OPUBB - BACSU - GREMLIN Contacts

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OPUBB - Choline transport system permease protein OpuBB

UniProt:	Q45461	Sequences: MHHIVQFLQTNGGELLYKTYEHITISLIAVILGVLVAVPLGVVLTRMKKGAGTIIGIVNIIQTLPSLAILAFFIPLLGVGKVPAIVALFFYSVLPILRNTYTGIRGVNKNLLESGKGIGMTPAEQVRLVELPLAAPVIMAGIRTSTIYLIGWATLASFIGGGGLGDYIFIGLNLYQPEYIIGGAVPVTILAIVIDYVLAVAERKLTPAGMQRLKELS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (189)
Sequences:	94131 (56718)
Seq/√Len:	4125.6

ECOLI - YEHY PROW TAUC SSUC CYSW METI MODB POTC POTH POTI CYST MALF YEHW YCJP PSTC PHNE YDCV YECS YCJO PSTA UGPA POTB YDCU YNJC UGPE THIP MALG GLNP HISM HISQ YHDY GLTK ARTQ GLTJ ARTM
BACSU - OPUBB OPUCB OPUCD OPUBD OPUAB SSUC YTLD TCYL ARAP GANP YXEN METP TCYB YVGM MDXF YTEP AMYD ARTQ YESP YURN LPLB GANQ YQGH YQGI MDXG YESQ AMYC YURM ARAQ YTCP GLNP LPLC YCKA GLNM TCYM
HALSA - Q9HNI9 Q9HML6 Q9HP01 Q9HP02 Q9HPK3 Q9HMT4 Q9HR05 Q9HS11 Q9HHQ7 Q9HHQ6 Q9HS12 Q9HML7
SULSO - Q97YY3 Q97UF3 Q97UZ0 Q97ZC1 Q97UY9 Q97VC0 Q97YY2 Q97UF4 Q97ZC2 Q97ZT6 Q97ZT7 Q97Z98 Q97VY5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_Y	24_T	3.373	1.00
124_E	128_L	3.361	1.00
116_K	125_Q	3.188	1.00
101_Y	105_R	2.706	1.00
121_T	124_E	2.625	1.00
115_G	125_Q	2.513	1.00
32_L	89_F	2.474	1.00
122_P	125_Q	2.376	1.00
17_Y	20_Y	2.370	1.00
112_L	130_E	2.266	1.00
123_A	127_R	2.260	1.00
103_G	137_V	2.254	1.00
16_L	20_Y	2.160	1.00
28_I	85_I	2.122	1.00
176_Q	179_Y	2.092	1.00
46_R	112_L	2.038	1.00
112_L	125_Q	1.992	1.00
45_T	105_R	1.985	1.00
111_L	133_L	1.968	1.00
162_G	170_I	1.948	1.00
24_T	81_K	1.946	1.00
112_L	116_K	1.928	1.00
120_M	124_E	1.911	1.00
100_T	138_I	1.890	1.00
18_K	167_Y	1.798	1.00
24_T	28_I	1.797	1.00
17_Y	21_E	1.781	1.00
124_E	127_R	1.754	1.00
196_Y	200_V	1.738	1.00
104_I	134_A	1.719	1.00
84_A	156_A	1.717	1.00
116_K	122_P	1.710	1.00
115_G	120_M	1.710	1.00
30_V	142_I	1.688	1.00
40_L	97_L	1.684	1.00
44_L	97_L	1.598	1.00
35_L	39_P	1.557	1.00
162_G	167_Y	1.546	1.00
96_I	145_S	1.543	1.00
38_V	100_T	1.505	1.00
21_E	24_T	1.501	1.00
109_K	112_L	1.478	1.00
14_E	17_Y	1.457	1.00
143_R	198_L	1.445	1.00
55_I	101_Y	1.443	1.00
37_A	96_I	1.440	1.00
96_I	141_G	1.435	1.00
45_T	104_I	1.425	1.00
41_G	100_T	1.423	1.00
26_S	146_T	1.414	1.00
115_G	129_V	1.403	1.00
166_D	170_I	1.360	1.00
167_Y	170_I	1.358	1.00
29_A	149_L	1.356	1.00
38_V	134_A	1.353	1.00
48_K	51_A	1.350	1.00
38_V	126_V	1.349	1.00
50_G	53_T	1.291	1.00
168_I	183_G	1.287	1.00
104_I	130_E	1.279	1.00
64_L	69_I	1.274	1.00
121_T	125_Q	1.261	1.00
34_V	142_I	1.254	1.00
109_K	113_E	1.235	1.00
140_A	144_T	1.225	1.00
175_Y	178_E	1.222	1.00
49_K	52_G	1.199	1.00
44_L	55_I	1.185	1.00
51_A	105_R	1.173	1.00
153_A	157_S	1.159	1.00
79_V	82_V	1.154	1.00
40_L	93_V	1.153	1.00
163_G	166_D	1.140	1.00
85_I	89_F	1.138	1.00
110_N	113_E	1.121	1.00
41_G	45_T	1.119	1.00
49_K	53_T	1.116	1.00
155_L	159_I	1.107	1.00
45_T	101_Y	1.104	1.00
122_P	126_V	1.100	1.00
107_V	133_L	1.099	1.00
93_V	97_L	1.089	1.00
30_V	146_T	1.071	1.00
39_P	43_V	1.063	1.00
32_L	85_I	1.060	1.00
53_T	56_G	1.059	1.00
112_L	122_P	1.052	1.00
28_I	31_I	1.048	1.00
162_G	166_D	1.047	1.00
131_L	138_I	1.044	1.00
31_I	35_L	1.027	1.00
53_T	57_I	1.026	1.00
82_V	86_V	1.014	1.00
33_G	145_S	1.014	1.00
42_V	104_I	1.013	1.00
28_I	32_L	1.005	1.00
29_A	33_G	1.002	1.00
46_R	109_K	0.996	1.00
162_G	165_G	0.991	1.00
196_Y	199_A	0.990	1.00
41_G	104_I	0.984	1.00
100_T	141_G	0.983	1.00
192_I	196_Y	0.982	1.00
120_M	125_Q	0.982	1.00
43_V	54_I	0.968	1.00
161_G	165_G	0.967	1.00
81_K	85_I	0.957	1.00
135_A	139_M	0.947	1.00
38_V	138_I	0.947	1.00
78_G	82_V	0.941	1.00
125_Q	130_E	0.938	1.00
197_V	200_V	0.934	1.00
29_A	88_L	0.928	1.00
84_A	88_L	0.927	1.00
25_I	81_K	0.913	1.00
165_G	168_I	0.911	1.00
133_L	136_P	0.908	1.00
72_F	76_L	0.897	1.00
125_Q	128_L	0.895	1.00
80_G	161_G	0.894	1.00
193_V	197_V	0.885	1.00
36_V	93_V	0.884	1.00
88_L	149_L	0.883	1.00
36_V	89_F	0.873	1.00
33_G	92_S	0.872	1.00
24_T	82_V	0.871	1.00
73_F	87_A	0.870	1.00
37_A	97_L	0.868	1.00
80_G	83_P	0.854	1.00
48_K	52_G	0.851	1.00
16_L	19_T	0.846	1.00
51_A	55_I	0.846	1.00
52_G	56_G	0.840	1.00
23_I	27_L	0.836	1.00
78_G	81_K	0.833	1.00
81_K	161_G	0.827	1.00
24_T	27_L	0.822	1.00
42_V	126_V	0.817	1.00
100_T	134_A	0.816	1.00
152_W	155_L	0.815	1.00
166_D	169_F	0.814	1.00
99_N	141_G	0.812	1.00
30_V	149_L	0.808	1.00
197_V	201_A	0.807	1.00
44_L	101_Y	0.806	1.00
28_I	89_F	0.806	1.00
19_T	23_I	0.799	1.00
31_I	142_I	0.799	1.00
32_L	35_L	0.796	1.00
156_A	163_G	0.790	1.00
27_L	31_I	0.789	1.00
96_I	100_T	0.789	1.00
178_E	181_I	0.788	1.00
20_Y	23_I	0.788	1.00
66_S	91_Y	0.788	1.00
165_G	169_F	0.783	1.00
120_M	128_L	0.781	1.00
171_G	174_L	0.778	1.00
33_G	96_I	0.777	1.00
167_Y	183_G	0.773	1.00
87_A	159_I	0.770	1.00
134_A	137_V	0.766	1.00
126_V	130_E	0.765	1.00
82_V	85_I	0.764	1.00
163_G	167_Y	0.761	1.00
36_V	39_P	0.758	1.00
52_G	55_I	0.751	1.00
137_V	141_G	0.750	1.00
79_V	83_P	0.746	1.00
22_H	150_I	0.741	1.00
21_E	161_G	0.740	1.00
34_V	100_T	0.736	1.00
163_G	168_I	0.733	1.00
29_A	89_F	0.732	1.00
58_V	97_L	0.732	1.00
188_T	192_I	0.730	1.00
100_T	137_V	0.728	1.00
26_S	150_I	0.725	1.00
19_T	164_L	0.721	1.00
42_V	122_P	0.720	1.00
109_K	116_K	0.719	1.00
46_R	122_P	0.716	1.00
41_G	97_L	0.715	1.00
77_L	83_P	0.715	1.00
127_R	131_L	0.713	1.00
152_W	156_A	0.713	1.00
114_S	118_I	0.711	1.00
126_V	131_L	0.703	1.00
73_F	76_L	0.702	1.00
130_E	133_L	0.697	1.00
22_H	164_L	0.692	1.00
19_T	190_L	0.686	1.00
171_G	180_I	0.685	1.00
103_G	134_A	0.685	1.00
92_S	145_S	0.683	1.00
69_I	91_Y	0.682	1.00
70_L	74_I	0.677	1.00
191_A	195_D	0.675	1.00
177_P	181_I	0.674	1.00
145_S	149_L	0.671	1.00
18_K	21_E	0.669	1.00
170_I	173_N	0.668	1.00
59_N	98_R	0.667	1.00
73_F	159_I	0.667	1.00
127_R	130_E	0.665	1.00
33_G	37_A	0.664	1.00
21_E	81_K	0.660	1.00
13_G	17_Y	0.659	1.00
43_V	47_M	0.659	1.00
35_L	38_V	0.658	1.00
44_L	54_I	0.656	1.00
37_A	100_T	0.656	1.00
47_M	122_P	0.650	1.00
59_N	62_Q	0.649	1.00
181_I	184_A	0.648	1.00
114_S	117_G	0.641	1.00
111_L	129_V	0.639	1.00
69_I	73_F	0.638	1.00
135_A	138_I	0.638	1.00
195_D	199_A	0.637	1.00
47_M	51_A	0.634	1.00
154_T	157_S	0.631	1.00
111_L	114_S	0.625	1.00
29_A	85_I	0.622	1.00
83_P	87_A	0.620	1.00
87_A	155_L	0.618	1.00
17_Y	24_T	0.616	1.00
157_S	166_D	0.612	1.00
25_I	84_A	0.604	1.00
66_S	154_T	0.602	1.00
74_I	78_G	0.600	1.00
30_V	34_V	0.599	1.00
162_G	169_F	0.597	1.00
145_S	148_Y	0.592	1.00
70_L	154_T	0.591	1.00
46_R	130_E	0.590	1.00
179_Y	183_G	0.585	1.00
34_V	138_I	0.583	1.00
57_I	61_I	0.582	1.00
31_I	34_V	0.582	1.00
80_G	160_G	0.581	1.00
108_N	111_L	0.581	1.00
153_A	169_F	0.577	1.00
44_L	51_A	0.576	1.00
138_I	142_I	0.569	1.00
148_Y	151_G	0.566	1.00
26_S	30_V	0.566	1.00
107_V	134_A	0.564	1.00
141_G	145_S	0.561	1.00
113_E	116_K	0.559	1.00
25_I	88_L	0.559	1.00
88_L	156_A	0.557	1.00
50_G	54_I	0.556	1.00
25_I	29_A	0.555	1.00
42_V	46_R	0.552	1.00
190_L	193_V	0.551	1.00
33_G	89_F	0.548	1.00
15_L	183_G	0.548	1.00
41_G	101_Y	0.543	1.00
54_I	58_V	0.542	1.00
125_Q	129_V	0.542	1.00
189_I	193_V	0.540	1.00
62_Q	94_L	0.538	1.00
64_L	68_A	0.538	1.00
14_E	18_K	0.537	1.00
193_V	196_Y	0.537	1.00
100_T	104_I	0.535	1.00
33_G	149_L	0.535	1.00
21_E	25_I	0.535	1.00
44_L	58_V	0.532	1.00
14_E	167_Y	0.530	1.00
40_L	43_V	0.527	1.00
103_G	141_G	0.527	1.00
13_G	16_L	0.521	1.00
190_L	194_I	0.515	1.00
177_P	180_I	0.514	1.00
55_I	59_N	0.514	1.00
69_I	90_F	0.512	1.00
28_I	81_K	0.512	1.00
37_A	41_G	0.509	1.00
34_V	38_V	0.509	1.00
19_T	186_P	0.507	1.00
173_N	176_Q	0.503	1.00
181_I	185_V	0.500	1.00

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
2onkC	2	0.9263	100	0.246	Contact Map
3d31C	2	0.9078	100	0.254	Contact Map
4tquM	1	0.9447	100	0.293	Contact Map
3rlfF	1	0.9032	100	0.31	Contact Map
4ymuD	2	0.9493	100	0.329	Contact Map
3rlfG	1	0.9724	99.9	0.348	Contact Map
3tuiA	2	0.9263	99.9	0.356	Contact Map
4tquN	1	0.9171	99.9	0.386	Contact Map
4mt1A	3	0.8111	28	0.92	Contact Map
3ne5A	3	0.8664	27.7	0.92	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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