YISU - BACSU - GREMLIN Contacts

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YISU - Putative amino-acid transporter YisU

UniProt:	O06730	Sequences: MTISLMIEKKCERSFFSMNAIIHGIVLAFGLILPLGVQNVFIFQQGALQKHIWRALPAVISASVCDTLLIVLAVAGVSVIVQELPVFETVMMAGGFLFLLYMGWVTWNIRPNTSQNEKHTFTPKKQAAFAAAVSLLNPHAILDTIGVIGTSSLQYSGLEKWLFMAACIAVSWIWFISLAIAGRLFQTIDTSGRLMLIVNKCSAAVMWAAAGYFGVSLFCN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	220 (195)
Sequences:	12519 (9133)
Seq/√Len:	654.0

ECOLI - YAHN LEUE RHTC ARGO RHTB EAMB
BACSU - YISU YRHP YCGF
SULSO - Q97ZW7

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_V	127_A	5.177	1.00
103_G	207_W	3.560	1.00
104_W	108_N	3.401	1.00
197_I	200_K	2.955	1.00
89_T	92_M	2.811	1.00
100_L	210_A	2.647	1.00
124_K	128_A	2.563	1.00
57_P	123_P	2.388	1.00
196_L	200_K	2.362	1.00
68_L	131_A	2.226	1.00
107_W	200_K	2.206	1.00
93_A	97_L	2.184	1.00
101_Y	105_V	2.170	1.00
96_F	214_G	2.063	1.00
46_G	55_A	2.044	1.00
158_L	161_W	2.033	1.00
107_W	203_A	2.029	1.00
27_L	147_V	2.018	1.00
41_F	58_A	2.001	1.00
204_A	208_A	1.874	1.00
105_V	108_N	1.865	1.00
110_R	200_K	1.852	1.00
103_G	203_A	1.838	1.00
159_E	162_L	1.831	1.00
65_C	135_L	1.767	1.00
86_V	89_T	1.754	1.00
25_I	170_V	1.719	1.00
100_L	207_W	1.716	1.00
96_F	210_A	1.713	1.00
38_Q	62_A	1.688	1.00
39_N	178_L	1.683	1.00
21_I	166_A	1.665	1.00
186_Q	190_T	1.662	1.00
45_Q	49_Q	1.647	1.00
54_R	126_Q	1.605	1.00
171_S	175_F	1.576	1.00
88_E	92_M	1.567	1.00
158_L	162_L	1.557	1.00
111_P	200_K	1.533	1.00
128_A	132_A	1.511	1.00
32_I	170_V	1.498	1.00
33_L	174_W	1.448	1.00
46_G	179_A	1.439	1.00
60_I	127_A	1.438	1.00
79_V	83_E	1.437	1.00
100_L	104_W	1.430	1.00
89_T	93_A	1.421	1.00
45_Q	58_A	1.416	1.00
58_A	130_A	1.356	1.00
184_L	187_T	1.343	1.00
197_I	201_C	1.340	1.00
127_A	131_A	1.335	1.00
122_T	125_K	1.334	1.00
59_V	179_A	1.329	1.00
164_M	167_C	1.313	1.00
86_V	90_V	1.304	1.00
56_L	180_I	1.297	1.00
43_F	182_G	1.290	1.00
90_V	94_G	1.279	1.00
55_A	179_A	1.249	1.00
93_A	96_F	1.224	1.00
193_R	197_I	1.209	1.00
131_A	135_L	1.208	1.00
98_F	102_M	1.204	1.00
93_A	214_G	1.194	1.00
191_S	194_L	1.182	1.00
71_V	75_A	1.179	1.00
41_F	133_V	1.173	1.00
194_L	197_I	1.172	1.00
49_Q	54_R	1.167	1.00
161_W	165_A	1.161	1.00
165_A	168_I	1.155	1.00
24_G	28_A	1.144	1.00
125_K	128_A	1.140	1.00
174_W	178_L	1.137	1.00
207_W	211_G	1.133	1.00
160_K	163_F	1.132	1.00
45_Q	129_F	1.128	1.00
38_Q	134_S	1.107	1.00
203_A	207_W	1.103	1.00
23_H	26_V	1.097	1.00
51_H	180_I	1.087	1.00
153_L	156_S	1.080	1.00
103_G	210_A	1.078	1.00
42_I	46_G	1.077	1.00
22_I	26_V	1.071	1.00
41_F	45_Q	1.071	1.00
68_L	135_L	1.068	1.00
20_A	23_H	1.067	1.00
56_L	176_I	1.066	1.00
63_S	172_W	1.061	1.00
38_Q	133_V	1.060	1.00
108_N	111_P	1.060	1.00
66_D	140_A	1.057	1.00
61_S	127_A	1.051	1.00
32_I	171_S	1.042	1.00
23_H	27_L	1.033	1.00
164_M	168_I	1.025	1.00
159_E	163_F	1.023	1.00
109_I	199_N	1.020	1.00
42_I	175_F	1.020	1.00
177_S	181_A	1.012	1.00
200_K	204_A	1.000	1.00
65_C	131_A	0.999	1.00
208_A	212_Y	0.995	1.00
159_E	166_A	0.992	1.00
76_G	81_V	0.989	1.00
98_F	101_Y	0.987	1.00
66_D	134_S	0.985	1.00
125_K	129_F	0.977	1.00
44_Q	48_L	0.969	1.00
55_A	59_V	0.969	1.00
172_W	176_I	0.963	1.00
201_C	204_A	0.962	1.00
25_I	29_F	0.957	1.00
39_N	175_F	0.956	1.00
193_R	196_L	0.955	1.00
161_W	164_M	0.941	1.00
29_F	170_V	0.939	1.00
184_L	188_I	0.936	1.00
40_V	202_S	0.928	1.00
51_H	183_R	0.926	1.00
38_Q	66_D	0.920	1.00
76_G	83_E	0.915	1.00
42_I	179_A	0.890	1.00
69_L	135_L	0.889	1.00
66_D	69_L	0.887	1.00
38_Q	171_S	0.886	1.00
132_A	136_L	0.871	1.00
21_I	169_A	0.869	1.00
175_F	178_L	0.863	1.00
121_F	125_K	0.863	1.00
47_A	182_G	0.860	1.00
162_L	166_A	0.859	1.00
106_T	203_A	0.859	1.00
211_G	215_V	0.851	1.00
69_L	141_I	0.847	1.00
40_V	44_Q	0.835	1.00
81_V	84_L	0.832	1.00
56_L	179_A	0.825	1.00
105_V	109_I	0.815	1.00
120_T	124_K	0.811	1.00
27_L	30_G	0.807	1.00
28_A	32_I	0.805	1.00
61_S	131_A	0.803	1.00
146_G	150_T	0.795	1.00
195_M	199_N	0.795	1.00
97_L	100_L	0.795	1.00
64_V	131_A	0.793	1.00
160_K	164_M	0.787	1.00
190_T	194_L	0.787	1.00
176_I	180_I	0.786	1.00
96_F	100_L	0.785	1.00
126_Q	129_F	0.785	1.00
181_A	184_L	0.783	1.00
87_F	90_V	0.773	1.00
26_V	30_G	0.771	1.00
185_F	189_D	0.765	1.00
46_G	182_G	0.764	1.00
62_A	66_D	0.760	1.00
207_W	210_A	0.759	1.00
21_I	25_I	0.758	1.00
51_H	179_A	0.757	1.00
78_S	82_Q	0.753	1.00
104_W	207_W	0.753	1.00
39_N	43_F	0.750	1.00
54_R	57_P	0.749	1.00
51_H	176_I	0.748	1.00
188_I	194_L	0.745	1.00
30_G	34_P	0.739	1.00
94_G	97_L	0.738	1.00
107_W	207_W	0.737	1.00
188_I	191_S	0.734	1.00
59_V	63_S	0.733	1.00
59_V	176_I	0.728	1.00
57_P	126_Q	0.727	1.00
70_I	144_T	0.727	1.00
38_Q	175_F	0.726	1.00
67_T	168_I	0.725	1.00
75_A	79_V	0.724	1.00
63_S	168_I	0.719	1.00
84_L	88_E	0.718	1.00
101_Y	104_W	0.717	1.00
63_S	171_S	0.710	1.00
108_N	112_N	0.710	1.00
49_Q	126_Q	0.710	1.00
25_I	166_A	0.709	1.00
56_L	59_V	0.704	1.00
39_N	174_W	0.703	1.00
161_W	166_A	0.702	1.00
22_I	25_I	0.700	1.00
69_L	140_A	0.700	1.00
85_P	89_T	0.700	1.00
114_S	117_E	0.699	1.00
70_I	175_F	0.698	1.00
64_V	68_L	0.697	1.00
84_L	87_F	0.694	1.00
198_V	202_S	0.683	1.00
32_I	39_N	0.683	1.00
69_L	145_I	0.683	1.00
42_I	58_A	0.683	1.00
42_I	62_A	0.682	1.00
212_Y	215_V	0.680	1.00
32_I	174_W	0.663	1.00
90_V	93_A	0.660	1.00
97_L	101_Y	0.659	1.00
182_G	185_F	0.657	1.00
69_L	73_A	0.654	1.00
136_L	145_I	0.652	1.00
32_I	175_F	0.652	1.00
62_A	134_S	0.645	1.00
111_P	196_L	0.644	1.00
58_A	126_Q	0.644	1.00
159_E	167_C	0.642	1.00
134_S	140_A	0.641	1.00
27_L	31_L	0.640	1.00
94_G	136_L	0.639	1.00
73_A	78_S	0.639	1.00
201_C	205_V	0.637	1.00
29_F	33_L	0.636	1.00
123_P	127_A	0.634	1.00
66_D	144_T	0.633	1.00
43_F	178_L	0.630	1.00
69_L	134_S	0.629	1.00
39_N	133_V	0.629	1.00
79_V	82_Q	0.624	1.00
162_L	165_A	0.624	1.00
187_T	190_T	0.623	1.00
187_T	191_S	0.616	1.00
65_C	134_S	0.615	1.00
45_Q	48_L	0.614	1.00
68_L	71_V	0.611	1.00
163_F	167_C	0.608	1.00
124_K	127_A	0.604	1.00
181_A	185_F	0.601	1.00
21_I	168_I	0.600	1.00
180_I	184_L	0.600	1.00
48_L	51_H	0.600	1.00
194_L	198_V	0.599	1.00
69_L	78_S	0.599	1.00
19_N	23_H	0.599	1.00
173_I	177_S	0.596	1.00
110_R	113_T	0.595	1.00
169_A	173_I	0.594	1.00
44_Q	199_N	0.594	1.00
34_P	39_N	0.593	1.00
66_D	171_S	0.591	1.00
143_D	147_V	0.590	1.00
35_L	139_H	0.587	1.00
54_R	122_T	0.587	1.00
54_R	123_P	0.585	1.00
144_T	171_S	0.581	1.00
160_K	167_C	0.581	1.00
32_I	66_D	0.581	1.00
38_Q	140_A	0.580	1.00
73_A	144_T	0.579	1.00
34_P	199_N	0.578	1.00
58_A	133_V	0.576	1.00
103_G	107_W	0.575	1.00
186_Q	189_D	0.574	1.00
144_T	167_C	0.571	1.00
107_W	204_A	0.570	1.00
120_T	123_P	0.569	1.00
95_G	142_L	0.562	1.00
175_F	179_A	0.562	1.00
105_V	129_F	0.555	1.00
25_I	28_A	0.551	1.00
141_I	145_I	0.550	1.00
129_F	133_V	0.548	1.00
209_A	212_Y	0.547	1.00
100_L	214_G	0.545	1.00
24_G	149_G	0.543	1.00
37_V	137_N	0.543	1.00
174_W	177_S	0.541	1.00
60_I	63_S	0.538	1.00
202_S	206_M	0.536	1.00
70_I	164_M	0.535	1.00
73_A	141_I	0.534	1.00
163_F	166_A	0.530	0.99
185_F	188_I	0.527	0.99
63_S	175_F	0.527	0.99
107_W	111_P	0.527	0.99
31_L	147_V	0.526	0.99
117_E	120_T	0.524	0.99
42_I	59_V	0.519	0.99
63_S	66_D	0.519	0.99
31_L	140_A	0.515	0.99
110_R	196_L	0.509	0.99
24_G	151_S	0.509	0.99
177_S	180_I	0.506	0.99
59_V	172_W	0.503	0.99
56_L	60_I	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
2cfqA	1	0.9182	15.6	0.938	Contact Map
4x5mA	2	0.4227	11	0.942	Contact Map
3j1zP	8	0.7909	7.2	0.946	Contact Map
4m64A	1	0.9455	7.1	0.947	Contact Map
2wdqD	2	0.1364	6.3	0.948	Contact Map
2gfpA	2	0.9	5.6	0.949	Contact Map
4xnjA	1	0.4227	4.7	0.951	Contact Map
3wdoA	1	0.4409	4.7	0.951	Contact Map
4w6vA	1	0.4545	4.6	0.951	Contact Map
3o7qA	1	0.9273	4.5	0.951	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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