TRPP - BACSU - GREMLIN Contacts

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TRPP - Probable tryptophan transport protein

UniProt:	O07515	Sequences: MKTKELVIMALFAAIGAALHSIIPPFLGGMKPDMMLIMMFMGILLFPRVQNVLVIGIVTGIISALTTAFPAGQIPNIIDKPVSAFLFFSLFLLFRKSRKTGAAAVLTVIGTILSGIVFLSSALLIVGLPGGFAALFAAVVLPAAVLNTISMIIIYPIVQTILRRSSFMEAAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (165)
Sequences:	181 (155)
Seq/√Len:	12.0

BACSU - TRPP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_A	73_Q	7.069	1.00
86_L	113_L	3.834	0.99
56_G	84_A	3.137	0.97
30_M	139_V	2.802	0.94
53_L	56_G	2.557	0.90
78_I	121_S	2.326	0.85
44_L	155_Y	2.295	0.84
49_V	85_F	2.188	0.81
82_V	101_G	2.179	0.81
126_V	129_P	2.111	0.79
42_G	55_I	2.103	0.78
20_H	66_T	2.100	0.78
18_A	143_A	1.981	0.74
2_K	5_E	1.976	0.74
79_D	121_S	1.878	0.70
129_P	135_L	1.867	0.69
75_P	121_S	1.863	0.69
69_F	122_A	1.833	0.68
107_T	151_M	1.830	0.68
43_I	91_F	1.821	0.67
31_K	68_A	1.796	0.66
69_F	135_L	1.780	0.66
35_M	39_M	1.758	0.65
25_P	29_G	1.693	0.61
67_T	73_Q	1.645	0.59
59_T	65_L	1.607	0.57
122_A	135_L	1.592	0.57
4_K	138_A	1.552	0.55
35_M	62_I	1.514	0.53
141_L	145_V	1.505	0.52
25_P	68_A	1.501	0.52
25_P	64_A	1.487	0.51
14_A	153_I	1.479	0.51
65_L	113_L	1.475	0.51
2_K	101_G	1.468	0.50
109_I	152_I	1.436	0.49
75_P	122_A	1.412	0.48
134_A	138_A	1.409	0.47
132_F	136_F	1.409	0.47
3_T	7_V	1.405	0.47
9_M	151_M	1.403	0.47
85_F	117_V	1.398	0.47
91_F	130_G	1.389	0.46
69_F	129_P	1.380	0.46
64_A	123_L	1.362	0.45
117_V	127_G	1.353	0.45
9_M	42_G	1.351	0.44
31_K	107_T	1.346	0.44
116_I	136_F	1.299	0.42
12_F	102_A	1.295	0.42
9_M	51_N	1.287	0.41
88_F	145_V	1.265	0.40
32_P	143_A	1.251	0.40
2_K	9_M	1.248	0.39
43_I	87_F	1.236	0.39
48_R	153_I	1.234	0.39
82_V	117_V	1.197	0.37
13_A	59_T	1.194	0.37
139_V	143_A	1.190	0.37
30_M	68_A	1.185	0.36
11_L	76_N	1.184	0.36
81_P	88_F	1.177	0.36
131_G	137_A	1.168	0.36
40_F	143_A	1.168	0.36
67_T	81_P	1.163	0.35
105_V	149_I	1.157	0.35
46_F	156_P	1.156	0.35
20_H	67_T	1.140	0.34
112_I	144_A	1.132	0.34
3_T	6_L	1.119	0.33
71_A	127_G	1.116	0.33
65_L	124_L	1.107	0.33
108_V	148_T	1.087	0.32
122_A	143_A	1.085	0.32
64_A	67_T	1.083	0.32
101_G	112_I	1.081	0.32
56_G	75_P	1.077	0.32
81_P	159_Q	1.058	0.31
43_I	74_I	1.051	0.30
45_L	164_R	1.035	0.30
65_L	105_V	1.016	0.29
13_A	55_I	1.016	0.29
25_P	148_T	1.009	0.29
25_P	73_Q	1.009	0.29
111_T	147_N	1.008	0.29
59_T	164_R	1.006	0.29
154_I	165_S	0.995	0.28
2_K	17_A	0.992	0.28
15_I	153_I	0.987	0.28
109_I	146_L	0.976	0.27
29_G	63_S	0.972	0.27
18_A	63_S	0.966	0.27
100_T	156_P	0.957	0.27
5_E	9_M	0.942	0.26
82_V	86_L	0.942	0.26
59_T	103_A	0.941	0.26
17_A	62_I	0.928	0.25
103_A	117_V	0.925	0.25
96_K	136_F	0.915	0.25
75_P	112_I	0.912	0.25
9_M	14_A	0.909	0.25
30_M	135_L	0.906	0.25
98_R	105_V	0.896	0.24
42_G	51_N	0.895	0.24
32_P	139_V	0.895	0.24
45_L	131_G	0.892	0.24
9_M	46_F	0.889	0.24
28_G	112_I	0.889	0.24
42_G	46_F	0.882	0.24
25_P	75_P	0.881	0.24
11_L	151_M	0.881	0.24
109_I	134_A	0.876	0.24
109_I	113_L	0.875	0.24
44_L	124_L	0.870	0.23
10_A	153_I	0.869	0.23
47_P	84_A	0.863	0.23
21_S	49_V	0.862	0.23
69_F	126_V	0.858	0.23
48_R	51_N	0.856	0.23
6_L	59_T	0.852	0.23
56_G	100_T	0.846	0.22
12_F	125_I	0.841	0.22
63_S	108_V	0.840	0.22
18_A	153_I	0.833	0.22
6_L	45_L	0.830	0.22
73_Q	123_L	0.827	0.22
105_V	141_L	0.826	0.22
75_P	125_I	0.820	0.22
74_I	120_S	0.819	0.22
107_T	148_T	0.819	0.22
75_P	78_I	0.808	0.21
104_A	152_I	0.806	0.21
48_R	104_A	0.804	0.21
34_M	41_M	0.803	0.21
39_M	55_I	0.799	0.21
63_S	161_I	0.795	0.21
133_A	149_I	0.795	0.21
34_M	151_M	0.794	0.21
88_F	123_L	0.784	0.20
44_L	105_V	0.777	0.20
148_T	152_I	0.772	0.20
116_I	134_A	0.769	0.20
2_K	67_T	0.766	0.20
148_T	159_Q	0.764	0.20
63_S	156_P	0.763	0.20
23_I	37_I	0.762	0.20
145_V	165_S	0.759	0.20
121_S	129_P	0.759	0.20
30_M	69_F	0.751	0.19
12_F	163_R	0.747	0.19
25_P	57_I	0.744	0.19
10_A	98_R	0.733	0.19
2_K	133_A	0.728	0.19
6_L	52_V	0.720	0.18
124_L	144_A	0.714	0.18
5_E	75_P	0.714	0.18
113_L	121_S	0.714	0.18
81_P	90_L	0.713	0.18
9_M	18_A	0.711	0.18
91_F	148_T	0.704	0.18
22_I	43_I	0.688	0.17
18_A	28_G	0.680	0.17
17_A	46_F	0.680	0.17
15_I	123_L	0.675	0.17
161_I	165_S	0.675	0.17
2_K	50_Q	0.667	0.17
43_I	55_I	0.664	0.17
7_V	11_L	0.660	0.17
61_I	149_I	0.657	0.17
56_G	99_K	0.651	0.16
105_V	153_I	0.649	0.16
5_E	8_I	0.647	0.16
43_I	109_I	0.643	0.16
16_G	20_H	0.641	0.16
66_T	151_M	0.633	0.16
86_L	93_L	0.632	0.16
34_M	130_G	0.623	0.16
90_L	109_I	0.619	0.16
96_K	150_S	0.619	0.16
9_M	55_I	0.618	0.15
71_A	74_I	0.617	0.15
58_V	67_T	0.614	0.15
14_A	160_T	0.611	0.15
151_M	156_P	0.611	0.15
145_V	161_I	0.609	0.15
18_A	22_I	0.606	0.15
41_M	151_M	0.604	0.15
10_A	61_I	0.603	0.15
6_L	32_P	0.603	0.15
13_A	18_A	0.602	0.15
4_K	10_A	0.600	0.15
27_L	31_K	0.598	0.15
17_A	95_R	0.597	0.15
87_F	95_R	0.597	0.15
25_P	38_M	0.595	0.15
45_L	59_T	0.595	0.15
27_L	34_M	0.592	0.15
160_T	163_R	0.592	0.15
34_M	81_P	0.591	0.15
75_P	116_I	0.588	0.15
76_N	83_S	0.585	0.15
6_L	164_R	0.583	0.15
112_I	153_I	0.582	0.15
153_I	156_P	0.578	0.14
143_A	162_L	0.576	0.14
31_K	66_T	0.575	0.14
86_L	138_A	0.573	0.14
32_P	38_M	0.571	0.14
49_V	156_P	0.571	0.14
83_S	147_N	0.566	0.14
84_A	87_F	0.566	0.14
12_F	155_Y	0.566	0.14
22_I	153_I	0.563	0.14
77_I	99_K	0.561	0.14
57_I	82_V	0.561	0.14
91_F	98_R	0.560	0.14
27_L	44_L	0.559	0.14
117_V	124_L	0.554	0.14
126_V	143_A	0.551	0.14
14_A	42_G	0.548	0.14
25_P	31_K	0.547	0.14
82_V	92_L	0.544	0.14
71_A	144_A	0.544	0.14
37_I	134_A	0.543	0.14
126_V	135_L	0.539	0.14
130_G	138_A	0.536	0.13
18_A	161_I	0.535	0.13
128_L	132_F	0.534	0.13
53_L	57_I	0.532	0.13
113_L	144_A	0.531	0.13
8_I	91_F	0.530	0.13
82_V	120_S	0.528	0.13
38_M	59_T	0.528	0.13
87_F	113_L	0.525	0.13
46_F	55_I	0.523	0.13
136_F	149_I	0.518	0.13
1_M	119_L	0.517	0.13
93_L	124_L	0.516	0.13
125_I	158_V	0.514	0.13
23_I	75_P	0.514	0.13
106_L	161_I	0.512	0.13
35_M	124_L	0.510	0.13
30_M	138_A	0.508	0.13
20_H	33_D	0.506	0.13
5_E	157_I	0.503	0.13
43_I	52_V	0.503	0.13
109_I	137_A	0.501	0.13
77_I	121_S	0.500	0.13

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
4rfsS	1	0.9244	98.9	0.823	Contact Map
3p5nA	2	0.8953	98.7	0.836	Contact Map
3rlbA	1	0.9419	98.6	0.841	Contact Map
4hzuS	1	0.9128	98.2	0.86	Contact Map
4tkrA	2	0.9244	97.8	0.872	Contact Map
4huqS	1	0.9012	97.7	0.876	Contact Map
4z7fA	2	0.9186	97.6	0.877	Contact Map
4dveA	3	0.9477	94.1	0.912	Contact Map
4czbA	2	0.8488	4.1	0.967	Contact Map
3hzqA	3	0.4419	3.7	0.968	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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