YCJP - ECOLI - GREMLIN Contacts

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YCJP - Inner membrane ABC transporter permease protein YcjP

UniProt:	P77716	Sequences: MATNKRTLSRIGFYCGLALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQWTLEHYVDIFNPMIFPFVDYFRNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGILLVVPLFKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIFRITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTPDYIWGRMMAASLVTALPVVIMYALSERFIKSGLTAGGVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13913
Length:	280 (253)
Sequences:	68277 (44577)
Seq/√Len:	2802.5

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
185_Q	189_R	3.932	1.00
75_R	79_V	3.148	1.00
177_M	186_I	3.056	1.00
162_K	166_D	2.992	1.00
73_Y	232_G	2.654	1.00
72_D	75_R	2.598	1.00
35_S	59_Y	2.596	1.00
101_R	173_E	2.515	1.00
182_N	185_Q	2.514	1.00
83_V	146_I	2.503	1.00
87_V	150_V	2.484	1.00
164_Y	198_G	2.479	1.00
176_A	186_I	2.466	1.00
227_F	235_A	2.416	1.00
60_V	64_N	2.396	1.00
173_E	191_T	2.372	1.00
71_V	75_R	2.347	1.00
183_R	186_I	2.282	1.00
85_S	203_F	2.276	1.00
57_E	60_V	2.273	1.00
184_L	188_F	2.180	1.00
161_L	199_L	2.178	1.00
243_I	246_R	2.129	1.00
57_E	61_D	2.126	1.00
104_F	107_R	2.095	1.00
181_L	185_Q	2.023	1.00
185_Q	188_F	2.014	1.00
157_A	202_V	1.957	1.00
93_I	187_I	1.941	1.00
79_V	142_E	1.931	1.00
100_S	166_D	1.890	1.00
172_I	194_L	1.880	1.00
165_F	195_A	1.864	1.00
111_N	162_K	1.847	1.00
176_A	181_L	1.847	1.00
29_F	33_M	1.829	1.00
33_M	37_K	1.828	1.00
89_V	203_F	1.813	1.00
93_I	195_A	1.809	1.00
72_D	76_N	1.728	1.00
177_M	183_R	1.699	1.00
173_E	186_I	1.675	1.00
84_S	210_A	1.669	1.00
224_A	227_F	1.660	1.00
81_S	207_F	1.655	1.00
92_G	157_A	1.637	1.00
79_V	83_V	1.631	1.00
95_G	158_V	1.609	1.00
93_I	161_L	1.600	1.00
142_E	226_N	1.595	1.00
173_E	177_M	1.581	1.00
61_D	246_R	1.559	1.00
14_Y	18_A	1.524	1.00
99_L	158_V	1.521	1.00
170_D	173_E	1.517	1.00
232_G	236_L	1.494	1.00
61_D	64_N	1.481	1.00
66_M	69_P	1.478	1.00
26_F	30_V	1.424	1.00
157_A	206_C	1.419	1.00
56_L	60_V	1.417	1.00
103_R	107_R	1.399	1.00
106_G	109_T	1.395	1.00
100_S	162_K	1.391	1.00
214_Y	218_S	1.386	1.00
32_L	252_L	1.373	1.00
90_F	94_L	1.352	1.00
80_V	228_T	1.348	1.00
192_V	199_L	1.347	1.00
30_V	34_T	1.339	1.00
69_P	72_D	1.335	1.00
165_F	191_T	1.326	1.00
96_A	161_L	1.326	1.00
201_S	205_Y	1.318	1.00
88_A	206_C	1.315	1.00
263_A	267_R	1.312	1.00
55_T	58_H	1.292	1.00
161_L	202_V	1.286	1.00
214_Y	234_N	1.273	1.00
170_D	174_E	1.268	1.00
101_R	170_D	1.262	1.00
216_F	220_F	1.246	1.00
93_I	199_L	1.238	1.00
227_F	232_G	1.238	1.00
171_E	174_E	1.215	1.00
148_T	220_F	1.195	1.00
236_L	243_I	1.188	1.00
176_A	190_I	1.186	1.00
109_T	112_A	1.181	1.00
133_I	144_A	1.180	1.00
97_Y	165_F	1.178	1.00
41_E	53_Q	1.178	1.00
168_I	194_L	1.177	1.00
86_V	90_F	1.175	1.00
221_L	226_N	1.167	1.00
89_V	199_L	1.166	1.00
77_S	229_L	1.161	1.00
61_D	65_P	1.145	1.00
196_M	200_I	1.144	1.00
236_L	241_D	1.141	1.00
76_N	79_V	1.135	1.00
83_V	86_V	1.133	1.00
235_A	239_T	1.126	1.00
18_A	22_I	1.115	1.00
223_S	226_N	1.087	1.00
182_N	186_I	1.082	1.00
9_S	13_F	1.080	1.00
31_M	252_L	1.072	1.00
154_L	158_V	1.070	1.00
38_G	41_E	1.069	1.00
109_T	113_S	1.067	1.00
267_R	270_K	1.059	1.00
87_V	146_I	1.057	1.00
145_L	217_A	1.054	1.00
11_I	15_C	1.053	1.00
161_L	198_G	1.040	1.00
141_T	226_N	1.038	1.00
131_K	135_A	1.036	1.00
213_D	216_F	1.032	1.00
30_V	33_M	1.028	1.00
173_E	183_R	1.027	1.00
146_I	150_V	1.023	1.00
100_S	165_F	1.015	1.00
228_T	231_V	1.015	1.00
83_V	87_V	1.010	1.00
59_Y	252_L	1.008	1.00
84_S	88_A	1.005	1.00
160_M	202_V	0.996	1.00
94_L	98_A	0.991	1.00
194_L	197_S	0.989	1.00
11_I	14_Y	0.988	1.00
65_P	69_P	0.987	1.00
63_F	71_V	0.985	1.00
232_G	235_A	0.985	1.00
10_R	14_Y	0.981	1.00
84_S	149_M	0.979	1.00
97_Y	187_I	0.978	1.00
143_M	147_I	0.978	1.00
78_L	82_V	0.977	1.00
97_Y	183_R	0.969	1.00
181_L	186_I	0.969	1.00
186_I	189_R	0.953	1.00
142_E	146_I	0.946	1.00
217_A	228_T	0.941	1.00
129_L	220_F	0.940	1.00
86_V	203_F	0.939	1.00
39_A	43_I	0.935	1.00
213_D	217_A	0.931	1.00
227_F	231_V	0.926	1.00
107_R	166_D	0.923	1.00
13_F	17_L	0.921	1.00
232_G	250_A	0.920	1.00
79_V	143_M	0.918	1.00
138_I	143_M	0.912	1.00
84_S	146_I	0.911	1.00
35_S	39_A	0.905	1.00
96_A	100_S	0.900	1.00
264_L	268_F	0.898	1.00
237_F	247_M	0.898	1.00
218_S	231_V	0.896	1.00
82_V	86_V	0.888	1.00
164_Y	195_A	0.885	1.00
34_T	248_M	0.884	1.00
34_T	37_K	0.883	1.00
129_L	148_T	0.880	1.00
76_N	142_E	0.880	1.00
79_V	82_V	0.879	1.00
108_M	111_N	0.879	1.00
74_F	229_L	0.877	1.00
80_V	142_E	0.872	1.00
21_L	25_L	0.870	1.00
258_V	262_Y	0.869	1.00
88_A	92_G	0.862	1.00
37_K	41_E	0.860	1.00
149_M	210_A	0.856	1.00
195_A	198_G	0.856	1.00
161_L	195_A	0.851	1.00
141_T	144_A	0.846	1.00
186_I	191_T	0.845	1.00
92_G	158_V	0.844	1.00
115_Y	159_F	0.843	1.00
234_N	238_S	0.835	1.00
36_F	54_W	0.834	1.00
74_F	78_L	0.834	1.00
105_K	108_M	0.831	1.00
62_I	253_V	0.828	1.00
99_L	111_N	0.824	1.00
87_V	90_F	0.823	1.00
187_I	192_V	0.822	1.00
148_T	216_F	0.820	1.00
188_F	192_V	0.820	1.00
157_A	161_L	0.819	1.00
196_M	199_L	0.817	1.00
130_F	134_T	0.816	1.00
126_V	215_L	0.811	1.00
75_R	78_L	0.807	1.00
69_P	224_A	0.805	1.00
206_C	210_A	0.804	1.00
80_V	149_M	0.802	1.00
63_F	66_M	0.801	1.00
122_G	152_Q	0.800	1.00
96_A	158_V	0.800	1.00
40_K	43_I	0.799	1.00
98_A	104_F	0.799	1.00
70_F	250_A	0.794	1.00
236_L	250_A	0.791	1.00
181_L	189_R	0.789	1.00
58_H	245_G	0.778	1.00
183_R	187_I	0.778	1.00
260_I	264_L	0.778	1.00
265_S	268_F	0.775	1.00
236_L	246_R	0.767	1.00
31_M	248_M	0.767	1.00
140_D	223_S	0.754	1.00
34_T	38_G	0.750	1.00
73_Y	76_N	0.749	1.00
96_A	165_F	0.744	1.00
95_G	154_L	0.744	1.00
172_I	190_I	0.738	1.00
83_V	150_V	0.738	1.00
248_M	252_L	0.736	1.00
58_H	61_D	0.735	1.00
88_A	157_A	0.735	1.00
196_M	268_F	0.731	1.00
254_T	258_V	0.726	1.00
143_M	146_I	0.722	1.00
37_K	51_P	0.720	1.00
38_G	53_Q	0.720	1.00
88_A	210_A	0.718	1.00
61_D	243_I	0.716	1.00
85_S	207_F	0.712	1.00
168_I	195_A	0.711	1.00
54_W	57_E	0.709	1.00
136_L	139_Y	0.709	1.00
89_V	161_L	0.707	1.00
134_T	139_Y	0.707	1.00
229_L	254_T	0.707	1.00
20_F	24_T	0.705	1.00
187_I	191_T	0.704	1.00
12_G	15_C	0.701	1.00
122_G	215_L	0.699	1.00
26_F	29_F	0.697	1.00
81_S	85_S	0.697	1.00
199_L	202_V	0.697	1.00
175_A	179_D	0.695	1.00
36_F	55_T	0.695	1.00
125_L	151_T	0.693	1.00
99_L	162_K	0.692	1.00
60_V	63_F	0.690	1.00
92_G	161_L	0.688	1.00
153_T	206_C	0.688	1.00
126_V	219_I	0.686	1.00
175_A	178_M	0.685	1.00
15_C	18_A	0.684	1.00
246_R	250_A	0.681	1.00
264_L	267_R	0.676	1.00
71_V	74_F	0.676	1.00
170_D	177_M	0.674	1.00
73_Y	229_L	0.674	1.00
115_Y	118_Y	0.673	1.00
233_L	250_A	0.673	1.00
231_V	235_A	0.672	1.00
161_L	165_F	0.671	1.00
55_T	59_Y	0.670	1.00
213_D	228_T	0.668	1.00
66_M	72_D	0.665	1.00
88_A	153_T	0.662	1.00
31_M	251_S	0.662	1.00
144_A	148_T	0.662	1.00
153_T	209_V	0.657	1.00
191_T	194_L	0.657	1.00
259_V	263_A	0.655	1.00
77_S	230_P	0.655	1.00
17_L	21_L	0.653	1.00
98_A	102_L	0.652	1.00
99_L	110_I	0.651	1.00
131_K	134_T	0.650	1.00
85_S	89_V	0.650	1.00
199_L	203_F	0.645	1.00
12_G	16_G	0.639	1.00
21_L	24_T	0.636	1.00
22_I	26_F	0.635	1.00
50_L	53_Q	0.632	1.00
198_G	202_V	0.631	1.00
56_L	59_Y	0.631	1.00
80_V	146_I	0.631	1.00
95_G	114_F	0.628	1.00
80_V	145_L	0.623	1.00
230_P	254_T	0.622	1.00
41_E	52_Q	0.621	1.00
111_N	159_F	0.620	1.00
91_L	150_V	0.619	1.00
123_I	219_I	0.616	1.00
104_F	110_I	0.613	1.00
91_L	154_L	0.610	1.00
245_G	248_M	0.609	1.00
248_M	251_S	0.609	1.00
16_G	20_F	0.609	1.00
76_N	226_N	0.607	1.00
38_G	52_Q	0.604	1.00
25_L	29_F	0.601	1.00
145_L	221_L	0.600	1.00
106_G	110_I	0.599	1.00
88_A	150_V	0.596	1.00
244_W	247_M	0.595	1.00
244_W	248_M	0.595	1.00
188_F	191_T	0.594	1.00
62_I	250_A	0.592	1.00
81_S	210_A	0.591	1.00
129_L	132_I	0.590	1.00
160_M	198_G	0.589	1.00
215_L	218_S	0.589	1.00
69_P	232_G	0.584	1.00
209_V	212_N	0.584	1.00
260_I	263_A	0.582	1.00
112_A	116_T	0.582	1.00
105_K	109_T	0.580	1.00
145_L	149_M	0.579	1.00
263_A	266_E	0.577	1.00
203_F	206_C	0.576	1.00
144_A	220_F	0.575	1.00
186_I	190_I	0.575	1.00
35_S	249_A	0.572	1.00
10_R	13_F	0.570	1.00
200_I	203_F	0.569	1.00
53_Q	57_E	0.567	1.00
102_L	183_R	0.567	1.00
118_Y	155_P	0.567	1.00
89_V	93_I	0.566	1.00
210_A	213_D	0.566	1.00
221_L	227_F	0.564	1.00
34_T	39_A	0.560	1.00
37_K	53_Q	0.560	1.00
96_A	162_K	0.559	1.00
81_S	211_W	0.558	1.00
103_R	108_M	0.558	1.00
231_V	234_N	0.556	1.00
60_V	65_P	0.555	1.00
59_Y	249_A	0.555	1.00
118_Y	156_T	0.554	1.00
108_M	112_A	0.554	1.00
97_Y	191_T	0.552	1.00
80_V	84_S	0.552	1.00
122_G	126_V	0.549	1.00
236_L	239_T	0.548	1.00
77_S	211_W	0.548	1.00
215_L	219_I	0.547	1.00
62_I	246_R	0.545	1.00
149_M	152_Q	0.543	1.00
37_K	52_Q	0.542	1.00
149_M	213_D	0.541	1.00
14_Y	17_L	0.541	1.00
262_Y	266_E	0.539	1.00
27_P	31_M	0.535	1.00
174_E	177_M	0.535	1.00
133_I	139_Y	0.534	1.00
137_G	140_D	0.532	1.00
242_Y	245_G	0.530	1.00
95_G	98_A	0.529	1.00
246_R	249_A	0.529	1.00
66_M	71_V	0.527	1.00
103_R	106_G	0.527	1.00
103_R	170_D	0.524	1.00
182_N	188_F	0.522	1.00
126_V	130_F	0.521	1.00
111_N	166_D	0.521	1.00
251_S	254_T	0.520	1.00
168_I	173_E	0.519	1.00
208_M	212_N	0.519	1.00
149_M	217_A	0.513	1.00
85_S	210_A	0.512	1.00
224_A	235_A	0.512	1.00
113_S	117_V	0.511	1.00
39_A	51_P	0.511	1.00
217_A	231_V	0.507	1.00
111_N	158_V	0.507	1.00
84_S	150_V	0.505	1.00
53_Q	56_L	0.504	1.00
257_P	260_I	0.504	1.00
32_L	36_F	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
3rlfG	1	0.9607	100	0.257	Contact Map
4tquN	1	0.9464	100	0.265	Contact Map
2onkC	2	0.8643	100	0.299	Contact Map
4tquM	1	0.9107	100	0.325	Contact Map
3d31C	2	0.8464	100	0.327	Contact Map
3rlfF	1	0.9179	100	0.369	Contact Map
4ymuD	2	0.7607	99.9	0.483	Contact Map
3tuiA	2	0.7429	99.9	0.524	Contact Map
3mktA	1	0.55	9.1	0.949	Contact Map
3dh4A	3	0.7536	6.5	0.953	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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