YTCP - BACSU - GREMLIN Contacts

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YTCP - Probable ABC transporter permease protein YtcP

UniProt:	P53561	Sequences: MKNRLFDMLIYGFLLMFALICVLPFIHVIAASFATVEEVVSKKFILIPTTFSLDAYRYIFSTDIIYKSLLVSVFVTVIGTAVSMFLSSLMAYGLSRRDLIGRQPLMFLVVFTMLFSGGMIPTFLVVKSLGLLDSYWALILPTAINAFNLIILKNFFQNIPSSLEESAKIDGCNDLGIFFKIVLPLSLPAIATISLFYAVTYWNTYMTAILYLNDSAKWPIQVLLRQIVIVSSGMQGDMSEMGSGSPPPEQTIKMAVIVVATIPVLLVYPFIQKHFAKGALLGSVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	286 (247)
Sequences:	66965 (44410)
Seq/√Len:	2825.8

ECOLI - YCJP UGPE MALG YDCV POTH UGPA YCJO YDCU POTB POTC POTI PSTC MALF PSTA THIP YNJC CYST CYSW MODB SSUC YEHY TAUC YEHW PHNE PROW METI
BACSU - YTCP LPLC ARAQ YESQ MDXG GANQ AMYC GANP YURM MDXF AMYD ARAP YURN YTEP YESP LPLB YQGH YQGI YVGM SSUC YTLD OPUAB METP TCYB YXEN TCYL OPUCB OPUBB OPUBD OPUCD
HALSA - Q9HML6 Q9HHQ6 Q9HP01 Q9HHQ7 Q9HP02 Q9HMT4 Q9HS11 Q9HPK3 Q9HR05 Q9HNI9 Q9HS12
SULSO - Q97UF3 Q97ZC1 Q97UY9 Q97YY3 Q97YY2 Q97UZ0 Q97VC0 Q97UF4 Q97ZT6 Q97ZT7 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
176_G	180_K	4.290	1.00
70_L	74_F	3.200	1.00
153_K	157_Q	3.103	1.00
32_S	56_Y	3.004	1.00
168_K	177_I	2.961	1.00
96_R	164_E	2.803	1.00
164_E	182_V	2.647	1.00
68_S	223_L	2.612	1.00
67_K	70_L	2.591	1.00
167_A	177_I	2.566	1.00
173_N	176_G	2.515	1.00
54_D	57_R	2.435	1.00
80_T	194_S	2.413	1.00
82_V	143_A	2.398	1.00
155_F	189_A	2.371	1.00
66_Y	70_L	2.367	1.00
57_R	61_S	2.335	1.00
152_L	190_I	2.329	1.00
54_D	58_Y	2.320	1.00
175_L	179_F	2.302	1.00
174_D	177_I	2.262	1.00
78_I	139_I	2.232	1.00
88_S	178_F	2.149	1.00
176_G	179_F	2.061	1.00
99_L	102_R	2.058	1.00
172_C	176_G	2.055	1.00
249_E	252_I	2.048	1.00
95_S	157_Q	2.047	1.00
148_N	193_I	2.039	1.00
156_F	186_S	2.016	1.00
163_L	185_L	1.952	1.00
167_A	172_C	1.848	1.00
84_M	194_S	1.845	1.00
30_A	34_A	1.836	1.00
88_S	186_S	1.828	1.00
76_T	198_A	1.788	1.00
74_F	135_Y	1.774	1.00
106_M	153_K	1.771	1.00
87_S	148_N	1.767	1.00
67_K	71_V	1.732	1.00
168_K	174_D	1.724	1.00
26_I	30_A	1.707	1.00
94_L	149_L	1.702	1.00
164_E	177_I	1.682	1.00
88_S	152_L	1.675	1.00
90_M	149_L	1.659	1.00
74_F	78_I	1.642	1.00
218_W	226_Q	1.638	1.00
79_G	201_Y	1.599	1.00
58_Y	252_I	1.530	1.00
164_E	168_K	1.526	1.00
29_I	258_V	1.511	1.00
23_L	27_H	1.510	1.00
98_D	102_R	1.475	1.00
91_A	152_L	1.462	1.00
161_S	164_E	1.429	1.00
58_Y	61_S	1.429	1.00
101_G	104_P	1.423	1.00
11_Y	15_L	1.420	1.00
192_T	196_F	1.413	1.00
183_L	190_I	1.409	1.00
95_S	153_K	1.408	1.00
148_N	197_Y	1.387	1.00
205_Y	209_I	1.377	1.00
52_S	55_A	1.370	1.00
207_T	211_Y	1.362	1.00
53_L	57_R	1.361	1.00
27_H	31_A	1.351	1.00
156_F	182_V	1.345	1.00
124_L	127_K	1.331	1.00
83_S	197_Y	1.326	1.00
152_L	193_I	1.326	1.00
123_F	127_K	1.311	1.00
161_S	165_E	1.288	1.00
139_I	143_A	1.283	1.00
167_A	181_I	1.281	1.00
85_F	89_L	1.276	1.00
96_R	161_S	1.258	1.00
141_P	211_Y	1.247	1.00
135_Y	217_K	1.209	1.00
88_S	190_I	1.203	1.00
225_R	229_I	1.196	1.00
92_Y	156_F	1.189	1.00
56_Y	258_V	1.184	1.00
159_I	185_L	1.184	1.00
264_V	268_Y	1.174	1.00
78_I	81_A	1.174	1.00
162_S	165_E	1.173	1.00
64_I	67_K	1.172	1.00
81_A	85_F	1.169	1.00
173_N	177_I	1.143	1.00
223_L	227_I	1.141	1.00
218_W	221_Q	1.139	1.00
269_P	273_K	1.129	1.00
135_Y	139_I	1.124	1.00
28_V	258_V	1.118	1.00
84_M	190_I	1.108	1.00
15_L	19_L	1.104	1.00
136_W	139_I	1.103	1.00
75_V	219_P	1.103	1.00
187_L	191_A	1.100	1.00
104_P	107_F	1.092	1.00
38_E	50_T	1.092	1.00
92_Y	178_F	1.084	1.00
226_Q	230_V	1.083	1.00
134_S	220_I	1.076	1.00
151_I	193_I	1.074	1.00
35_T	38_E	1.069	1.00
152_L	189_A	1.069	1.00
185_L	188_P	1.059	1.00
204_T	208_A	1.054	1.00
220_I	224_L	1.050	1.00
71_V	74_F	1.050	1.00
55_A	251_T	1.049	1.00
164_E	174_D	1.047	1.00
60_F	66_Y	1.044	1.00
212_L	217_K	1.038	1.00
104_P	108_L	1.036	1.00
79_G	83_S	1.020	1.00
78_I	82_V	1.007	1.00
221_Q	229_I	0.999	1.00
95_S	156_F	0.997	1.00
89_L	93_G	0.983	1.00
92_Y	174_D	0.981	1.00
58_Y	62_T	0.979	1.00
73_V	77_V	0.975	1.00
32_S	36_V	0.974	1.00
270_F	274_H	0.969	1.00
204_T	207_T	0.969	1.00
216_A	220_I	0.968	1.00
223_L	226_Q	0.964	1.00
136_W	140_L	0.964	1.00
126_V	137_A	0.955	1.00
221_Q	225_R	0.955	1.00
172_C	177_I	0.952	1.00
102_R	157_Q	0.950	1.00
138_L	208_A	0.948	1.00
226_Q	229_I	0.945	1.00
221_Q	224_L	0.943	1.00
177_I	180_K	0.942	1.00
79_G	142_T	0.939	1.00
27_H	30_A	0.935	1.00
219_P	222_V	0.933	1.00
8_M	12_G	0.932	1.00
10_I	14_L	0.931	1.00
130_G	133_D	0.928	1.00
131_L	136_W	0.923	1.00
8_M	11_Y	0.908	1.00
7_D	11_Y	0.904	1.00
142_T	201_Y	0.900	1.00
148_N	152_L	0.900	1.00
186_S	189_A	0.899	1.00
155_F	186_S	0.898	1.00
100_I	103_Q	0.892	1.00
141_P	207_T	0.890	1.00
91_A	95_S	0.888	1.00
77_V	81_A	0.881	1.00
65_I	256_V	0.878	1.00
82_V	139_I	0.878	1.00
31_A	254_M	0.874	1.00
152_L	186_S	0.872	1.00
252_I	256_V	0.860	1.00
83_S	87_S	0.859	1.00
187_L	190_I	0.858	1.00
81_A	194_S	0.853	1.00
110_V	150_I	0.852	1.00
69_L	73_V	0.848	1.00
71_V	135_Y	0.847	1.00
18_A	22_V	0.844	1.00
94_L	106_M	0.844	1.00
36_V	40_V	0.837	1.00
87_S	149_L	0.837	1.00
33_F	51_F	0.836	1.00
31_A	34_A	0.833	1.00
178_F	183_L	0.830	1.00
82_V	85_F	0.819	1.00
103_Q	106_M	0.818	1.00
218_W	223_L	0.818	1.00
59_I	259_V	0.816	1.00
34_A	38_E	0.816	1.00
179_F	183_L	0.815	1.00
79_G	139_I	0.812	1.00
74_F	77_V	0.810	1.00
214_D	217_K	0.808	1.00
137_A	141_P	0.804	1.00
91_A	149_L	0.801	1.00
33_F	52_S	0.800	1.00
197_Y	201_Y	0.800	1.00
205_Y	225_R	0.793	1.00
28_V	254_M	0.788	1.00
93_G	99_L	0.781	1.00
187_L	274_H	0.778	1.00
266_L	270_F	0.776	1.00
220_I	223_L	0.775	1.00
74_F	136_W	0.773	1.00
177_I	182_V	0.770	1.00
271_I	274_H	0.770	1.00
122_T	125_V	0.768	1.00
37_E	40_V	0.768	1.00
128_S	131_L	0.767	1.00
91_A	156_F	0.764	1.00
163_L	181_I	0.764	1.00
124_L	128_S	0.759	1.00
215_S	218_W	0.759	1.00
70_L	73_V	0.758	1.00
174_D	178_F	0.758	1.00
23_L	26_I	0.757	1.00
152_L	156_F	0.756	1.00
224_L	227_I	0.752	1.00
58_Y	249_E	0.748	1.00
123_F	126_V	0.745	1.00
138_L	142_T	0.745	1.00
84_M	152_L	0.740	1.00
223_L	228_V	0.740	1.00
75_V	142_T	0.739	1.00
230_V	247_P	0.738	1.00
75_V	135_Y	0.737	1.00
110_V	113_M	0.733	1.00
94_L	105_L	0.733	1.00
47_I	50_T	0.729	1.00
78_I	143_A	0.725	1.00
250_Q	253_K	0.724	1.00
178_F	182_V	0.723	1.00
222_V	225_R	0.721	1.00
260_A	264_V	0.720	1.00
139_I	142_T	0.720	1.00
254_M	258_V	0.715	1.00
133_D	214_D	0.708	1.00
161_S	168_K	0.707	1.00
68_S	71_V	0.707	1.00
12_G	15_L	0.703	1.00
83_S	145_N	0.701	1.00
83_S	148_N	0.697	1.00
80_T	198_A	0.691	1.00
17_F	21_C	0.691	1.00
250_Q	254_M	0.690	1.00
159_I	186_S	0.688	1.00
251_T	254_M	0.688	1.00
76_T	80_T	0.687	1.00
220_I	227_I	0.684	1.00
94_L	153_K	0.683	1.00
35_T	49_T	0.683	1.00
190_I	193_I	0.680	1.00
28_V	257_I	0.680	1.00
117_G	206_M	0.679	1.00
34_A	48_P	0.678	1.00
270_F	273_K	0.671	1.00
208_A	219_P	0.670	1.00
87_S	152_L	0.669	1.00
31_A	35_T	0.668	1.00
59_I	256_V	0.668	1.00
93_G	97_R	0.666	1.00
216_A	219_P	0.666	1.00
252_I	255_A	0.665	1.00
268_Y	272_Q	0.661	1.00
225_R	228_V	0.660	1.00
59_I	252_I	0.660	1.00
69_L	220_I	0.659	1.00
66_Y	69_L	0.658	1.00
145_N	197_Y	0.657	1.00
35_T	50_T	0.655	1.00
72_S	221_Q	0.651	1.00
9_L	13_F	0.648	1.00
106_M	150_I	0.647	1.00
127_K	132_L	0.646	1.00
80_T	84_M	0.644	1.00
129_L	132_L	0.641	1.00
248_P	252_I	0.641	1.00
122_T	211_Y	0.638	1.00
190_I	194_S	0.636	1.00
166_S	170_D	0.635	1.00
172_C	180_K	0.634	1.00
113_M	146_A	0.634	1.00
51_F	54_D	0.632	1.00
182_V	185_L	0.632	1.00
212_L	218_W	0.631	1.00
142_T	145_N	0.630	1.00
135_Y	138_L	0.630	1.00
62_T	66_Y	0.627	1.00
57_R	60_F	0.626	1.00
189_A	193_I	0.625	1.00
55_A	58_Y	0.624	1.00
134_S	137_A	0.621	1.00
137_A	211_Y	0.621	1.00
9_L	12_G	0.621	1.00
56_Y	255_A	0.617	1.00
217_K	221_Q	0.616	1.00
34_A	50_T	0.616	1.00
166_S	169_I	0.616	1.00
76_T	201_Y	0.612	1.00
220_I	225_R	0.611	1.00
216_A	228_V	0.611	1.00
145_N	200_T	0.610	1.00
13_F	17_F	0.608	1.00
115_F	119_M	0.606	1.00
14_L	18_A	0.606	1.00
83_S	201_Y	0.602	1.00
38_E	49_T	0.598	1.00
126_V	132_L	0.596	1.00
90_M	109_V	0.595	1.00
136_W	143_A	0.594	1.00
118_G	210_L	0.592	1.00
31_A	36_V	0.590	1.00
113_M	147_F	0.587	1.00
101_G	105_L	0.587	1.00
138_L	143_A	0.586	1.00
50_T	53_L	0.583	1.00
107_F	111_F	0.582	1.00
18_A	21_C	0.579	1.00
206_M	210_L	0.577	1.00
97_R	100_I	0.576	1.00
99_L	105_L	0.575	1.00
254_M	257_I	0.575	1.00
199_V	203_N	0.574	1.00
53_L	56_Y	0.573	1.00
151_I	189_A	0.573	1.00
64_I	218_W	0.571	1.00
60_F	63_D	0.569	1.00
141_P	144_I	0.567	1.00
257_I	260_A	0.563	1.00
135_Y	141_P	0.562	1.00
142_T	208_A	0.561	1.00
108_L	112_T	0.560	1.00
109_V	146_A	0.560	1.00
220_I	229_I	0.559	1.00
75_V	139_I	0.559	1.00
134_S	143_A	0.556	1.00
98_D	103_Q	0.555	1.00
72_S	202_W	0.554	1.00
173_N	179_F	0.546	1.00
29_I	33_F	0.544	1.00
80_T	201_Y	0.543	1.00
159_I	164_E	0.543	1.00
32_S	255_A	0.541	1.00
220_I	226_Q	0.540	1.00
138_L	212_L	0.540	1.00
91_A	153_K	0.539	1.00
123_F	132_L	0.537	1.00
98_D	161_S	0.535	1.00
11_Y	14_L	0.534	1.00
200_T	203_N	0.534	1.00
75_V	79_G	0.533	1.00
134_S	138_L	0.531	1.00
48_P	51_F	0.530	1.00
34_A	49_T	0.527	1.00
265_L	269_P	0.527	1.00
105_L	109_V	0.527	1.00
80_T	85_F	0.527	1.00
7_D	10_I	0.524	1.00
197_Y	200_T	0.523	1.00
19_L	23_L	0.523	1.00
112_T	146_A	0.522	1.00
127_K	130_G	0.519	1.00
63_D	66_Y	0.519	1.00
75_V	138_L	0.518	1.00
76_T	202_W	0.517	1.00
220_I	228_V	0.512	1.00
62_T	252_I	0.511	1.00
263_P	266_L	0.511	1.00
103_Q	107_F	0.510	1.00
52_S	56_Y	0.510	1.00
230_V	249_E	0.510	1.00
63_D	67_K	0.509	1.00
32_S	35_T	0.509	1.00
84_M	89_L	0.508	1.00
206_M	209_I	0.508	1.00
79_G	143_A	0.505	1.00
90_M	93_G	0.504	1.00
36_V	48_P	0.503	1.00
128_S	132_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
4tquN	1	0.965	100	0.257	Contact Map
3rlfG	1	0.9231	100	0.311	Contact Map
2onkC	2	0.8322	100	0.356	Contact Map
4tquM	1	0.8671	100	0.376	Contact Map
3d31C	2	0.8147	100	0.384	Contact Map
3rlfF	1	0.8811	100	0.414	Contact Map
4ymuD	2	0.7308	99.9	0.517	Contact Map
3tuiA	2	0.7133	99.9	0.552	Contact Map
2a65A	2	0.7972	8.5	0.952	Contact Map
4xp4A	1	0.8077	5.5	0.956	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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