√Len:	635.3

ECOLI - TPX AHPC BCP DSBE
BACSU - TPX AHPC BCP YKUU YKUV RESA STOA YNEN
HALSA - Q9HQE6 Q9HP28 Q9HN00 Q9HRG4
SULSO - Q97VL0 Q97WG5 Q97WP9 TDXH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_R	140_E	3.446	1.00
29_T	37_D	3.014	1.00
25_A	118_Y	2.634	1.00
56_I	91_Q	2.631	1.00
46_K	79_V	2.569	1.00
69_N	101_N	2.536	1.00
32_A	36_S	2.493	1.00
139_D	145_I	2.371	1.00
29_T	39_T	2.369	1.00
72_A	76_D	2.234	1.00
24_K	143_N	2.197	1.00
122_I	132_A	2.084	1.00
71_L	74_E	2.079	1.00
27_T	41_G	2.021	1.00
20_Q	23_S	2.011	1.00
110_R	113_E	1.949	1.00
39_T	42_Q	1.928	1.00
113_E	117_A	1.910	1.00
33_K	95_C	1.874	1.00
31_V	37_D	1.820	1.00
139_D	143_N	1.809	1.00
115_L	131_A	1.758	1.00
27_T	39_T	1.719	1.00
72_A	101_N	1.662	1.00
32_A	38_V	1.656	1.00
38_V	43_F	1.653	1.00
67_K	71_L	1.652	1.00
85_A	115_L	1.564	1.00
146_F	165_V	1.546	1.00
48_K	142_D	1.502	1.00
71_L	159_Y	1.456	1.00
65_V	100_L	1.448	1.00
85_A	111_N	1.448	1.00
25_A	138_I	1.436	1.00
57_D	98_E	1.431	1.00
57_D	93_R	1.375	1.00
48_K	79_V	1.368	1.00
49_V	137_V	1.366	1.00
32_A	104_I	1.355	1.00
43_F	81_L	1.355	1.00
30_L	106_L	1.346	1.00
85_A	131_A	1.298	1.00
30_L	114_F	1.285	1.00
44_A	48_K	1.283	1.00
43_F	48_K	1.281	1.00
47_R	78_T	1.264	1.00
160_E	164_A	1.251	1.00
92_S	96_G	1.243	1.00
71_L	160_E	1.237	1.00
76_D	79_V	1.229	1.00
111_N	116_Q	1.224	1.00
69_N	103_V	1.210	1.00
116_Q	121_A	1.192	1.00
48_K	81_L	1.179	1.00
66_R	70_Q	1.177	1.00
78_T	166_L	1.170	1.00
138_I	144_V	1.168	1.00
47_R	145_I	1.118	1.00
44_A	142_D	1.106	1.00
120_V	134_A	1.076	1.00
21_A	146_F	1.073	1.00
67_K	70_Q	1.057	1.00
73_T	76_D	1.057	1.00
79_V	104_I	1.054	1.00
51_N	65_V	1.045	1.00
27_T	40_L	1.043	1.00
52_I	83_I	1.040	1.00
63_A	156_E	1.035	1.00
161_A	164_A	1.022	1.00
41_G	44_A	1.006	1.00
145_I	151_D	0.996	1.00
32_A	106_L	0.995	1.00
57_D	97_A	0.985	1.00
120_V	136_V	0.984	1.00
93_R	96_G	0.981	1.00
132_A	149_L	0.976	1.00
111_N	121_A	0.976	1.00
114_F	118_Y	0.974	1.00
89_F	93_R	0.957	1.00
82_C	105_T	0.949	1.00
34_D	92_S	0.948	1.00
77_N	140_E	0.948	1.00
113_E	116_Q	0.948	1.00
49_V	135_V	0.946	1.00
134_A	149_L	0.943	1.00
66_R	69_N	0.941	1.00
148_Q	165_V	0.933	1.00
62_A	98_E	0.927	1.00
88_P	107_S	0.919	1.00
81_L	106_L	0.912	1.00
74_E	163_L	0.903	1.00
53_F	82_C	0.902	1.00
87_L	90_A	0.901	1.00
48_K	138_I	0.900	1.00
92_S	95_C	0.896	1.00
137_V	165_V	0.895	1.00
25_A	144_V	0.892	1.00
137_V	146_F	0.889	1.00
57_D	90_A	0.887	1.00
19_P	144_V	0.884	1.00
51_N	103_V	0.882	1.00
50_L	138_I	0.869	1.00
47_R	77_N	0.865	1.00
24_K	44_A	0.852	1.00
21_A	147_S	0.837	1.00
157_P	160_E	0.830	1.00
28_F	118_Y	0.830	1.00
65_V	82_C	0.823	1.00
63_A	66_R	0.821	1.00
68_F	80_V	0.816	1.00
66_R	98_E	0.812	1.00
40_L	48_K	0.803	1.00
136_V	144_V	0.799	1.00
28_F	114_F	0.793	1.00
115_L	121_A	0.787	1.00
38_V	81_L	0.787	1.00
151_D	155_T	0.786	1.00
52_I	120_V	0.785	1.00
33_K	92_S	0.784	1.00
148_Q	161_A	0.779	1.00
31_V	109_F	0.776	1.00
132_A	150_V	0.775	1.00
20_Q	147_S	0.774	1.00
47_R	166_L	0.773	1.00
148_Q	162_A	0.768	1.00
49_V	78_T	0.760	1.00
53_F	56_I	0.745	1.00
19_P	23_S	0.734	1.00
64_S	135_V	0.733	1.00
83_I	114_F	0.732	1.00
25_A	40_L	0.732	1.00
111_N	115_L	0.722	1.00
124_D	128_K	0.719	1.00
85_A	108_T	0.717	1.00
34_D	95_C	0.711	1.00
21_A	144_V	0.705	1.00
87_L	109_F	0.701	1.00
146_F	161_A	0.699	1.00
157_P	161_A	0.692	1.00
40_L	43_F	0.690	1.00
69_N	72_A	0.684	1.00
137_V	148_Q	0.676	1.00
68_F	162_A	0.675	1.00
138_I	142_D	0.664	1.00
91_Q	94_F	0.663	1.00
31_V	88_P	0.660	1.00
73_T	101_N	0.659	1.00
43_F	79_V	0.654	1.00
45_G	140_E	0.653	1.00
28_F	40_L	0.653	1.00
64_S	68_F	0.651	1.00
75_I	78_T	0.651	1.00
135_V	162_A	0.648	1.00
122_I	128_K	0.646	1.00
58_T	133_R	0.639	1.00
52_I	114_F	0.637	1.00
50_L	118_Y	0.634	1.00
88_P	92_S	0.633	1.00
101_N	104_I	0.633	1.00
25_A	114_F	0.627	1.00
55_S	130_L	0.627	1.00
51_N	64_S	0.625	1.00
90_A	93_R	0.624	1.00
55_S	86_D	0.623	1.00
38_V	106_L	0.611	1.00
156_E	159_Y	0.603	1.00
154_T	157_P	0.595	1.00
72_A	79_V	0.593	1.00
134_A	147_S	0.593	1.00
89_F	92_S	0.590	1.00
52_I	118_Y	0.590	1.00
63_A	67_K	0.587	1.00
53_F	91_Q	0.587	1.00
95_C	105_T	0.586	1.00
47_R	137_V	0.584	1.00
67_K	159_Y	0.581	1.00
114_F	117_A	0.577	1.00
69_N	73_T	0.574	1.00
94_F	98_E	0.570	1.00
60_V	154_T	0.570	1.00
75_I	163_L	0.566	1.00
148_Q	158_D	0.566	1.00
158_D	161_A	0.566	1.00
33_K	104_I	0.559	1.00
85_A	121_A	0.554	1.00
91_Q	105_T	0.553	1.00
60_V	155_T	0.553	1.00
68_F	159_Y	0.546	1.00
35_L	88_P	0.545	1.00
71_L	75_I	0.543	1.00
115_L	120_V	0.543	1.00
136_V	147_S	0.543	1.00
49_V	162_A	0.541	1.00
49_V	68_F	0.538	0.99
56_I	90_A	0.538	0.99
54_P	58_T	0.532	0.99
80_V	103_V	0.530	0.99
109_F	129_G	0.528	0.99
27_T	44_A	0.527	0.99
51_N	82_C	0.517	0.99
38_V	42_Q	0.513	0.99
67_K	156_E	0.513	0.99
23_S	147_S	0.512	0.99
44_A	141_N	0.511	0.99
55_S	87_L	0.510	0.99
55_S	58_T	0.508	0.99
26_Q	117_A	0.507	0.99
123_A	128_K	0.507	0.99
132_A	153_I	0.506	0.99
33_K	88_P	0.506	0.99
56_I	105_T	0.504	0.99
145_I	165_V	0.503	0.99
53_F	94_F	0.500	0.99

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
3zrdA	2	0.9821	100	0.298	Contact Map
1xiyA	1	0.875	100	0.302	Contact Map
2v2gA	2	0.875	100	0.303	Contact Map
3a2vA	5	0.881	100	0.304	Contact Map
3w6gA	6	0.8512	100	0.304	Contact Map
1prxA	2	0.8869	100	0.307	Contact Map
1q98A	2	0.9643	100	0.308	Contact Map
2yzhA	3	0.9821	100	0.31	Contact Map
1xvqA	2	0.9345	100	0.314	Contact Map
1xccA	2	0.875	100	0.314	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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