YTPP - BACSU - GREMLIN Contacts

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YTPP - Thioredoxin-like protein YtpP

UniProt:	O34357	Sequences: MKKIESTQELEKAVKDDWSVFMFSADWCPDCRFVEPFLPELEANFPEFTYYYVDRDKFIDTCAEWEIYGIPSFVVFNEGKEVNRFVSKDRKTKEEIEQFLTDSLAKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	107 (96)
Sequences:	8749 (5613)
Seq/√Len:	572.9

ECOLI - THIO2 THIO YBBN
BACSU - YTPP YDBP THIO YDFQ YUSE BDBA STOA YNEN
HALSA - O46709 Q9HMD0 Q9HQ69
SULSO - Q97WI4 Q980T5 Q980E5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_R	62_C	2.824	1.00
40_E	93_K	2.346	1.00
11_E	64_E	2.340	1.00
74_V	84_R	2.176	1.00
92_T	95_E	2.077	1.00
19_S	49_T	2.059	1.00
7_T	60_D	2.052	1.00
44_N	93_K	2.003	1.00
5_E	51_Y	1.871	1.00
7_T	61_T	1.835	1.00
54_D	57_K	1.816	1.00
44_N	97_E	1.793	1.00
22_M	52_Y	1.787	1.00
81_E	84_R	1.770	1.00
28_C	31_C	1.735	1.00
37_F	40_E	1.674	1.00
74_V	81_E	1.665	1.00
65_W	76_F	1.640	1.00
38_L	50_Y	1.637	1.00
18_W	75_V	1.609	1.00
45_F	97_E	1.594	1.00
20_V	38_L	1.555	1.00
7_T	58_F	1.533	1.00
37_F	93_K	1.528	1.00
20_V	73_F	1.519	1.00
13_A	49_T	1.502	1.00
90_R	95_E	1.488	1.00
55_R	70_I	1.477	1.00
41_L	50_Y	1.476	1.00
26_D	54_D	1.425	1.00
9_E	13_A	1.405	1.00
85_F	91_K	1.374	1.00
95_E	98_Q	1.368	1.00
45_F	101_T	1.352	1.00
41_L	97_E	1.338	1.00
19_S	51_Y	1.336	1.00
97_E	101_T	1.298	1.00
6_S	9_E	1.269	1.00
34_V	73_F	1.263	1.00
85_F	99_F	1.212	1.00
5_E	13_A	1.155	1.00
34_V	37_F	1.154	1.00
53_V	61_T	1.135	1.00
83_N	99_F	1.130	1.00
22_M	35_E	1.127	1.00
21_F	76_F	1.117	1.00
41_L	93_K	1.111	1.00
13_A	19_S	1.104	1.00
35_E	39_P	1.090	1.00
75_V	99_F	1.079	1.00
6_S	58_F	1.051	1.00
35_E	52_Y	1.029	1.00
11_E	15_K	1.020	1.00
34_V	96_I	1.012	1.00
59_I	63_A	1.004	1.00
53_V	62_C	0.987	1.00
18_W	77_N	0.985	1.00
93_K	97_E	0.966	1.00
38_L	73_F	0.946	1.00
39_P	52_Y	0.946	1.00
91_K	95_E	0.937	1.00
41_L	45_F	0.907	1.00
43_A	46_P	0.895	1.00
33_F	90_R	0.853	1.00
48_F	100_L	0.849	1.00
20_V	50_Y	0.843	1.00
75_V	100_L	0.839	1.00
5_E	9_E	0.835	1.00
13_A	17_D	0.822	1.00
77_N	82_V	0.810	1.00
41_L	96_I	0.809	1.00
29_P	32_R	0.806	1.00
23_F	65_W	0.805	1.00
94_E	98_Q	0.794	1.00
12_K	16_D	0.794	1.00
10_L	65_W	0.793	1.00
73_F	96_I	0.786	1.00
5_E	21_F	0.779	1.00
45_F	48_F	0.778	1.00
14_V	19_S	0.772	1.00
24_S	52_Y	0.769	1.00
9_E	51_Y	0.767	1.00
37_F	92_T	0.752	1.00
10_L	23_F	0.752	1.00
60_D	64_E	0.748	1.00
98_Q	101_T	0.746	1.00
17_D	78_E	0.735	1.00
34_V	91_K	0.731	1.00
91_K	99_F	0.727	1.00
58_F	61_T	0.718	1.00
26_D	56_D	0.714	1.00
22_M	34_V	0.708	1.00
22_M	30_D	0.703	1.00
42_E	50_Y	0.687	1.00
24_S	70_I	0.673	1.00
18_W	78_E	0.667	1.00
20_V	96_I	0.665	1.00
67_I	72_S	0.663	1.00
34_V	38_L	0.661	1.00
27_W	32_R	0.658	1.00
37_F	41_L	0.653	1.00
26_D	32_R	0.651	1.00
17_D	49_T	0.644	1.00
40_E	43_A	0.633	1.00
68_Y	84_R	0.630	1.00
11_E	16_D	0.615	1.00
23_F	55_R	0.614	1.00
10_L	61_T	0.611	1.00
59_I	62_C	0.611	1.00
24_S	54_D	0.607	1.00
20_V	100_L	0.606	1.00
30_D	33_F	0.605	1.00
23_F	74_V	0.600	1.00
25_A	56_D	0.599	1.00
21_F	53_V	0.596	1.00
61_T	64_E	0.596	1.00
21_F	51_Y	0.595	1.00
38_L	100_L	0.593	1.00
30_D	69_G	0.591	1.00
77_N	80_K	0.588	1.00
55_R	67_I	0.580	1.00
29_P	33_F	0.580	1.00
14_V	17_D	0.579	1.00
20_V	75_V	0.578	1.00
62_C	65_W	0.576	1.00
9_E	12_K	0.564	0.99
44_N	101_T	0.555	0.99
94_E	97_E	0.545	0.99
48_F	52_Y	0.543	0.99
10_L	21_F	0.540	0.99
76_F	81_E	0.534	0.99
60_D	63_A	0.534	0.99
83_N	102_D	0.526	0.99
99_F	102_D	0.526	0.99
66_E	84_R	0.517	0.99
85_F	95_E	0.516	0.99
53_V	58_F	0.513	0.99
23_F	67_I	0.511	0.99
25_A	36_P	0.507	0.99
38_L	96_I	0.506	0.99
30_D	91_K	0.505	0.99
40_E	44_N	0.505	0.99
27_W	56_D	0.503	0.99
69_G	86_V	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
3f8uA	2	0.9813	99.8	0.194	Contact Map
2r2jA	2	0.9626	99.8	0.197	Contact Map
3apoA	1	0.9065	99.8	0.2	Contact Map
2b5eA	1	0.9813	99.8	0.206	Contact Map
3wgdA	3	0.972	99.8	0.237	Contact Map
4i6xA	1	0.972	99.8	0.238	Contact Map
4tveA	1	0.9813	99.8	0.239	Contact Map
4ekzA	1	0.9813	99.8	0.24	Contact Map
3ed3A	1	0.9813	99.8	0.24	Contact Map
4tw5A	3	0.9813	99.8	0.244	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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