YCBN - BACSU - GREMLIN Contacts

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YCBN - Uncharacterized ABC transporter ATP-binding protein YcbN

UniProt:	P42246	Sequences: MTYIVQTNGLTKTYQGKEVVSNVSMHIKKGEIYGFLGPNGAGKTTIMKMLTSLVKPTSGEIIILGNKFTHTSYEVLGNIGSMIEYPIFYENLTAEENLDLHCEYMGYHNKKAIQEVLDMVNLKQIDKKPVKTFSLGMKQRLGIARAILTKPDLLILDEPVNGLDPLGIKKIRQLFQVLSKEYGMTLLISSHLLGEIEQIADTIGVIRDGRLLEEVSMEDVRGQNTEYIELVTPNQTRACFVLEKELQLTNFKILNEKTIRIYEAEASQAAISKALILNDVDIESMNKKYTSLEDYFIKLINGNSISA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	307 (240)
Sequences:	77872 (47974)
Seq/√Len:	3096.7

ECOLI - YADG PROV METN YDCT FBPC POTG MALK YCJV CYSA POTA UGPC MACB MODC YEHX OPPD RBSA SAPD DPPF OPPF ARAG DPPD DDPD DDPF UUP YHES PHNC MLAF GSIA FEPC ZNUC TAUB MDLA MDLB SAPF SSUB FECE HISP FHUC LSRA YTFR NIKE XYLG YECC YOJI GLNQ CYDC MSBA LPTB CYDD YHDZ GLTL LIVF YPHE LIVG PHNK ARTP SUFC ALSA ETTA PSTB MODF FTSE THIQ NIKD MGLA LOLD BTUD FETA YBBA CCMA PHNL YDDA YNJD YBHF YEJF YBIT YHIH
BACSU - YCBN YHCH YDBJ YFIL YVRA YXLF OPUCA YVFR OPUAA OPUBA METN YHAQ YURJ MSMX TAGH YTRB DPPD APPD YKFD OPPD APPF OPPF YFMM YKPA RBSA ECFA1 YUSV YFMR YDIF YFMF FHUC YXDL YCLP SUNT YHEH TCYN ECSA SSUB YFIC YLMA CYDD YFIB YGAD BMRA YKNV SUFC YWJA YKNU SKFE ECFA2 BCEA YXEO YTLC NATA YHEI YKOD YTHP GLNQ FTSE ARTM ALBC CYDC YVCR YJKB TCYC PSTB1 MNTB YUFO PSTB2 YVRO YHCG YYBJ YKNY ZNUC EXPZ YCLH YYDI YTRE
HALSA - Q9HRJ6 Q9HMU8 BTUDA Q9HR06 Q9HMX3 Q9HMW0 Q9HNZ9 Q9HHQ5 Q9HMT3 Q9HMX2 Q9HRH8 Q9HMG1 PHNC Q9HSQ7 Q9HHM2 PSTB2 Q9HMG6 Q9HNY3 Y1631 Q9HRZ9 Y2317 Q9HRV7 PSTB1 Q9HHR7 Q9HS04 Q9HR96 Q9HQA8 Q9HT03 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q7LX64 Q97X18 Q97YK2 Q97UF2 Q97YY4 Q97VH6 Q97UY8 Q97ZC0 Q97VK8 Q97VC1 Q97YQ7 Q97UH3 Q97YP7 Q97VF5 Q97VK9 Q97UD4 Q97YP3 Q97UJ9 Q97YP8 Q97VF4 Q97U54 Q97Z03 Q980W0 Y2030 Q7LY07 Q97UH4 Q97V00 Y1893 PSTB Q97W42 Q97V01 Q97VM2 Q7LXM4 Q7LX80 Q97VY4 Q97Z56 Q97UG5 Q97UC2 Q97Z96 Q97YP4 Q980K5 Q97ZU0 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
31_E	202_T	3.705	1.00
33_Y	204_G	3.179	1.00
78_N	152_D	3.164	1.00
18_E	21_S	3.095	1.00
6_Q	26_H	3.067	1.00
9_G	22_N	2.892	1.00
8_N	60_E	2.797	1.00
34_G	200_A	2.779	1.00
13_T	18_E	2.766	1.00
202_T	214_E	2.691	1.00
60_E	67_K	2.585	1.00
6_Q	62_I	2.538	1.00
28_K	31_E	2.526	1.00
12_K	49_M	2.436	1.00
11_T	58_S	2.387	1.00
216_S	219_D	2.350	1.00
64_L	152_D	2.330	1.00
215_V	219_D	2.323	1.00
11_T	18_E	2.301	1.00
204_G	211_L	2.207	1.00
21_S	210_R	2.198	1.00
119_M	182_Y	2.141	1.00
11_T	22_N	2.121	1.00
125_I	128_K	2.118	1.00
8_N	62_I	2.059	1.00
7_T	10_L	2.025	1.00
29_K	152_D	1.959	1.00
204_G	214_E	1.946	1.00
177_V	181_E	1.903	1.00
94_A	133_F	1.886	1.00
112_A	150_K	1.825	1.00
47_M	189_S	1.809	1.00
128_K	132_T	1.809	1.00
14_Y	19_V	1.743	1.00
115_E	119_M	1.722	1.00
14_Y	45_T	1.702	1.00
47_M	155_I	1.669	1.00
112_A	115_E	1.661	1.00
197_E	218_E	1.657	1.00
95_E	99_D	1.630	1.00
176_Q	198_Q	1.625	1.00
64_L	78_N	1.619	1.00
190_S	196_I	1.612	1.00
150_K	184_M	1.603	1.00
118_D	123_K	1.588	1.00
12_K	54_V	1.587	1.00
12_K	57_T	1.568	1.00
95_E	127_K	1.565	1.00
99_D	113_I	1.512	1.00
110_K	114_Q	1.508	1.00
215_V	220_V	1.508	1.00
9_G	24_S	1.500	1.00
123_K	126_D	1.493	1.00
11_T	21_S	1.492	1.00
67_K	70_H	1.492	1.00
13_T	57_T	1.486	1.00
178_L	184_M	1.474	1.00
119_M	181_E	1.471	1.00
25_M	204_G	1.438	1.00
114_Q	118_D	1.411	1.00
7_T	25_M	1.388	1.00
33_Y	214_E	1.370	1.00
31_E	201_D	1.368	1.00
10_L	56_P	1.361	1.00
150_K	182_Y	1.347	1.00
116_V	148_L	1.346	1.00
119_M	177_V	1.327	1.00
62_I	67_K	1.320	1.00
93_T	96_E	1.312	1.00
219_D	223_Q	1.300	1.00
23_V	46_I	1.293	1.00
27_I	33_Y	1.284	1.00
28_K	202_T	1.281	1.00
34_G	196_I	1.281	1.00
99_D	110_K	1.277	1.00
156_L	186_L	1.267	1.00
92_L	96_E	1.259	1.00
4_I	64_L	1.227	1.00
25_M	46_I	1.226	1.00
112_A	116_V	1.220	1.00
7_T	50_L	1.219	1.00
32_I	179_S	1.219	1.00
66_N	71_T	1.218	1.00
98_L	117_L	1.207	1.00
8_N	26_H	1.176	1.00
95_E	110_K	1.176	1.00
172_R	195_E	1.161	1.00
93_T	127_K	1.153	1.00
84_E	135_L	1.136	1.00
116_V	120_V	1.129	1.00
33_Y	202_T	1.128	1.00
49_M	56_P	1.117	1.00
95_E	113_I	1.117	1.00
111_K	115_E	1.116	1.00
116_V	144_A	1.113	1.00
224_N	228_I	1.113	1.00
207_R	212_L	1.112	1.00
114_Q	126_D	1.107	1.00
51_T	81_S	1.100	1.00
29_K	64_L	1.099	1.00
8_N	24_S	1.093	1.00
52_S	55_K	1.091	1.00
35_F	187_L	1.081	1.00
35_F	46_I	1.077	1.00
117_L	126_D	1.072	1.00
20_V	49_M	1.054	1.00
48_K	54_V	1.053	1.00
229_E	232_T	1.041	1.00
97_N	145_R	1.040	1.00
229_E	233_P	1.026	1.00
32_I	186_L	1.022	1.00
218_E	222_G	1.020	1.00
179_S	186_L	1.012	1.00
114_Q	122_L	1.010	1.00
226_E	230_L	1.001	1.00
82_M	156_L	0.993	1.00
105_M	149_T	0.991	1.00
96_E	99_D	0.990	1.00
174_L	177_V	0.985	1.00
176_Q	179_S	0.984	1.00
169_K	173_Q	0.983	1.00
213_E	223_Q	0.983	1.00
163_L	171_I	0.982	1.00
226_E	229_E	0.982	1.00
120_V	144_A	0.970	1.00
130_V	141_L	0.967	1.00
219_D	222_G	0.964	1.00
110_K	113_I	0.956	1.00
203_I	217_M	0.953	1.00
175_F	186_L	0.948	1.00
32_I	200_A	0.947	1.00
168_I	195_E	0.945	1.00
99_D	103_E	0.943	1.00
98_L	148_L	0.941	1.00
115_E	118_D	0.941	1.00
133_F	141_L	0.940	1.00
95_E	126_D	0.936	1.00
93_T	129_P	0.934	1.00
121_N	170_K	0.933	1.00
7_T	46_I	0.931	1.00
154_L	184_M	0.930	1.00
168_I	192_L	0.928	1.00
102_C	148_L	0.920	1.00
74_E	77_G	0.917	1.00
87_I	138_K	0.912	1.00
95_E	114_Q	0.912	1.00
156_L	175_F	0.909	1.00
9_G	58_S	0.906	1.00
80_G	146_A	0.906	1.00
225_T	228_I	0.894	1.00
29_K	183_G	0.883	1.00
228_I	232_T	0.875	1.00
91_N	131_K	0.874	1.00
48_K	53_L	0.873	1.00
38_P	207_R	0.870	1.00
80_G	151_P	0.869	1.00
7_T	61_I	0.865	1.00
172_R	198_Q	0.861	1.00
129_P	132_T	0.861	1.00
46_I	206_I	0.860	1.00
217_M	221_R	0.853	1.00
114_Q	124_Q	0.851	1.00
106_G	109_N	0.849	1.00
82_M	146_A	0.845	1.00
154_L	186_L	0.845	1.00
94_A	141_L	0.844	1.00
5_V	50_L	0.843	1.00
121_N	177_V	0.842	1.00
173_Q	176_Q	0.841	1.00
50_L	187_L	0.840	1.00
66_N	78_N	0.839	1.00
32_I	188_I	0.838	1.00
35_F	204_G	0.838	1.00
51_T	155_I	0.838	1.00
122_L	126_D	0.837	1.00
32_I	176_Q	0.831	1.00
101_H	145_R	0.830	1.00
71_T	74_E	0.830	1.00
179_S	201_D	0.829	1.00
126_D	133_F	0.827	1.00
49_M	54_V	0.826	1.00
75_V	79_I	0.826	1.00
197_E	221_R	0.825	1.00
158_E	191_H	0.822	1.00
228_I	231_V	0.817	1.00
56_P	69_T	0.810	1.00
224_N	227_Y	0.809	1.00
12_K	45_T	0.801	1.00
88_F	138_K	0.798	1.00
36_L	196_I	0.794	1.00
102_C	106_G	0.793	1.00
93_T	97_N	0.789	1.00
10_L	49_M	0.788	1.00
82_M	143_I	0.787	1.00
41_A	206_I	0.786	1.00
207_R	230_L	0.783	1.00
97_N	130_V	0.780	1.00
116_V	119_M	0.780	1.00
133_F	137_M	0.777	1.00
22_N	58_S	0.772	1.00
113_I	116_V	0.771	1.00
13_T	21_S	0.770	1.00
176_Q	199_I	0.765	1.00
170_K	173_Q	0.764	1.00
91_N	96_E	0.763	1.00
92_L	97_N	0.760	1.00
160_V	171_I	0.758	1.00
213_E	220_V	0.757	1.00
27_I	185_T	0.755	1.00
227_Y	230_L	0.754	1.00
237_R	240_F	0.752	1.00
49_M	61_I	0.751	1.00
23_V	211_L	0.750	1.00
227_Y	231_V	0.746	1.00
155_I	187_L	0.746	1.00
118_D	124_Q	0.739	1.00
20_V	23_V	0.739	1.00
28_K	185_T	0.738	1.00
121_N	124_Q	0.738	1.00
22_N	210_R	0.733	1.00
5_V	153_L	0.728	1.00
211_L	214_E	0.727	1.00
27_I	153_L	0.722	1.00
224_N	229_E	0.721	1.00
67_K	71_T	0.717	1.00
92_L	100_L	0.717	1.00
33_Y	187_L	0.715	1.00
66_N	74_E	0.713	1.00
111_K	114_Q	0.705	1.00
20_V	46_I	0.704	1.00
12_K	20_V	0.699	1.00
4_I	29_K	0.697	1.00
217_M	227_Y	0.695	1.00
102_C	109_N	0.691	1.00
13_T	19_V	0.684	1.00
152_D	184_M	0.683	1.00
205_V	220_V	0.681	1.00
32_I	199_I	0.680	1.00
98_L	113_I	0.679	1.00
197_E	217_M	0.678	1.00
116_V	147_I	0.677	1.00
64_L	153_L	0.677	1.00
200_A	203_I	0.676	1.00
173_Q	177_V	0.673	1.00
60_E	69_T	0.670	1.00
212_L	225_T	0.667	1.00
27_I	187_L	0.666	1.00
102_C	108_H	0.663	1.00
55_K	69_T	0.662	1.00
14_Y	54_V	0.661	1.00
230_L	234_N	0.659	1.00
173_Q	198_Q	0.658	1.00
117_L	122_L	0.657	1.00
79_I	153_L	0.657	1.00
19_V	45_T	0.657	1.00
36_L	205_V	0.654	1.00
188_I	200_A	0.654	1.00
122_L	125_I	0.650	1.00
105_M	108_H	0.650	1.00
153_L	185_T	0.649	1.00
207_R	210_R	0.645	1.00
9_G	12_K	0.637	1.00
86_P	142_G	0.636	1.00
195_E	199_I	0.635	1.00
193_L	221_R	0.629	1.00
190_S	195_E	0.629	1.00
188_I	199_I	0.628	1.00
5_V	63_I	0.628	1.00
62_I	65_G	0.626	1.00
26_H	214_E	0.622	1.00
49_M	57_T	0.619	1.00
13_T	16_G	0.618	1.00
102_C	105_M	0.617	1.00
18_E	22_N	0.614	1.00
13_T	58_S	0.611	1.00
74_E	78_N	0.606	1.00
90_E	131_K	0.600	1.00
239_C	242_L	0.598	1.00
36_L	193_L	0.596	1.00
200_A	217_M	0.595	1.00
102_C	107_Y	0.594	1.00
143_I	171_I	0.593	1.00
110_K	127_K	0.593	1.00
160_V	195_E	0.591	1.00
80_G	149_T	0.590	1.00
105_M	109_N	0.587	1.00
227_Y	233_P	0.585	1.00
89_Y	92_L	0.584	1.00
194_G	198_Q	0.583	1.00
63_I	78_N	0.581	1.00
118_D	121_N	0.580	1.00
118_D	126_D	0.579	1.00
135_L	140_R	0.577	1.00
213_E	224_N	0.576	1.00
235_Q	239_C	0.574	1.00
68_F	75_V	0.574	1.00
85_Y	138_K	0.573	1.00
101_H	104_Y	0.572	1.00
32_I	201_D	0.571	1.00
50_L	61_I	0.569	1.00
175_F	188_I	0.569	1.00
90_E	138_K	0.568	1.00
167_G	170_K	0.567	1.00
220_V	228_I	0.566	1.00
115_E	150_K	0.565	1.00
71_T	75_V	0.564	1.00
44_T	48_K	0.563	1.00
100_L	104_Y	0.560	1.00
4_I	63_I	0.560	1.00
235_Q	238_A	0.560	1.00
4_I	28_K	0.559	1.00
4_I	185_T	0.557	1.00
60_E	70_H	0.557	1.00
153_L	187_L	0.556	1.00
177_V	182_Y	0.554	1.00
134_S	137_M	0.554	1.00
179_S	182_Y	0.554	1.00
53_L	83_I	0.553	1.00
241_V	244_K	0.552	1.00
111_K	118_D	0.552	1.00
66_N	75_V	0.552	1.00
63_I	75_V	0.550	1.00
51_T	79_I	0.544	1.00
215_V	221_R	0.544	1.00
196_I	200_A	0.543	1.00
4_I	153_L	0.541	1.00
139_Q	162_G	0.538	1.00
230_L	233_P	0.537	1.00
240_F	243_E	0.535	1.00
213_E	228_I	0.535	1.00
12_K	15_Q	0.534	1.00
112_A	119_M	0.534	1.00
82_M	142_G	0.533	1.00
117_L	120_V	0.533	1.00
114_Q	123_K	0.532	1.00
101_H	149_T	0.532	1.00
10_L	61_I	0.530	1.00
233_P	236_T	0.529	1.00
48_K	81_S	0.529	1.00
77_G	106_G	0.525	1.00
208_D	230_L	0.522	1.00
64_L	68_F	0.519	1.00
121_N	126_D	0.519	1.00
39_N	158_E	0.517	1.00
73_Y	77_G	0.515	1.00
231_V	234_N	0.515	1.00
196_I	203_I	0.514	1.00
89_Y	97_N	0.513	1.00
101_H	105_M	0.513	1.00
39_N	167_G	0.512	1.00
83_I	86_P	0.510	1.00
218_E	221_R	0.509	1.00
127_K	130_V	0.509	1.00
225_T	229_E	0.509	1.00
52_S	69_T	0.509	1.00
202_T	216_S	0.509	1.00
192_L	195_E	0.503	1.00
130_V	138_K	0.501	1.00
11_T	57_T	0.500	1.00
172_R	199_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	0.9023	100	0.124	Contact Map
3tuiC	2	0.9935	100	0.182	Contact Map
4u00A	1	0.7622	100	0.197	Contact Map
4rvcA	4	0.772	100	0.201	Contact Map
2oljA	2	0.7622	100	0.204	Contact Map
3d31A	2	0.9772	100	0.208	Contact Map
3fvqA	2	0.9935	100	0.21	Contact Map
1v43A	2	0.9479	100	0.211	Contact Map
4mkiB	2	0.8795	100	0.212	Contact Map
2it1A	1	0.9837	100	0.212	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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