OPUCB - BACSU - GREMLIN Contacts

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OPUCB - Glycine betaine/carnitine/choline transport system permease protein OpuCB

UniProt:	O34878	Sequences: MNQMMTFLQTNGGELLYKTGEHLYISLIAVVLGIIVAVPLGVALTRMKKGAGAVIGFVNIVQTLPSLAILAFFIPLLGVGKVPAIVALFFYSVLPILRNTYTGIKGVNKNLLESGKGIGMTGWEQIRLVEIPLAIPIIMAGIRTSTIYLIGWATLASFIGGGGLGDYIFIGLNLYQPEYIIGGAVPVTILAIIIDYVLAVTERKVTPKGLQGMKEVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (190)
Sequences:	93514 (56775)
Seq/√Len:	4118.9

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_E	128_L	3.353	1.00
20_G	24_Y	3.343	1.00
116_K	125_Q	3.202	1.00
101_Y	105_K	2.687	1.00
121_T	124_E	2.604	1.00
115_G	125_Q	2.525	1.00
32_L	89_F	2.480	1.00
17_Y	20_G	2.397	1.00
122_G	125_Q	2.352	1.00
103_G	137_I	2.251	1.00
112_L	130_E	2.251	1.00
123_W	127_R	2.250	1.00
28_I	85_I	2.197	1.00
16_L	20_G	2.149	1.00
176_Q	179_Y	2.089	1.00
46_R	112_L	2.026	1.00
162_G	170_I	1.987	1.00
112_L	125_Q	1.982	1.00
45_T	105_K	1.962	1.00
111_L	133_L	1.959	1.00
24_Y	81_K	1.942	1.00
112_L	116_K	1.929	1.00
120_M	124_E	1.923	1.00
100_T	138_I	1.895	1.00
18_K	167_Y	1.890	1.00
17_Y	21_E	1.793	1.00
24_Y	28_I	1.793	1.00
124_E	127_R	1.758	1.00
84_A	156_A	1.740	1.00
196_Y	200_V	1.733	1.00
115_G	120_M	1.726	1.00
104_I	134_A	1.710	1.00
116_K	122_G	1.682	1.00
40_L	97_L	1.678	1.00
30_V	142_I	1.671	1.00
35_I	39_P	1.562	1.00
96_I	145_S	1.542	1.00
44_L	97_L	1.536	1.00
38_V	100_T	1.517	1.00
21_E	24_Y	1.501	1.00
162_G	167_Y	1.494	1.00
14_E	17_Y	1.494	1.00
109_K	112_L	1.476	1.00
143_R	198_L	1.455	1.00
55_I	101_Y	1.444	1.00
96_I	141_G	1.443	1.00
166_D	170_I	1.442	1.00
37_A	96_I	1.429	1.00
41_G	100_T	1.427	1.00
167_Y	170_I	1.426	1.00
26_S	146_T	1.395	1.00
38_V	134_A	1.391	1.00
45_T	104_I	1.383	1.00
168_I	183_G	1.366	1.00
115_G	129_V	1.358	1.00
29_A	149_L	1.340	1.00
38_V	126_I	1.334	1.00
48_K	51_A	1.310	1.00
175_Y	178_E	1.290	1.00
50_G	53_A	1.282	1.00
64_L	69_I	1.260	1.00
121_T	125_Q	1.255	1.00
34_I	142_I	1.246	1.00
104_I	130_E	1.243	1.00
109_K	113_E	1.225	1.00
140_A	144_T	1.221	1.00
44_L	55_I	1.184	1.00
49_K	52_G	1.181	1.00
153_A	157_S	1.139	1.00
40_L	93_V	1.138	1.00
45_T	101_Y	1.125	1.00
107_V	133_L	1.115	1.00
163_G	166_D	1.115	1.00
32_L	85_I	1.111	1.00
110_N	113_E	1.108	1.00
51_A	105_K	1.107	1.00
49_K	53_A	1.100	1.00
122_G	126_I	1.095	1.00
155_L	159_I	1.091	1.00
53_A	56_G	1.087	1.00
93_V	97_L	1.082	1.00
85_I	89_F	1.082	1.00
41_G	45_T	1.075	1.00
30_V	146_T	1.055	1.00
79_V	82_V	1.049	1.00
131_I	138_I	1.046	1.00
112_L	122_G	1.045	1.00
39_P	43_A	1.044	1.00
31_V	35_I	1.044	1.00
28_I	31_V	1.020	1.00
53_A	57_F	1.014	1.00
29_A	33_G	1.012	1.00
82_V	86_V	1.009	1.00
46_R	109_K	1.007	1.00
33_G	145_S	0.999	1.00
42_V	104_I	0.997	1.00
192_I	196_Y	0.990	1.00
100_T	141_G	0.990	1.00
43_A	54_V	0.989	1.00
162_G	166_D	0.986	1.00
28_I	32_L	0.979	1.00
120_M	125_Q	0.976	1.00
196_Y	199_A	0.974	1.00
41_G	104_I	0.969	1.00
29_A	88_L	0.967	1.00
12_G	16_L	0.944	1.00
38_V	138_I	0.942	1.00
125_Q	130_E	0.940	1.00
135_I	139_M	0.939	1.00
197_V	200_V	0.924	1.00
81_K	85_I	0.916	1.00
81_K	161_G	0.915	1.00
78_G	82_V	0.910	1.00
36_V	93_V	0.904	1.00
133_L	136_P	0.904	1.00
88_L	149_L	0.899	1.00
24_Y	82_V	0.897	1.00
125_Q	128_L	0.896	1.00
166_D	169_F	0.892	1.00
162_G	165_G	0.889	1.00
161_G	165_G	0.888	1.00
36_V	89_F	0.878	1.00
80_G	161_G	0.877	1.00
33_G	92_S	0.872	1.00
16_L	19_T	0.871	1.00
84_A	88_L	0.869	1.00
165_G	168_I	0.865	1.00
73_F	87_A	0.865	1.00
87_A	159_I	0.861	1.00
25_I	81_K	0.859	1.00
51_A	55_I	0.855	1.00
193_I	197_V	0.852	1.00
66_S	91_Y	0.849	1.00
48_K	52_G	0.847	1.00
42_V	126_I	0.841	1.00
156_A	163_G	0.841	1.00
52_G	56_G	0.840	1.00
78_G	81_K	0.839	1.00
165_G	169_F	0.836	1.00
163_G	168_I	0.835	1.00
37_A	97_L	0.835	1.00
24_Y	27_L	0.831	1.00
96_I	100_T	0.830	1.00
23_L	27_L	0.828	1.00
31_V	142_I	0.825	1.00
100_T	134_A	0.819	1.00
99_N	141_G	0.810	1.00
72_F	76_L	0.807	1.00
32_L	35_I	0.804	1.00
197_V	201_T	0.802	1.00
120_M	128_L	0.797	1.00
30_V	149_L	0.797	1.00
19_T	23_L	0.789	1.00
19_T	164_L	0.786	1.00
21_E	161_G	0.785	1.00
167_Y	183_G	0.783	1.00
27_L	31_V	0.783	1.00
44_L	101_Y	0.781	1.00
20_G	23_L	0.777	1.00
82_V	85_I	0.776	1.00
171_G	174_L	0.774	1.00
80_G	83_P	0.771	1.00
152_W	155_L	0.769	1.00
33_G	96_I	0.768	1.00
28_I	89_F	0.767	1.00
29_A	89_F	0.766	1.00
126_I	130_E	0.760	1.00
134_A	137_I	0.759	1.00
52_G	55_I	0.759	1.00
137_I	141_G	0.757	1.00
22_H	150_I	0.750	1.00
58_V	97_L	0.749	1.00
36_V	39_P	0.748	1.00
77_L	83_P	0.747	1.00
22_H	164_L	0.738	1.00
163_G	167_Y	0.737	1.00
34_I	100_T	0.735	1.00
188_T	192_I	0.732	1.00
127_R	131_I	0.729	1.00
178_E	181_I	0.720	1.00
26_S	150_I	0.716	1.00
42_V	122_G	0.716	1.00
41_G	97_L	0.713	1.00
170_I	173_N	0.707	1.00
130_E	133_L	0.705	1.00
100_T	137_I	0.701	1.00
73_F	76_L	0.700	1.00
69_I	91_Y	0.699	1.00
152_W	156_A	0.699	1.00
114_S	118_I	0.698	1.00
69_I	73_F	0.694	1.00
177_P	181_I	0.690	1.00
126_I	131_I	0.688	1.00
109_K	116_K	0.688	1.00
114_S	117_G	0.688	1.00
19_T	190_L	0.686	1.00
21_E	81_K	0.683	1.00
92_S	145_S	0.680	1.00
46_R	122_G	0.680	1.00
127_R	130_E	0.678	1.00
171_G	180_I	0.675	1.00
59_N	98_R	0.673	1.00
145_S	149_L	0.671	1.00
70_L	74_I	0.670	1.00
33_G	37_A	0.669	1.00
103_G	134_A	0.669	1.00
195_D	199_A	0.666	1.00
18_K	21_E	0.665	1.00
29_A	85_I	0.665	1.00
157_S	166_D	0.665	1.00
43_A	47_M	0.663	1.00
191_A	195_D	0.660	1.00
35_I	38_V	0.660	1.00
47_M	122_G	0.660	1.00
37_A	100_T	0.657	1.00
79_V	83_P	0.655	1.00
135_I	138_I	0.651	1.00
59_N	62_Q	0.651	1.00
181_I	184_A	0.648	1.00
87_A	155_L	0.648	1.00
80_G	160_G	0.643	1.00
162_G	169_F	0.637	1.00
13_G	17_Y	0.637	1.00
44_L	54_V	0.626	1.00
111_L	129_V	0.625	1.00
154_T	157_S	0.622	1.00
111_L	114_S	0.621	1.00
153_A	169_F	0.619	1.00
179_Y	183_G	0.618	1.00
66_S	154_T	0.618	1.00
34_I	138_I	0.616	1.00
17_Y	24_Y	0.615	1.00
44_L	51_A	0.613	1.00
57_F	61_V	0.610	1.00
190_L	193_I	0.608	1.00
145_S	148_Y	0.604	1.00
47_M	51_A	0.603	1.00
74_I	78_G	0.600	1.00
26_S	30_V	0.598	1.00
73_F	159_I	0.594	1.00
70_L	154_T	0.591	1.00
25_I	88_L	0.589	1.00
25_I	84_A	0.586	1.00
30_V	34_I	0.580	1.00
107_V	134_A	0.568	1.00
138_I	142_I	0.568	1.00
31_V	34_I	0.567	1.00
148_Y	151_G	0.566	1.00
193_I	196_Y	0.566	1.00
141_G	145_S	0.566	1.00
50_G	54_V	0.565	1.00
83_P	87_A	0.562	1.00
15_L	183_G	0.561	1.00
54_V	58_V	0.561	1.00
108_N	111_L	0.560	1.00
100_T	104_I	0.560	1.00
69_I	90_F	0.557	1.00
46_R	130_E	0.556	1.00
88_L	156_A	0.555	1.00
25_I	29_A	0.555	1.00
125_Q	129_V	0.549	1.00
41_G	101_Y	0.549	1.00
14_E	18_K	0.545	1.00
113_E	116_K	0.542	1.00
64_L	68_A	0.541	1.00
103_G	141_G	0.539	1.00
37_A	41_G	0.537	1.00
14_E	167_Y	0.534	1.00
33_G	89_F	0.532	1.00
13_G	16_L	0.530	1.00
44_L	58_V	0.529	1.00
163_G	169_F	0.529	1.00
42_V	46_R	0.526	1.00
194_I	198_L	0.526	1.00
62_Q	94_L	0.523	1.00
40_L	43_A	0.521	1.00
189_I	193_I	0.521	1.00
177_P	180_I	0.520	1.00
25_I	163_G	0.519	1.00
55_I	59_N	0.516	1.00
181_I	185_V	0.510	1.00
19_T	186_P	0.508	1.00
34_I	38_V	0.507	1.00
175_Y	179_Y	0.501	1.00
33_G	149_L	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	0.244	Contact Map
3d31C	2	0.9078	100	0.256	Contact Map
4tquM	1	0.9447	100	0.294	Contact Map
3rlfF	1	0.9032	100	0.313	Contact Map
4ymuD	2	0.9447	99.9	0.35	Contact Map
3rlfG	1	0.9724	99.9	0.35	Contact Map
3tuiA	2	0.9263	99.9	0.361	Contact Map
4tquN	1	0.9217	99.9	0.39	Contact Map
3w9iA	3	0.8341	41.9	0.913	Contact Map
4mt1A	3	0.8249	37.1	0.916	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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