YDBJ - BACSU - GREMLIN Contacts

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YDBJ - Uncharacterized ABC transporter ATP-binding protein YdbJ

UniProt:	P96605	Sequences: MAEPILHIEGLDKKIGSKQILKQISMDVMEGEIIGLLGPNGSGKTTLIRIIVGLLKQNSGSVTISGFQHDTEFEKAMEAVGAIVENPEFYPYLTGWENLKHFANMHKKIADERLDEVVERVGLTSAIHDKVKTYSLGMRQRLGIAQAILHRPKLLILDEPTNGLDPAGMKDFRDHIKELAEMEGTAVLFATHLLREVEDLCDRVIIIQKGEIKAEVSLQGTDQTTEKAIIEVQPQEKALNWLTGNQYQAESQDGTIVVEVAKENIPELNRSLVGQDLNVFSITPYTQSLEDEFIKATTAHQEEGEELV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (240)
Sequences:	74743 (45535)
Seq/√Len:	2939.3

ECOLI - YADG PROV FBPC METN CYSA MALK POTG YCJV UGPC POTA YDCT MACB MODC YEHX DDPD SAPD ARAG DPPF RBSA OPPF DPPD OPPD UUP YHES SAPF HISP DDPF FEPC YTFR GSIA MLAF TAUB MDLA MDLB LSRA YECC FECE PHNC YPHE FHUC PHNK LIVG SSUB CYDC LIVF MSBA NIKE YOJI LPTB GLNQ ALSA YHDZ GLTL CYDD ZNUC LOLD XYLG ARTP MODF SUFC PSTB FTSE ETTA MGLA THIQ BTUD FETA NIKD YBBA CCMA PHNL YNJD YDDA YBHF YEJF YBIT YHIH
BACSU - YDBJ YHCH YCBN YFIL YVRA YVFR OPUCA OPUBA OPUAA YXLF YHAQ YURJ METN MSMX TAGH YTRB YKFD OPPF OPPD APPD DPPD YUSV APPF YFMM RBSA ECFA1 YKPA YFMR FHUC YFMF SUFC YDIF TCYN YHEH ECSA YCLP YFIC YLMA SUNT BMRA SKFE YKNV BCEA YGAD YWJA NATA YXEO YHEI YKNU YFIB YTLC YKOD YXDL CYDD SSUB ECFA2 GLNQ TCYC ALBC YVCR ARTM YJKB FTSE PSTB1 YTHP CYDC MNTB YVRO YYBJ PSTB2 YHCG YKNY ZNUC YUFO YCLH EXPZ YYDI YTRE
HALSA - Q9HMU8 BTUDA Q9HRJ6 Q9HMX3 Q9HMW0 Q9HHQ5 Q9HR06 Q9HNZ9 Q9HMT3 Q9HMX2 Q9HRH8 Q9HMG1 PSTB2 Q9HNY3 Q9HHM2 Q9HSQ7 Q9HMG6 PHNC Q9HRZ9 Y1631 Y2317 Q9HRV7 PSTB1 Q9HHR7 Q9HS04 Q9HR96 Q9HQA8 Q9HT03 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q7LX64 Q97UF2 Q97UY8 Q97YY4 Q97VH6 Q97X18 Q97YK2 Q97ZC0 Q97VC1 Q97YQ7 Q97UH3 Q97VK9 Q97VK8 Q97VF5 Q97YP7 Q97UD4 Q97YP8 Q97YP3 Q97UJ9 Q97VF4 Q7LY07 Q97Z03 Q97U54 Q97UH4 Y2030 Q97V00 Y1893 Q980W0 PSTB Q97V01 Q97W42 Q97VM2 Q7LXM4 Q97VY4 Q7LX80 Q97Z56 Q97UG5 Q97Z96 Q97YP4 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_E	203_R	3.696	1.00
34_I	205_I	3.109	1.00
19_Q	22_K	3.054	1.00
79_A	153_K	3.036	1.00
7_H	27_D	2.980	1.00
126_A	129_D	2.893	1.00
10_G	23_Q	2.807	1.00
9_E	61_S	2.719	1.00
14_K	19_Q	2.702	1.00
35_G	201_C	2.624	1.00
203_R	215_E	2.538	1.00
13_K	50_I	2.498	1.00
29_M	32_E	2.454	1.00
7_H	63_T	2.445	1.00
61_S	68_Q	2.395	1.00
12_D	59_S	2.337	1.00
217_S	220_G	2.280	1.00
65_S	153_K	2.277	1.00
12_D	19_Q	2.217	1.00
216_V	220_G	2.207	1.00
205_I	212_I	2.154	1.00
22_K	211_E	2.113	1.00
120_R	183_E	2.091	1.00
12_D	23_Q	2.020	1.00
8_I	11_L	2.003	1.00
9_E	63_T	1.977	1.00
205_I	215_E	1.913	1.00
30_E	153_K	1.909	1.00
115_D	127_I	1.906	1.00
113_R	151_R	1.868	1.00
96_W	127_I	1.850	1.00
95_G	134_Y	1.796	1.00
15_I	46_T	1.769	1.00
113_R	116_E	1.754	1.00
48_I	190_A	1.728	1.00
129_D	133_T	1.714	1.00
116_E	120_R	1.696	1.00
15_I	20_I	1.678	1.00
48_I	156_I	1.678	1.00
198_E	219_Q	1.636	1.00
65_S	79_A	1.593	1.00
96_W	128_H	1.572	1.00
151_R	185_T	1.562	1.00
177_K	199_D	1.558	1.00
13_K	55_L	1.523	1.00
111_D	115_D	1.520	1.00
96_W	100_K	1.511	1.00
191_T	197_V	1.503	1.00
13_K	58_N	1.485	1.00
119_E	124_T	1.482	1.00
100_K	110_A	1.467	1.00
216_V	221_T	1.466	1.00
12_D	22_K	1.448	1.00
10_G	25_S	1.436	1.00
72_E	75_K	1.436	1.00
68_Q	71_T	1.435	1.00
118_V	127_I	1.426	1.00
8_I	26_M	1.408	1.00
11_L	57_Q	1.398	1.00
117_V	149_L	1.396	1.00
26_M	205_I	1.395	1.00
94_T	97_E	1.381	1.00
99_L	118_V	1.367	1.00
34_I	215_E	1.366	1.00
93_L	97_E	1.356	1.00
151_R	183_E	1.354	1.00
67_F	72_E	1.347	1.00
35_G	197_V	1.344	1.00
220_G	224_T	1.327	1.00
32_E	202_D	1.314	1.00
14_K	58_N	1.299	1.00
100_K	114_L	1.277	1.00
24_I	47_L	1.261	1.00
73_F	77_M	1.250	1.00
157_L	187_V	1.250	1.00
33_I	180_A	1.244	1.00
104_N	110_A	1.243	1.00
29_M	203_R	1.241	1.00
26_M	47_L	1.226	1.00
28_V	34_I	1.210	1.00
96_W	111_D	1.198	1.00
8_I	51_I	1.184	1.00
63_T	68_Q	1.178	1.00
9_E	27_D	1.163	1.00
112_E	116_E	1.157	1.00
126_A	134_Y	1.157	1.00
117_V	145_A	1.157	1.00
115_D	119_E	1.155	1.00
100_K	111_D	1.149	1.00
5_I	65_S	1.149	1.00
52_V	82_A	1.139	1.00
173_R	196_E	1.136	1.00
53_G	73_F	1.123	1.00
117_V	121_V	1.122	1.00
94_T	128_H	1.121	1.00
34_I	203_R	1.118	1.00
50_I	57_Q	1.116	1.00
208_Q	213_K	1.095	1.00
36_L	188_L	1.092	1.00
109_I	112_E	1.092	1.00
177_K	180_A	1.090	1.00
98_N	146_Q	1.090	1.00
53_G	56_K	1.086	1.00
122_G	171_D	1.072	1.00
49_R	55_L	1.069	1.00
30_E	65_S	1.066	1.00
120_R	178_E	1.065	1.00
36_L	47_L	1.051	1.00
180_A	187_V	1.039	1.00
33_I	187_V	1.039	1.00
9_E	25_S	1.038	1.00
21_L	50_I	1.034	1.00
85_E	136_L	1.029	1.00
219_Q	223_Q	1.028	1.00
113_R	117_V	1.026	1.00
33_I	201_C	1.010	1.00
96_W	114_L	1.007	1.00
100_K	104_N	1.001	1.00
170_K	174_D	0.996	1.00
180_A	202_D	0.985	1.00
83_I	157_L	0.980	1.00
164_L	172_F	0.977	1.00
92_Y	132_K	0.977	1.00
220_G	223_Q	0.974	1.00
176_I	187_V	0.974	1.00
116_E	119_E	0.958	1.00
227_K	230_I	0.957	1.00
103_A	149_L	0.954	1.00
55_L	58_N	0.953	1.00
121_V	145_A	0.952	1.00
204_V	218_L	0.951	1.00
225_T	229_I	0.950	1.00
96_W	115_D	0.949	1.00
169_M	196_E	0.949	1.00
131_V	142_L	0.949	1.00
109_I	113_R	0.948	1.00
155_L	185_T	0.947	1.00
175_H	178_E	0.944	1.00
134_Y	142_L	0.943	1.00
10_G	59_S	0.942	1.00
115_D	123_L	0.938	1.00
157_L	176_I	0.926	1.00
103_A	110_A	0.925	1.00
107_K	110_A	0.921	1.00
106_H	150_H	0.918	1.00
93_L	98_N	0.915	1.00
169_M	193_L	0.913	1.00
111_D	127_I	0.911	1.00
8_I	47_L	0.911	1.00
94_T	130_K	0.909	1.00
228_A	231_E	0.908	1.00
47_L	207_I	0.908	1.00
99_L	149_L	0.906	1.00
14_K	17_S	0.900	1.00
212_I	215_E	0.898	1.00
95_G	142_L	0.894	1.00
49_R	54_L	0.892	1.00
130_K	133_T	0.890	1.00
231_E	235_Q	0.886	1.00
110_A	114_L	0.884	1.00
97_E	100_K	0.883	1.00
108_K	112_E	0.882	1.00
81_G	152_P	0.882	1.00
122_G	178_E	0.878	1.00
75_K	78_E	0.876	1.00
67_F	79_A	0.874	1.00
155_L	187_V	0.866	1.00
94_T	98_N	0.862	1.00
30_E	184_G	0.861	1.00
230_I	234_P	0.856	1.00
33_I	177_K	0.856	1.00
117_V	120_R	0.853	1.00
173_R	199_D	0.852	1.00
83_I	144_I	0.852	1.00
81_G	147_A	0.849	1.00
177_K	181_E	0.846	1.00
52_V	156_I	0.842	1.00
126_A	138_M	0.842	1.00
230_I	233_Q	0.840	1.00
6_L	51_I	0.836	1.00
208_Q	232_V	0.833	1.00
159_E	192_H	0.831	1.00
11_L	50_I	0.813	1.00
174_D	177_K	0.813	1.00
36_L	205_I	0.808	1.00
14_K	22_K	0.807	1.00
67_F	75_K	0.805	1.00
83_I	147_A	0.804	1.00
8_I	62_V	0.797	1.00
50_I	55_L	0.797	1.00
93_L	101_H	0.796	1.00
177_K	200_L	0.795	1.00
102_F	146_Q	0.793	1.00
39_P	208_Q	0.792	1.00
104_N	107_K	0.790	1.00
98_N	131_V	0.789	1.00
33_I	189_F	0.788	1.00
134_Y	138_M	0.787	1.00
124_T	127_I	0.787	1.00
107_K	111_D	0.784	1.00
110_A	113_R	0.783	1.00
92_Y	97_E	0.783	1.00
76_A	80_V	0.783	1.00
13_K	46_T	0.781	1.00
198_E	222_D	0.780	1.00
218_L	222_D	0.779	1.00
51_I	188_L	0.778	1.00
28_V	186_A	0.778	1.00
23_Q	59_S	0.774	1.00
37_L	197_V	0.766	1.00
89_F	139_R	0.766	1.00
42_S	207_I	0.765	1.00
239_L	242_L	0.761	1.00
57_Q	70_D	0.759	1.00
99_L	114_L	0.751	1.00
24_I	212_I	0.748	1.00
33_I	200_L	0.748	1.00
29_M	186_A	0.746	1.00
153_K	185_T	0.744	1.00
241_W	244_G	0.742	1.00
213_K	227_K	0.741	1.00
111_D	114_L	0.740	1.00
156_I	188_L	0.737	1.00
198_E	218_L	0.727	1.00
21_L	47_L	0.721	1.00
228_A	232_V	0.720	1.00
28_V	154_L	0.720	1.00
50_I	62_V	0.718	1.00
23_Q	211_E	0.713	1.00
161_T	172_F	0.712	1.00
189_F	201_C	0.712	1.00
201_C	204_V	0.712	1.00
214_A	224_T	0.712	1.00
179_L	185_T	0.711	1.00
21_L	24_I	0.701	1.00
232_V	235_Q	0.699	1.00
203_R	214_A	0.696	1.00
118_V	123_L	0.696	1.00
229_I	233_Q	0.695	1.00
171_D	174_D	0.692	1.00
37_L	206_I	0.692	1.00
208_Q	211_E	0.691	1.00
15_I	55_L	0.686	1.00
180_A	183_E	0.685	1.00
34_I	188_L	0.683	1.00
117_V	148_I	0.681	1.00
206_I	221_T	0.679	1.00
13_K	21_L	0.677	1.00
225_T	228_A	0.676	1.00
20_I	46_T	0.670	1.00
10_G	13_K	0.669	1.00
112_E	115_D	0.669	1.00
231_E	234_P	0.666	1.00
75_K	79_A	0.666	1.00
90_Y	93_L	0.663	1.00
6_L	154_L	0.660	1.00
218_L	228_A	0.660	1.00
6_L	64_I	0.655	1.00
61_S	70_D	0.653	1.00
189_F	200_L	0.649	1.00
196_E	200_L	0.647	1.00
65_S	154_L	0.643	1.00
5_I	30_E	0.641	1.00
14_K	20_I	0.640	1.00
80_V	154_L	0.637	1.00
191_T	196_E	0.635	1.00
114_L	117_V	0.631	1.00
14_K	59_S	0.631	1.00
102_F	105_M	0.628	1.00
50_I	58_N	0.627	1.00
232_V	236_E	0.626	1.00
19_Q	23_Q	0.622	1.00
27_D	215_E	0.621	1.00
56_K	70_D	0.620	1.00
174_D	199_D	0.619	1.00
218_L	221_T	0.618	1.00
81_G	150_H	0.617	1.00
161_T	196_E	0.614	1.00
102_F	150_H	0.609	1.00
222_D	225_T	0.609	1.00
101_H	105_M	0.608	1.00
154_L	188_L	0.606	1.00
33_I	202_D	0.605	1.00
154_L	186_A	0.604	1.00
135_S	138_M	0.600	1.00
116_E	151_R	0.599	1.00
174_D	178_E	0.599	1.00
87_P	143_G	0.598	1.00
54_L	84_V	0.597	1.00
28_V	188_L	0.597	1.00
103_A	113_R	0.596	1.00
194_L	222_D	0.596	1.00
64_I	76_A	0.595	1.00
91_P	132_K	0.595	1.00
45_T	49_R	0.591	1.00
201_C	218_L	0.590	1.00
5_I	29_M	0.589	1.00
51_I	62_V	0.587	1.00
63_T	66_G	0.587	1.00
206_I	225_T	0.586	1.00
221_T	225_T	0.583	1.00
144_I	172_F	0.580	1.00
49_R	82_A	0.577	1.00
37_L	194_L	0.577	1.00
5_I	154_L	0.576	1.00
5_I	64_I	0.573	1.00
64_I	79_A	0.567	1.00
125_S	129_D	0.566	1.00
111_D	128_H	0.566	1.00
52_V	80_V	0.566	1.00
221_T	230_I	0.564	1.00
67_F	76_A	0.557	1.00
83_I	143_G	0.556	1.00
197_V	204_V	0.555	1.00
168_G	171_D	0.554	1.00
209_K	232_V	0.551	1.00
102_F	106_H	0.548	1.00
213_K	228_A	0.548	1.00
195_R	199_D	0.548	1.00
89_F	98_N	0.547	1.00
61_S	71_T	0.546	1.00
136_L	141_R	0.545	1.00
91_P	139_R	0.544	1.00
114_L	127_I	0.542	1.00
203_R	217_S	0.542	1.00
5_I	186_A	0.541	1.00
240_N	243_T	0.539	1.00
236_E	239_L	0.537	1.00
76_A	79_A	0.537	1.00
236_E	240_N	0.535	1.00
214_A	221_T	0.534	1.00
89_F	131_V	0.534	1.00
14_K	18_K	0.533	1.00
129_D	134_Y	0.531	1.00
51_I	156_I	0.530	1.00
73_F	76_A	0.529	1.00
90_Y	98_N	0.529	1.00
180_A	184_G	0.528	1.00
112_E	119_E	0.527	1.00
64_I	154_L	0.526	1.00
30_E	186_A	0.525	1.00
214_A	225_T	0.525	1.00
101_H	104_N	0.523	1.00
242_L	245_N	0.523	1.00
131_V	139_R	0.520	1.00
128_H	131_V	0.518	1.00
197_V	201_C	0.517	1.00
127_I	130_K	0.516	1.00
140_Q	163_G	0.516	1.00
123_L	126_A	0.515	1.00
69_H	76_A	0.515	1.00
18_K	209_K	0.511	1.00
95_G	99_L	0.510	1.00
11_L	62_V	0.508	1.00
31_G	186_A	0.506	1.00
53_G	70_D	0.506	1.00
239_L	243_T	0.504	1.00
224_T	228_A	0.501	1.00
220_G	226_E	0.501	1.00
40_N	168_G	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	0.9123	100	0.134	Contact Map
3tuiC	2	0.9903	100	0.178	Contact Map
4u00A	1	0.763	100	0.2	Contact Map
1b0uA	2	0.776	100	0.2	Contact Map
2oljA	2	0.763	100	0.203	Contact Map
4mkiB	2	0.8669	100	0.203	Contact Map
4rvcA	4	0.7695	100	0.203	Contact Map
4ymuJ	2	0.7565	100	0.208	Contact Map
1v43A	2	0.9513	100	0.208	Contact Map
1g291	4	0.9058	100	0.21	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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