YADG - ECOLI - GREMLIN Contacts

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YADG - Uncharacterized ABC transporter ATP-binding protein YadG

UniProt:	P36879	Sequences: MTIALELQQLKKTYPGGVQALRGIDLQVEAGDFYALLGPNGAGKSTTIGIISSLVNKTSGRVSVFGYDLEKDVVNAKRQLGLVPQEFNFNPFETVQQIVVNQAGYYGVERKEAYIRSEKYLKQLDLWGKRNERARMLSGGMKRRLMIARALMHEPKLLILDEPTAGVDIELRRSMWGFLKDLNDKGTTIILTTHYLEEAEMLCRNIGIIQHGELVENTSMKALLAKLKSETFILDLAPKSPLPKLDGYQYRLVDTATLEVEVLREQGINSVFTQLSEQGIQVLSMRNKANRLEELFVSLVNEKQGDRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12320
Length:	308 (236)
Sequences:	92042 (54519)
Seq/√Len:	3548.9

ECOLI - YADG METN PROV YDCT UGPC FBPC YCJV MALK POTG POTA CYSA MACB RBSA YEHX ARAG DPPF OPPD SAPD MODC DPPD DDPD OPPF DDPF PHNC MLAF TAUB FEPC SAPF YTFR HISP NIKE FHUC GSIA FECE YECC YHES UUP XYLG LSRA GLNQ MDLB SSUB YHDZ LPTB ZNUC YPHE GLTL CYDC MDLA MSBA FTSE CYDD PHNK YOJI ARTP LIVF THIQ LIVG ALSA SUFC MODF MGLA PSTB NIKD BTUD LOLD YBBA ETTA FETA PHNL CCMA YBHF YDDA YNJD YEJF YBIT YHIH
BACSU - YFIL YHCH YCBN OPUBA YVRA YDBJ OPUCA YHAQ YVFR YXLF METN OPUAA TAGH MSMX YURJ APPD DPPD YKFD OPPD APPF YTRB YFMM RBSA ECFA1 YKPA OPPF YUSV YFMF TCYN YXDL FHUC ECSA YFMR YLMA YCLP YDIF ECFA2 YTHP NATA SUFC SKFE YFIC YXEO BCEA GLNQ FTSE YHEH TCYC YVCR YKNV YFIB YTLC YWJA SUNT ARTM YGAD CYDD SSUB YUFO BMRA YKNU YKOD ALBC MNTB YVRO PSTB1 YJKB YHEI PSTB2 YKNY CYDC ZNUC YYBJ YCLH YHCG EXPZ YTRE YYDI
HALSA - Q9HRJ6 Q9HMU8 BTUDA Q9HMX3 Q9HMW0 Q9HHQ5 Q9HNZ9 Q9HR06 Q9HRH8 Q9HMT3 Q9HMX2 Q9HMG1 Q9HHM2 Q9HMG6 PHNC PSTB2 Q9HSQ7 Q9HNY3 Q9HRZ9 Y2317 Y1631 Q9HRV7 PSTB1 Q9HHR7 Q9HS04 Q9HR96 Q9HR21 Q9HQA8 Q9HT03 Q9HMC1 Q9HMW1
SULSO - Q7LX64 Q97UF2 Q97VH6 Q97YY4 Q97UY8 Q97YK2 Q97X18 Q97ZC0 Q97VC1 Q97VK8 Q97UH3 Q97YQ7 Q97VF5 Q97YP3 Q97YP8 Q97VK9 Q97YP7 Q97UD4 Q97VF4 Q97UJ9 Q97U54 Q97Z03 Q97UH4 Q7LY07 Q97W42 Y2030 PSTB Q980W0 Y1893 Q97V00 Q97V01 Q97VY4 Q7LXM4 Q97VM2 Q7LX80 Q97Z56 Q97UG5 Q97YP4 Q97Z96 Q97UC2 Q97ZU0 Q980K5 Q980E6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_D	205_N	3.577	1.00
19_Q	22_R	3.056	1.00
79_Q	156_K	3.019	1.00
6_E	27_Q	2.994	1.00
34_Y	207_G	2.955	1.00
205_N	217_N	2.861	1.00
9_Q	23_G	2.790	1.00
8_Q	61_R	2.779	1.00
13_T	19_Q	2.705	1.00
29_E	32_D	2.583	1.00
35_A	203_C	2.569	1.00
61_R	68_D	2.539	1.00
6_E	63_S	2.513	1.00
11_K	59_S	2.430	1.00
129_K	132_E	2.314	1.00
11_K	19_Q	2.303	1.00
219_S	222_A	2.298	1.00
12_K	50_I	2.245	1.00
218_T	222_A	2.208	1.00
8_Q	63_S	2.197	1.00
22_R	213_E	2.184	1.00
65_F	156_K	2.125	1.00
11_K	23_G	2.089	1.00
207_G	214_L	2.057	1.00
207_G	217_N	2.031	1.00
109_E	112_E	1.933	1.00
7_L	10_L	1.904	1.00
118_E	130_R	1.847	1.00
118_E	126_L	1.832	1.00
30_A	156_K	1.827	1.00
72_D	75_N	1.783	1.00
96_Q	130_R	1.708	1.00
96_Q	100_V	1.708	1.00
48_I	192_T	1.684	1.00
95_V	137_L	1.667	1.00
154_E	187_T	1.642	1.00
48_I	159_I	1.639	1.00
14_Y	46_T	1.628	1.00
116_R	154_E	1.613	1.00
14_Y	20_A	1.610	1.00
180_K	201_M	1.610	1.00
132_E	136_M	1.598	1.00
181_D	185_K	1.581	1.00
200_E	221_K	1.578	1.00
118_E	122_K	1.563	1.00
119_K	123_Q	1.562	1.00
116_R	119_K	1.536	1.00
96_Q	131_N	1.503	1.00
12_K	55_V	1.496	1.00
65_F	79_Q	1.476	1.00
9_Q	25_D	1.456	1.00
218_T	223_L	1.454	1.00
26_L	207_G	1.454	1.00
100_V	113_A	1.446	1.00
193_T	199_A	1.444	1.00
11_K	22_R	1.434	1.00
103_A	106_Y	1.422	1.00
12_K	58_T	1.421	1.00
114_Y	118_E	1.401	1.00
32_D	204_R	1.369	1.00
7_L	26_L	1.368	1.00
10_L	57_K	1.366	1.00
28_V	34_Y	1.354	1.00
13_T	58_T	1.337	1.00
4_A	65_F	1.323	1.00
227_L	231_T	1.317	1.00
121_L	130_R	1.304	1.00
123_Q	185_K	1.300	1.00
34_Y	217_N	1.291	1.00
26_L	47_T	1.269	1.00
222_A	226_K	1.264	1.00
29_E	205_N	1.263	1.00
63_S	68_D	1.260	1.00
68_D	71_K	1.258	1.00
94_T	97_Q	1.251	1.00
122_K	127_W	1.240	1.00
33_F	183_N	1.230	1.00
53_S	56_N	1.228	1.00
35_A	199_A	1.224	1.00
210_Q	215_V	1.224	1.00
7_L	51_I	1.224	1.00
34_Y	205_N	1.216	1.00
120_Y	152_M	1.205	1.00
229_S	232_F	1.204	1.00
24_I	47_T	1.203	1.00
230_E	233_I	1.153	1.00
92_F	97_Q	1.152	1.00
160_L	189_I	1.149	1.00
216_E	226_K	1.149	1.00
93_E	97_Q	1.146	1.00
231_T	235_D	1.141	1.00
100_V	117_S	1.139	1.00
99_V	121_L	1.132	1.00
8_Q	27_Q	1.120	1.00
36_L	47_T	1.118	1.00
52_S	82_L	1.115	1.00
33_F	203_C	1.104	1.00
123_Q	181_D	1.101	1.00
109_E	113_A	1.100	1.00
110_R	114_Y	1.096	1.00
100_V	114_Y	1.094	1.00
220_M	230_E	1.091	1.00
67_Y	75_N	1.085	1.00
173_R	177_G	1.075	1.00
30_A	65_F	1.068	1.00
176_W	198_E	1.061	1.00
183_N	189_I	1.058	1.00
73_V	77_K	1.057	1.00
111_K	115_I	1.051	1.00
115_I	119_K	1.051	1.00
33_F	189_I	1.041	1.00
94_T	131_N	1.039	1.00
33_F	191_L	1.036	1.00
97_Q	100_V	1.025	1.00
112_E	115_I	1.018	1.00
96_Q	114_Y	1.016	1.00
50_I	57_K	1.012	1.00
8_Q	25_D	1.011	1.00
73_V	76_A	1.007	1.00
221_K	225_A	1.000	1.00
67_Y	72_D	0.999	1.00
49_G	55_V	0.998	1.00
119_K	122_K	0.996	1.00
21_L	50_I	0.994	1.00
120_Y	148_A	0.989	1.00
98_I	149_R	0.983	1.00
206_I	220_M	0.979	1.00
178_F	181_D	0.976	1.00
7_L	47_T	0.973	1.00
167_V	175_M	0.962	1.00
222_A	225_A	0.962	1.00
47_T	209_I	0.961	1.00
116_R	120_Y	0.961	1.00
216_E	227_L	0.952	1.00
104_G	113_A	0.952	1.00
81_G	155_P	0.948	1.00
99_V	152_M	0.946	1.00
110_R	113_A	0.938	1.00
4_A	30_A	0.936	1.00
172_R	195_Y	0.934	1.00
39_P	210_Q	0.932	1.00
85_Q	139_G	0.930	1.00
180_K	183_N	0.923	1.00
117_S	120_Y	0.921	1.00
36_L	190_I	0.920	1.00
137_L	145_L	0.916	1.00
215_V	229_S	0.915	1.00
172_R	198_E	0.915	1.00
158_L	187_T	0.907	1.00
81_G	150_A	0.897	1.00
134_A	145_L	0.896	1.00
36_L	207_G	0.896	1.00
230_E	234_L	0.883	1.00
83_V	160_L	0.880	1.00
9_Q	59_S	0.871	1.00
96_Q	117_S	0.870	1.00
162_E	194_H	0.860	1.00
108_V	112_E	0.860	1.00
67_Y	79_Q	0.857	1.00
12_K	46_T	0.854	1.00
13_T	17_G	0.851	1.00
103_A	152_M	0.848	1.00
158_L	189_I	0.847	1.00
51_I	190_I	0.846	1.00
95_V	145_L	0.844	1.00
33_F	180_K	0.842	1.00
106_Y	153_H	0.841	1.00
124_L	148_A	0.838	1.00
176_W	201_M	0.835	1.00
56_N	70_E	0.832	1.00
7_L	62_V	0.832	1.00
103_A	113_A	0.827	1.00
113_A	117_S	0.826	1.00
83_V	147_I	0.824	1.00
5_L	51_I	0.823	1.00
83_V	150_A	0.820	1.00
55_V	58_T	0.818	1.00
96_Q	118_E	0.817	1.00
133_R	136_M	0.817	1.00
42_A	209_I	0.814	1.00
30_A	186_G	0.812	1.00
125_D	174_S	0.811	1.00
127_W	130_R	0.811	1.00
94_T	133_R	0.810	1.00
160_L	179_L	0.807	1.00
4_A	27_Q	0.805	1.00
103_A	107_G	0.801	1.00
177_G	180_K	0.800	1.00
216_E	228_K	0.798	1.00
13_T	22_R	0.798	1.00
120_Y	124_L	0.797	1.00
183_N	204_R	0.791	1.00
92_F	135_R	0.788	1.00
179_L	189_I	0.787	1.00
52_S	159_I	0.783	1.00
89_F	142_K	0.782	1.00
109_E	118_E	0.781	1.00
113_A	118_E	0.779	1.00
50_I	55_V	0.777	1.00
210_Q	234_L	0.776	1.00
72_D	76_A	0.776	1.00
10_L	50_I	0.770	1.00
102_Q	149_R	0.766	1.00
220_M	224_L	0.764	1.00
75_N	78_R	0.763	1.00
233_I	237_A	0.762	1.00
23_G	213_E	0.761	1.00
120_Y	123_Q	0.759	1.00
114_Y	130_R	0.757	1.00
21_L	24_I	0.753	1.00
112_E	126_L	0.750	1.00
13_T	20_A	0.750	1.00
112_E	116_R	0.750	1.00
174_S	177_G	0.750	1.00
49_G	54_L	0.749	1.00
156_K	187_T	0.748	1.00
159_I	190_I	0.744	1.00
23_G	59_S	0.744	1.00
93_E	98_I	0.740	1.00
191_L	203_C	0.733	1.00
57_K	70_E	0.732	1.00
100_V	104_G	0.731	1.00
182_L	187_T	0.727	1.00
214_L	217_N	0.727	1.00
53_S	73_V	0.725	1.00
137_L	141_M	0.724	1.00
50_I	62_V	0.724	1.00
28_V	188_T	0.723	1.00
24_I	214_L	0.722	1.00
28_V	190_I	0.722	1.00
98_I	134_A	0.720	1.00
232_F	235_D	0.715	1.00
37_L	199_A	0.712	1.00
200_E	224_L	0.705	1.00
29_E	188_T	0.705	1.00
4_A	29_E	0.699	1.00
200_E	220_M	0.699	1.00
93_E	101_N	0.699	1.00
229_S	233_I	0.697	1.00
125_D	181_D	0.695	1.00
94_T	98_I	0.693	1.00
232_F	236_L	0.688	1.00
180_K	202_L	0.682	1.00
34_Y	190_I	0.678	1.00
177_G	181_D	0.678	1.00
114_Y	117_S	0.678	1.00
216_E	223_L	0.670	1.00
33_F	202_L	0.669	1.00
75_N	79_Q	0.666	1.00
157_L	188_T	0.664	1.00
122_K	128_G	0.663	1.00
164_T	175_M	0.655	1.00
53_S	76_A	0.655	1.00
210_Q	229_S	0.653	1.00
61_R	70_E	0.649	1.00
80_L	157_L	0.649	1.00
108_V	113_A	0.649	1.00
21_L	47_T	0.641	1.00
12_K	21_L	0.641	1.00
27_Q	217_N	0.639	1.00
65_F	157_L	0.638	1.00
19_Q	23_G	0.634	1.00
70_E	73_V	0.634	1.00
115_I	118_E	0.632	1.00
5_L	64_V	0.630	1.00
37_L	196_L	0.627	1.00
208_I	223_L	0.627	1.00
96_Q	127_W	0.626	1.00
210_Q	213_E	0.624	1.00
139_G	144_R	0.623	1.00
63_S	66_G	0.622	1.00
28_V	157_L	0.622	1.00
203_C	206_I	0.621	1.00
234_L	238_P	0.621	1.00
102_Q	153_H	0.619	1.00
227_L	230_E	0.614	1.00
99_V	117_S	0.613	1.00
5_L	157_L	0.612	1.00
196_L	224_L	0.612	1.00
234_L	237_A	0.609	1.00
19_Q	59_S	0.609	1.00
20_A	46_T	0.608	1.00
9_Q	12_K	0.606	1.00
81_G	153_H	0.605	1.00
37_L	208_I	0.604	1.00
112_E	121_L	0.604	1.00
193_T	198_E	0.602	1.00
171_L	174_S	0.602	1.00
198_E	202_L	0.601	1.00
177_G	201_M	0.591	1.00
223_L	232_F	0.591	1.00
14_Y	55_V	0.587	1.00
13_T	59_S	0.584	1.00
13_T	18_V	0.582	1.00
224_L	227_L	0.580	1.00
52_S	80_L	0.576	1.00
121_L	126_L	0.574	1.00
76_A	80_L	0.570	1.00
164_T	198_E	0.568	1.00
40_N	171_L	0.566	1.00
191_L	202_L	0.563	1.00
51_I	62_V	0.561	1.00
104_G	110_R	0.561	1.00
118_E	128_G	0.557	1.00
125_D	128_G	0.550	1.00
199_A	203_C	0.550	1.00
4_A	157_L	0.549	1.00
32_D	217_N	0.549	1.00
87_F	142_K	0.547	1.00
205_N	219_S	0.545	1.00
65_F	69_L	0.544	1.00
33_F	204_R	0.544	1.00
64_V	79_Q	0.542	1.00
50_I	58_T	0.542	1.00
91_P	135_R	0.540	1.00
4_A	188_T	0.540	1.00
119_K	154_E	0.539	1.00
103_A	108_V	0.539	1.00
138_S	141_M	0.538	1.00
99_V	112_E	0.537	1.00
86_E	142_K	0.537	1.00
83_V	146_M	0.536	1.00
91_P	142_K	0.536	1.00
157_L	190_I	0.534	1.00
45_S	49_G	0.534	1.00
120_Y	151_L	0.531	1.00
197_E	201_M	0.528	1.00
203_C	220_M	0.527	1.00
227_L	232_F	0.524	1.00
4_A	64_V	0.524	1.00
226_K	229_S	0.522	1.00
222_A	228_K	0.522	1.00
18_V	211_H	0.522	1.00
231_T	234_L	0.521	1.00
147_I	175_M	0.521	1.00
108_V	116_R	0.520	1.00
40_N	162_E	0.517	1.00
208_I	227_L	0.517	1.00
87_F	146_M	0.517	1.00
129_K	141_M	0.515	1.00
233_I	236_L	0.514	1.00
199_A	220_M	0.511	1.00
31_G	188_T	0.510	1.00
227_L	235_D	0.509	1.00
151_L	187_T	0.507	1.00
215_V	230_E	0.506	1.00
154_E	185_K	0.506	1.00
51_I	159_I	0.503	1.00
6_E	25_D	0.503	1.00
216_E	231_T	0.502	1.00
22_R	211_H	0.502	1.00
64_V	157_L	0.501	1.00
30_A	188_T	0.500	1.00
90_N	98_I	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
4yerA	2	0.9058	100	0.119	Contact Map
3tuiC	2	0.9935	100	0.184	Contact Map
4u00A	1	0.7727	100	0.199	Contact Map
4rvcA	4	0.7792	100	0.204	Contact Map
2oljA	2	0.7727	100	0.204	Contact Map
4mkiB	2	0.8864	100	0.206	Contact Map
4huqB	1	0.8799	100	0.213	Contact Map
1b0uA	2	0.7857	100	0.214	Contact Map
3fvqA	2	0.987	100	0.215	Contact Map
1vplA	2	0.7727	100	0.215	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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