AMYC - BACSU - GREMLIN Contacts

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AMYC - Putative ABC transporter permease protein AmyC

UniProt:	O34518	Sequences: MRAARTKSMRIITLLAAIVACAHFIPFYILLTTSLKAKGDYSSKWIFPADISFHNFSEAWERASLGNSFINTMIITGFSALLLIIFGSLAAYPLARRETKLNKAVFALLISIMIIPPLTSMVPLYRMVVDAGMVNTHAIAIFINTAAYMPLTVFLYSGFIRSTIPKELVEAARIDGAGMLKIFFTIVFPLLKPITATICIISCVFIWNDYQFAIFFLQDQKVQTLTVAMAGFFGENANNLHLVAAAALMAMLPMVVLFLALQKYFIAGLSSGAVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	276 (251)
Sequences:	71180 (46488)
Seq/√Len:	2934.3

ECOLI - YCJP MALG UGPE POTH POTI UGPA YCJO THIP YDCV YDCU POTC PSTA PSTC POTB YNJC CYST CYSW MALF MODB SSUC TAUC PHNE YEHY YEHW METI PROW YECS GLNP
BACSU - AMYC MDXG GANQ ARAQ YURM YESQ YTCP LPLC GANP AMYD ARAP MDXF YTEP YURN LPLB YQGH YQGI YESP YVGM YTLD SSUC OPUAB TCYB METP TCYL YXEN OPUCB OPUBD OPUCD OPUBB ARTQ GLNP
HALSA - Q9HMT4 Q9HML6 Q9HHQ6 Q9HP02 Q9HHQ7 Q9HP01 Q9HS11 Q9HR05 Q9HPK3 Q9HNI9 Q9HS12
SULSO - Q97UF3 Q97UY9 Q97ZC1 Q97YY3 Q97YY2 Q97ZT6 Q97VC0 Q97UZ0 Q97ZC2 Q97ZT7 Q97UF4 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
181_K	185_T	3.965	1.00
70_I	74_I	3.324	1.00
173_R	182_I	3.171	1.00
157_S	161_R	3.043	1.00
67_N	70_I	2.668	1.00
68_S	228_A	2.612	1.00
96_R	169_V	2.591	1.00
178_G	181_K	2.549	1.00
172_A	182_I	2.532	1.00
159_F	194_I	2.477	1.00
78_F	141_I	2.462	1.00
34_S	56_F	2.452	1.00
169_V	187_V	2.425	1.00
223_Q	231_G	2.384	1.00
66_G	70_I	2.381	1.00
57_S	61_E	2.365	1.00
179_M	182_I	2.343	1.00
54_H	57_S	2.337	1.00
180_L	184_F	2.248	1.00
80_A	199_C	2.243	1.00
156_Y	195_T	2.229	1.00
99_T	102_N	2.183	1.00
54_H	58_E	2.122	1.00
239_N	242_L	2.122	1.00
82_L	145_T	2.072	1.00
177_A	181_K	2.027	1.00
181_K	184_F	1.988	1.00
168_L	190_L	1.972	1.00
88_S	183_F	1.964	1.00
95_A	161_R	1.960	1.00
152_T	198_I	1.956	1.00
160_I	191_L	1.938	1.00
172_A	177_A	1.893	1.00
32_T	36_K	1.878	1.00
28_Y	32_T	1.830	1.00
106_F	157_S	1.812	1.00
88_S	191_L	1.810	1.00
67_N	71_N	1.790	1.00
169_V	182_I	1.788	1.00
84_I	199_C	1.738	1.00
173_R	179_M	1.728	1.00
74_I	78_F	1.698	1.00
220_Q	223_Q	1.695	1.00
88_S	156_Y	1.694	1.00
87_G	152_T	1.693	1.00
79_S	206_I	1.683	1.00
169_V	173_R	1.671	1.00
76_T	203_C	1.667	1.00
90_A	153_V	1.627	1.00
94_L	153_V	1.601	1.00
58_E	242_L	1.549	1.00
228_A	232_F	1.534	1.00
13_T	17_A	1.520	1.00
25_I	29_I	1.493	1.00
58_E	61_E	1.492	1.00
166_K	169_V	1.482	1.00
152_T	202_S	1.459	1.00
101_L	104_A	1.440	1.00
98_E	102_N	1.422	1.00
91_A	156_Y	1.411	1.00
210_Y	214_I	1.394	1.00
85_I	89_L	1.391	1.00
197_T	201_I	1.390	1.00
75_I	224_T	1.373	1.00
29_I	33_T	1.371	1.00
53_F	57_S	1.369	1.00
160_I	187_V	1.367	1.00
95_A	157_S	1.366	1.00
31_L	248_L	1.343	1.00
52_S	55_N	1.343	1.00
83_L	202_S	1.342	1.00
64_S	67_N	1.323	1.00
166_K	170_E	1.302	1.00
156_Y	198_I	1.299	1.00
135_N	139_I	1.282	1.00
188_F	195_T	1.281	1.00
172_A	186_I	1.278	1.00
96_R	166_K	1.261	1.00
212_F	216_F	1.250	1.00
167_E	170_E	1.244	1.00
223_Q	228_A	1.243	1.00
88_S	195_T	1.236	1.00
104_A	107_A	1.233	1.00
137_H	222_V	1.231	1.00
217_L	222_V	1.231	1.00
71_N	74_I	1.229	1.00
178_G	182_I	1.219	1.00
210_Y	230_A	1.208	1.00
143_I	216_F	1.208	1.00
259_L	263_K	1.205	1.00
232_F	239_N	1.205	1.00
231_G	235_E	1.198	1.00
81_L	85_I	1.195	1.00
164_I	190_L	1.190	1.00
92_Y	160_I	1.187	1.00
140_A	213_A	1.185	1.00
72_T	225_L	1.179	1.00
78_F	81_L	1.173	1.00
219_D	222_V	1.166	1.00
136_T	139_I	1.156	1.00
17_A	21_C	1.125	1.00
84_I	195_T	1.113	1.00
192_K	196_A	1.113	1.00
232_F	237_A	1.104	1.00
224_T	227_V	1.103	1.00
37_A	40_D	1.096	1.00
40_D	50_D	1.092	1.00
169_V	179_M	1.089	1.00
29_I	32_T	1.081	1.00
104_A	108_L	1.077	1.00
30_L	248_L	1.074	1.00
78_F	82_L	1.067	1.00
149_M	153_V	1.066	1.00
95_A	160_I	1.059	1.00
223_Q	227_V	1.052	1.00
79_S	83_L	1.050	1.00
10_R	14_L	1.039	1.00
89_L	93_P	1.021	1.00
156_Y	194_I	1.021	1.00
79_S	144_N	1.019	1.00
126_R	130_D	1.017	1.00
190_L	193_P	1.011	1.00
82_L	141_I	0.999	1.00
60_W	66_G	0.999	1.00
209_D	212_F	0.988	1.00
155_L	198_I	0.988	1.00
228_A	231_G	0.984	1.00
92_Y	179_M	0.984	1.00
12_I	16_A	0.978	1.00
260_A	264_Y	0.978	1.00
92_Y	183_F	0.975	1.00
58_E	62_R	0.973	1.00
177_A	182_I	0.969	1.00
73_M	77_G	0.960	1.00
9_M	13_T	0.960	1.00
133_M	138_A	0.959	1.00
10_R	13_T	0.949	1.00
213_A	224_T	0.947	1.00
33_T	36_K	0.944	1.00
124_L	216_F	0.934	1.00
102_N	161_R	0.927	1.00
209_D	213_A	0.927	1.00
124_L	143_I	0.919	1.00
74_I	137_H	0.919	1.00
77_G	81_L	0.917	1.00
141_I	145_T	0.914	1.00
182_I	185_T	0.913	1.00
81_L	199_C	0.911	1.00
34_S	38_K	0.907	1.00
74_I	77_G	0.906	1.00
20_A	24_F	0.906	1.00
100_K	103_K	0.906	1.00
94_L	106_F	0.905	1.00
91_A	95_A	0.905	1.00
152_T	156_Y	0.896	1.00
228_A	246_A	0.893	1.00
55_N	241_H	0.893	1.00
56_F	248_L	0.892	1.00
69_F	225_L	0.891	1.00
233_F	243_V	0.889	1.00
110_I	154_F	0.885	1.00
87_G	153_V	0.874	1.00
230_A	234_G	0.873	1.00
214_I	227_V	0.868	1.00
144_N	206_I	0.865	1.00
156_Y	191_L	0.865	1.00
159_F	191_L	0.861	1.00
79_S	141_I	0.860	1.00
36_K	40_D	0.860	1.00
82_L	85_I	0.859	1.00
83_L	87_G	0.857	1.00
135_N	219_D	0.857	1.00
69_F	73_M	0.854	1.00
47_F	50_D	0.851	1.00
179_M	183_F	0.845	1.00
183_F	188_F	0.843	1.00
103_K	106_F	0.842	1.00
191_L	194_I	0.840	1.00
33_T	37_A	0.835	1.00
70_I	73_M	0.828	1.00
83_L	148_Y	0.817	1.00
184_F	188_F	0.816	1.00
91_A	160_I	0.814	1.00
182_I	187_V	0.813	1.00
227_V	231_G	0.811	1.00
35_L	51_I	0.811	1.00
244_A	248_L	0.809	1.00
192_K	195_T	0.809	1.00
75_I	144_N	0.807	1.00
202_S	206_I	0.804	1.00
91_A	153_V	0.802	1.00
65_L	246_A	0.802	1.00
117_P	147_A	0.800	1.00
51_I	54_H	0.796	1.00
30_L	244_A	0.794	1.00
93_P	99_T	0.794	1.00
53_F	56_F	0.792	1.00
256_V	260_A	0.788	1.00
192_K	264_Y	0.785	1.00
83_L	152_T	0.785	1.00
143_I	212_F	0.779	1.00
177_A	185_T	0.777	1.00
50_D	53_F	0.776	1.00
90_A	149_M	0.775	1.00
125_Y	129_V	0.775	1.00
254_M	258_F	0.769	1.00
33_T	244_A	0.765	1.00
87_G	156_Y	0.763	1.00
64_S	220_Q	0.763	1.00
183_F	187_V	0.758	1.00
140_A	144_N	0.748	1.00
38_K	42_S	0.744	1.00
250_A	254_M	0.744	1.00
129_V	134_V	0.743	1.00
168_L	186_I	0.738	1.00
39_G	42_S	0.734	1.00
86_F	145_T	0.733	1.00
58_E	239_N	0.733	1.00
121_M	211_Q	0.731	1.00
242_L	246_A	0.729	1.00
59_A	249_M	0.729	1.00
68_S	71_N	0.729	1.00
241_H	244_A	0.728	1.00
166_K	173_R	0.724	1.00
232_F	246_A	0.722	1.00
255_V	259_L	0.722	1.00
121_M	215_F	0.719	1.00
217_L	223_Q	0.719	1.00
84_I	156_Y	0.718	1.00
194_I	198_I	0.717	1.00
25_I	28_Y	0.715	1.00
62_R	66_G	0.713	1.00
94_L	105_V	0.709	1.00
171_A	175_D	0.709	1.00
66_G	69_F	0.705	1.00
40_D	49_A	0.700	1.00
232_F	242_L	0.700	1.00
135_N	138_A	0.697	1.00
131_A	134_V	0.697	1.00
80_A	203_C	0.694	1.00
63_A	67_N	0.693	1.00
75_I	140_A	0.693	1.00
11_I	15_L	0.690	1.00
94_L	157_S	0.689	1.00
83_L	206_I	0.688	1.00
100_K	104_A	0.686	1.00
171_A	174_I	0.686	1.00
79_S	145_T	0.685	1.00
261_L	264_Y	0.682	1.00
19_V	23_H	0.680	1.00
124_L	127_M	0.677	1.00
35_L	52_S	0.676	1.00
11_I	14_L	0.672	1.00
14_L	17_A	0.671	1.00
76_T	80_A	0.671	1.00
55_N	58_E	0.670	1.00
140_A	217_L	0.670	1.00
36_K	48_P	0.666	1.00
117_P	211_Q	0.666	1.00
156_Y	160_I	0.664	1.00
187_V	190_L	0.663	1.00
57_S	60_W	0.662	1.00
37_A	49_A	0.662	1.00
195_T	198_I	0.659	1.00
37_A	50_D	0.658	1.00
110_I	113_M	0.656	1.00
50_D	54_H	0.655	1.00
20_A	23_H	0.651	1.00
148_Y	202_S	0.648	1.00
164_I	191_L	0.647	1.00
75_I	141_I	0.640	1.00
52_S	56_F	0.639	1.00
80_A	84_I	0.638	1.00
209_D	224_T	0.637	1.00
98_E	103_K	0.636	1.00
244_A	247_A	0.636	1.00
240_L	244_A	0.635	1.00
232_F	235_E	0.632	1.00
260_A	263_K	0.631	1.00
204_V	208_N	0.630	1.00
225_L	250_A	0.629	1.00
259_L	262_Q	0.627	1.00
68_S	225_L	0.627	1.00
24_F	28_Y	0.623	1.00
21_C	25_I	0.621	1.00
15_L	19_V	0.620	1.00
72_T	226_T	0.617	1.00
247_A	250_A	0.617	1.00
126_R	129_V	0.616	1.00
195_T	199_C	0.615	1.00
90_A	109_L	0.613	1.00
101_L	105_V	0.613	1.00
75_I	137_H	0.609	1.00
211_Q	214_I	0.607	1.00
30_L	247_A	0.607	1.00
99_T	105_V	0.607	1.00
106_F	154_F	0.606	1.00
26_P	30_L	0.602	1.00
26_P	33_T	0.602	1.00
78_F	145_T	0.599	1.00
80_A	206_I	0.599	1.00
117_P	121_M	0.599	1.00
16_A	20_A	0.597	1.00
72_T	207_W	0.597	1.00
205_F	208_N	0.596	1.00
120_S	146_A	0.593	1.00
184_F	187_V	0.592	1.00
109_L	150_P	0.591	1.00
229_M	246_A	0.589	1.00
75_I	79_S	0.587	1.00
86_F	149_M	0.587	1.00
113_M	150_P	0.586	1.00
63_A	66_G	0.586	1.00
148_Y	205_F	0.578	1.00
258_F	262_Q	0.576	1.00
93_P	97_R	0.576	1.00
9_M	12_I	0.575	1.00
211_Q	215_F	0.575	1.00
48_P	51_I	0.573	1.00
155_L	194_I	0.572	1.00
199_C	202_S	0.572	1.00
118_L	215_F	0.571	1.00
13_T	16_A	0.570	1.00
91_A	157_S	0.569	1.00
196_A	199_C	0.569	1.00
83_L	145_T	0.568	1.00
76_T	207_W	0.565	1.00
76_T	206_I	0.564	1.00
242_L	245_A	0.563	1.00
33_T	38_K	0.561	1.00
182_I	186_I	0.558	1.00
240_L	243_V	0.557	1.00
226_T	250_A	0.557	1.00
97_R	179_M	0.556	1.00
92_Y	187_V	0.555	1.00
22_A	26_P	0.555	1.00
103_K	107_A	0.555	1.00
144_N	209_D	0.551	1.00
71_N	222_V	0.550	1.00
107_A	111_S	0.550	1.00
115_I	120_S	0.550	1.00
67_N	74_I	0.547	1.00
106_F	161_R	0.543	1.00
170_E	173_R	0.543	1.00
128_V	134_V	0.542	1.00
59_A	246_A	0.542	1.00
38_K	48_P	0.541	1.00
64_S	228_A	0.541	1.00
85_I	88_S	0.540	1.00
113_M	151_L	0.539	1.00
121_M	125_Y	0.538	1.00
36_K	50_D	0.538	1.00
59_A	242_L	0.533	1.00
90_A	93_P	0.529	1.00
226_T	229_M	0.527	1.00
133_M	136_T	0.526	1.00
108_L	112_I	0.525	1.00
105_V	109_L	0.524	1.00
26_P	29_I	0.521	1.00
102_N	106_F	0.519	1.00
202_S	205_F	0.518	1.00
227_V	230_A	0.516	1.00
112_I	150_P	0.515	1.00
62_R	242_L	0.513	1.00
198_I	202_S	0.511	1.00
187_V	191_L	0.509	1.00
206_I	209_D	0.509	1.00
98_E	166_K	0.508	1.00
253_P	256_V	0.508	1.00
36_K	49_A	0.508	1.00
256_V	259_L	0.508	1.00
34_S	245_A	0.503	1.00
60_W	63_A	0.503	1.00
47_F	51_I	0.503	1.00
98_E	101_L	0.500	1.00
109_L	153_V	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	0.9674	100	0.23	Contact Map
4tquN	1	0.9493	100	0.247	Contact Map
2onkC	2	0.8768	100	0.277	Contact Map
4tquM	1	0.9203	100	0.301	Contact Map
3d31C	2	0.8587	100	0.306	Contact Map
3rlfF	1	0.9203	100	0.357	Contact Map
4ymuD	2	0.7717	99.9	0.455	Contact Map
3tuiA	2	0.7536	99.9	0.504	Contact Map
4hfiA	3	0.4348	9.4	0.946	Contact Map
3hd7A	1	0.1196	7.3	0.949	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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