YDCV - ECOLI - GREMLIN Contacts

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YDCV - Inner membrane ABC transporter permease protein YdcV

UniProt:	P0AFR9	Sequences: MHSERAPFFLKLAAWGGVVFLHFPILIIAAYAFNTEDAAFSFPPQGLTLRWFSVAAQRSDILDAVTLSLKVAALATLIALVLGTLAAAALWRRDFFGKNAISLLLLLPIALPGIVTGLALLTAFKTINLEPGFFTIVVGHATFCVVVVFNNVIARFRRTSWSLVEASMDLGANGWQTFRYVVLPNLSSALLAGGMLAFALSFDEIIVTTFTAGHERTLPLWLLNQLGRPRDVPVTNVVALLVMLVTTLPILGAWWLTREGDNGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13765
Length:	264 (248)
Sequences:	72209 (46567)
Seq/√Len:	2957.0

ECOLI - YDCV POTH YCJO YCJP YDCU POTC UGPE POTB UGPA PSTA MALG PSTC POTI THIP CYST YNJC CYSW MALF MODB SSUC TAUC YEHY YEHW METI PHNE PROW YECS GLNP
BACSU - YTCP GANP AMYD MDXF YTEP MDXG GANQ ARAP LPLB AMYC YURN YESQ ARAQ YURM YQGI YQGH YESP LPLC YVGM YTLD SSUC METP OPUAB TCYB YXEN TCYL OPUCB OPUBB OPUBD OPUCD ARTQ GLNP YCKA
HALSA - Q9HP02 Q9HML6 Q9HP01 Q9HMT4 Q9HHQ7 Q9HS11 Q9HHQ6 Q9HPK3 Q9HR05 Q9HNI9 Q9HS12 Q9HML7
SULSO - Q97UZ0 Q97YY2 Q97ZC1 Q97UF3 Q97UY9 Q97YY3 Q97UF4 Q97ZT6 Q97ZT7 Q97ZC2 Q97VC0 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_Q	180_Y	3.885	1.00
66_T	70_K	3.249	1.00
168_M	177_T	3.116	1.00
153_I	157_R	3.018	1.00
64_A	221_W	2.657	1.00
155_R	189_A	2.599	1.00
63_D	66_T	2.593	1.00
74_L	137_V	2.557	1.00
92_R	164_V	2.533	1.00
32_A	52_F	2.516	1.00
167_S	177_T	2.499	1.00
216_R	224_N	2.482	1.00
164_V	182_V	2.476	1.00
173_N	176_Q	2.463	1.00
78_I	141_A	2.448	1.00
53_S	57_Q	2.362	1.00
50_R	53_S	2.338	1.00
62_L	66_T	2.338	1.00
174_G	177_T	2.328	1.00
231_D	234_V	2.265	1.00
175_W	179_R	2.244	1.00
76_T	194_G	2.226	1.00
152_V	190_L	2.196	1.00
50_R	54_V	2.146	1.00
95_F	98_K	2.113	1.00
172_A	176_Q	2.039	1.00
176_Q	179_R	1.991	1.00
70_K	133_F	1.942	1.00
91_W	157_R	1.919	1.00
84_T	178_F	1.899	1.00
167_S	172_A	1.886	1.00
156_F	186_L	1.883	1.00
148_V	193_G	1.883	1.00
102_S	153_I	1.861	1.00
26_L	30_A	1.845	1.00
163_L	185_N	1.825	1.00
30_A	34_N	1.825	1.00
84_T	186_L	1.804	1.00
80_L	194_G	1.786	1.00
164_V	177_T	1.759	1.00
63_D	67_L	1.731	1.00
251_L	255_W	1.729	1.00
168_M	174_G	1.724	1.00
72_A	198_F	1.670	1.00
164_V	168_M	1.642	1.00
221_W	225_Q	1.633	1.00
83_G	148_V	1.632	1.00
70_K	74_L	1.604	1.00
75_A	201_S	1.602	1.00
54_V	234_V	1.595	1.00
86_A	149_F	1.588	1.00
84_T	152_V	1.584	1.00
90_L	149_F	1.568	1.00
11_K	15_W	1.513	1.00
81_V	85_L	1.506	1.00
161_W	164_V	1.504	1.00
23_F	27_I	1.474	1.00
148_V	197_A	1.467	1.00
71_V	217_T	1.441	1.00
97_G	100_A	1.421	1.00
29_A	240_L	1.414	1.00
60_D	63_D	1.411	1.00
54_V	57_Q	1.396	1.00
94_D	98_K	1.376	1.00
87_A	152_V	1.367	1.00
91_W	153_I	1.365	1.00
205_I	209_T	1.345	1.00
156_F	182_V	1.332	1.00
192_A	196_L	1.330	1.00
183_L	190_L	1.329	1.00
49_L	53_S	1.319	1.00
161_W	165_E	1.318	1.00
27_I	31_Y	1.308	1.00
79_A	197_A	1.300	1.00
152_V	193_G	1.293	1.00
48_T	51_W	1.289	1.00
84_T	190_L	1.249	1.00
167_S	181_V	1.241	1.00
216_R	221_W	1.234	1.00
88_A	156_F	1.233	1.00
100_A	103_L	1.229	1.00
92_R	161_W	1.227	1.00
205_I	223_L	1.226	1.00
162_S	165_E	1.225	1.00
225_Q	231_D	1.224	1.00
139_G	211_T	1.217	1.00
225_Q	229_P	1.190	1.00
207_V	211_T	1.184	1.00
74_L	77_L	1.184	1.00
77_L	81_V	1.176	1.00
67_L	70_K	1.171	1.00
159_T	185_N	1.167	1.00
80_L	190_L	1.159	1.00
224_N	228_R	1.158	1.00
91_W	156_F	1.151	1.00
38_A	46_G	1.145	1.00
173_N	177_T	1.127	1.00
124_F	135_T	1.127	1.00
68_S	218_L	1.121	1.00
145_V	149_F	1.119	1.00
187_S	191_L	1.113	1.00
28_I	240_L	1.113	1.00
15_W	19_V	1.112	1.00
35_T	38_A	1.092	1.00
100_A	104_L	1.091	1.00
208_T	217_T	1.086	1.00
54_V	58_R	1.079	1.00
136_I	208_T	1.079	1.00
78_I	137_V	1.071	1.00
8_F	11_K	1.050	1.00
74_L	78_I	1.037	1.00
27_I	30_A	1.032	1.00
152_V	189_A	1.031	1.00
70_K	134_F	1.027	1.00
217_T	220_L	1.026	1.00
252_G	256_L	1.019	1.00
137_V	141_A	1.016	1.00
8_F	12_L	1.016	1.00
221_W	238_V	1.011	1.00
151_N	193_G	1.010	1.00
122_T	126_T	1.008	1.00
75_A	140_H	1.008	1.00
75_A	79_A	1.007	1.00
88_A	178_F	1.001	1.00
164_V	174_G	0.993	1.00
85_L	89_A	0.992	1.00
172_A	177_T	0.991	1.00
177_T	180_Y	0.984	1.00
221_W	224_N	0.984	1.00
216_R	220_L	0.982	1.00
185_N	188_S	0.982	1.00
204_E	207_V	0.981	1.00
56_A	62_L	0.978	1.00
133_F	137_V	0.972	1.00
65_V	218_L	0.971	1.00
134_F	138_V	0.967	1.00
223_L	227_G	0.959	1.00
88_A	174_G	0.956	1.00
10_L	14_A	0.950	1.00
69_L	73_A	0.949	1.00
226_L	235_T	0.947	1.00
31_Y	236_N	0.935	1.00
98_K	157_R	0.930	1.00
87_A	91_W	0.922	1.00
77_L	194_G	0.919	1.00
32_A	36_E	0.916	1.00
75_A	137_V	0.905	1.00
83_G	149_F	0.905	1.00
204_E	208_T	0.904	1.00
106_L	150_N	0.890	1.00
209_T	220_L	0.882	1.00
120_L	211_T	0.882	1.00
172_A	180_Y	0.882	1.00
67_L	133_F	0.882	1.00
96_F	99_N	0.879	1.00
252_G	255_W	0.879	1.00
43_P	46_G	0.878	1.00
61_I	238_V	0.871	1.00
34_N	38_A	0.871	1.00
70_K	73_A	0.870	1.00
73_A	77_L	0.869	1.00
71_V	133_F	0.869	1.00
139_G	207_V	0.869	1.00
121_L	125_K	0.865	1.00
18_V	22_H	0.865	1.00
113_G	143_F	0.864	1.00
140_H	201_S	0.864	1.00
52_F	240_L	0.862	1.00
225_Q	234_V	0.862	1.00
177_T	182_V	0.861	1.00
132_G	135_T	0.859	1.00
152_V	186_L	0.859	1.00
99_N	102_S	0.857	1.00
31_Y	34_N	0.856	1.00
65_V	69_L	0.854	1.00
129_L	134_F	0.849	1.00
186_L	189_A	0.849	1.00
89_A	95_F	0.845	1.00
66_T	69_L	0.840	1.00
187_S	190_L	0.840	1.00
79_A	83_G	0.839	1.00
155_R	186_L	0.838	1.00
37_D	40_F	0.837	1.00
225_Q	238_V	0.833	1.00
179_R	183_L	0.829	1.00
212_A	216_R	0.820	1.00
120_L	139_G	0.819	1.00
33_F	47_L	0.817	1.00
220_L	224_N	0.806	1.00
76_T	198_F	0.805	1.00
90_L	102_S	0.803	1.00
87_A	156_F	0.802	1.00
178_F	183_L	0.797	1.00
78_I	81_V	0.791	1.00
36_E	40_F	0.789	1.00
197_A	201_S	0.789	1.00
87_A	149_F	0.783	1.00
79_A	148_V	0.782	1.00
71_V	140_H	0.781	1.00
248_L	252_G	0.780	1.00
74_L	141_A	0.770	1.00
134_F	137_V	0.765	1.00
55_A	241_L	0.765	1.00
117_G	206_I	0.765	1.00
148_V	152_V	0.761	1.00
28_I	236_N	0.755	1.00
79_A	144_C	0.751	1.00
31_Y	35_T	0.751	1.00
174_G	178_F	0.746	1.00
131_P	214_H	0.744	1.00
163_L	181_V	0.743	1.00
246_T	250_I	0.743	1.00
59_S	63_D	0.741	1.00
23_F	26_L	0.739	1.00
90_L	153_I	0.737	1.00
47_L	50_R	0.736	1.00
253_A	256_L	0.733	1.00
83_G	152_V	0.725	1.00
178_F	182_V	0.725	1.00
51_W	233_P	0.720	1.00
125_K	130_E	0.715	1.00
116_T	142_T	0.715	1.00
80_L	152_V	0.715	1.00
144_C	197_A	0.709	1.00
54_V	231_D	0.708	1.00
64_A	67_L	0.708	1.00
49_L	52_F	0.708	1.00
53_S	56_A	0.706	1.00
182_V	185_N	0.702	1.00
102_S	150_N	0.702	1.00
46_G	50_R	0.701	1.00
113_G	206_I	0.699	1.00
90_L	101_I	0.698	1.00
35_T	46_G	0.697	1.00
9_F	12_L	0.696	1.00
82_L	141_A	0.695	1.00
86_A	145_V	0.695	1.00
166_A	170_L	0.692	1.00
72_A	76_T	0.691	1.00
190_L	193_G	0.686	1.00
117_G	210_F	0.686	1.00
161_W	168_M	0.685	1.00
12_L	15_W	0.684	1.00
64_A	218_L	0.682	1.00
218_L	242_V	0.680	1.00
234_V	238_V	0.679	1.00
79_A	201_S	0.678	1.00
9_F	13_A	0.671	1.00
128_N	131_P	0.671	1.00
144_C	200_L	0.668	1.00
247_T	251_L	0.668	1.00
68_S	202_F	0.668	1.00
38_A	45_Q	0.667	1.00
204_E	217_T	0.667	1.00
35_T	45_Q	0.666	1.00
34_N	44_P	0.665	1.00
89_A	93_R	0.665	1.00
106_L	109_I	0.664	1.00
62_L	65_V	0.662	1.00
51_W	54_V	0.662	1.00
17_G	21_L	0.659	1.00
166_A	169_D	0.658	1.00
28_I	239_A	0.656	1.00
33_F	48_T	0.655	1.00
222_L	238_V	0.654	1.00
219_P	242_V	0.654	1.00
135_T	139_G	0.653	1.00
95_F	101_I	0.645	1.00
19_V	23_F	0.644	1.00
152_V	156_F	0.643	1.00
71_V	137_V	0.640	1.00
71_V	136_I	0.640	1.00
136_I	140_H	0.639	1.00
24_P	28_I	0.638	1.00
159_T	186_L	0.636	1.00
187_S	256_L	0.635	1.00
136_I	212_A	0.633	1.00
18_V	21_L	0.633	1.00
236_N	240_L	0.632	1.00
14_A	18_V	0.631	1.00
48_T	52_F	0.630	1.00
59_S	62_L	0.628	1.00
190_L	194_G	0.625	1.00
96_F	100_A	0.624	1.00
88_A	182_V	0.620	1.00
189_A	193_G	0.620	1.00
60_D	221_W	0.619	1.00
13_A	17_G	0.618	1.00
120_L	123_A	0.618	1.00
68_S	219_P	0.614	1.00
122_T	125_K	0.613	1.00
206_I	210_F	0.610	1.00
127_I	130_E	0.609	1.00
242_V	246_T	0.608	1.00
86_A	105_L	0.606	1.00
105_L	146_V	0.602	1.00
151_N	189_A	0.602	1.00
34_N	46_G	0.600	1.00
114_I	210_F	0.598	1.00
99_N	103_L	0.597	1.00
194_G	197_A	0.594	1.00
31_Y	36_E	0.594	1.00
46_G	49_L	0.592	1.00
191_L	194_G	0.592	1.00
79_A	141_A	0.587	1.00
179_R	182_V	0.587	1.00
76_T	80_L	0.586	1.00
220_L	223_L	0.586	1.00
36_E	44_P	0.584	1.00
232_V	236_N	0.584	1.00
60_D	216_R	0.581	1.00
206_I	209_T	0.580	1.00
236_N	239_A	0.579	1.00
109_I	146_V	0.577	1.00
87_A	153_I	0.571	1.00
22_H	26_L	0.571	1.00
97_G	101_I	0.565	1.00
71_V	75_A	0.564	1.00
55_A	234_V	0.562	1.00
75_A	141_A	0.560	1.00
200_L	203_D	0.559	1.00
80_L	84_T	0.559	1.00
72_A	202_F	0.559	1.00
11_K	14_A	0.559	1.00
82_L	145_V	0.558	1.00
76_T	201_S	0.558	1.00
250_I	254_W	0.558	1.00
103_L	107_L	0.558	1.00
177_T	181_V	0.552	1.00
135_T	211_T	0.552	1.00
113_G	117_G	0.550	1.00
124_F	130_E	0.549	1.00
93_R	174_G	0.549	1.00
32_A	237_V	0.543	1.00
34_N	45_Q	0.541	1.00
208_T	220_L	0.541	1.00
193_G	197_A	0.536	1.00
86_A	89_A	0.535	1.00
94_D	99_N	0.534	1.00
102_S	157_R	0.533	1.00
140_H	204_E	0.531	1.00
55_A	238_V	0.531	1.00
58_R	62_L	0.530	1.00
109_I	147_V	0.530	1.00
108_P	146_V	0.530	1.00
38_A	41_S	0.530	1.00
81_V	84_T	0.529	1.00
222_L	239_A	0.526	1.00
95_F	99_N	0.524	1.00
233_P	236_N	0.523	1.00
199_A	203_D	0.523	1.00
94_D	161_W	0.522	1.00
44_P	47_L	0.521	1.00
82_L	85_L	0.519	1.00
63_D	70_K	0.517	1.00
232_V	235_T	0.516	1.00
201_S	204_E	0.515	1.00
98_K	102_S	0.514	1.00
83_G	145_V	0.510	1.00
165_E	168_M	0.510	1.00
143_F	207_V	0.510	1.00
230_R	234_V	0.510	1.00
117_G	121_L	0.509	1.00
72_A	201_S	0.508	1.00
60_D	64_A	0.504	1.00
52_F	237_V	0.504	1.00
140_H	208_T	0.502	1.00
53_S	58_R	0.502	1.00
173_N	179_R	0.502	1.00
123_A	130_E	0.501	1.00
32_A	240_L	0.500	1.00
37_D	41_S	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
2onkC	2	0.9167	100	0.238	Contact Map
4tquM	1	0.9394	100	0.252	Contact Map
3d31C	2	0.8977	100	0.263	Contact Map
3rlfG	1	0.9811	100	0.295	Contact Map
4tquN	1	0.9659	100	0.307	Contact Map
3rlfF	1	0.9356	100	0.323	Contact Map
4ymuD	2	0.8068	99.9	0.43	Contact Map
3tuiA	2	0.7879	99.9	0.453	Contact Map
2a65A	2	0.8674	16.9	0.938	Contact Map
2m20A	2	0.1402	13.8	0.94	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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