YCKA - BACSU - GREMLIN Contacts

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YCKA - Probable amino-acid ABC transporter permease protein YckA

UniProt:	P42399	Sequences: MINSIQWEYIFNTKLAIESFPYVIKGIGYTLLISFVSMFAGTVIGLFISLARMSKLALLRWPAKLYISFMRGVPILVILFILYFGFPYIGIEFSAVTAALIGFSLNSAAYIAEINRSAISSVEKGQWEAASSLGLSYWQTMRGIILPQSIRIALPPLANVLLDLIKASSLAAMITVPELLQHAKIIGGREFDYMTMYILTALIYWAICSIAAVFQNILEKKYAHYV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	226 (206)
Sequences:	18394 (11011)
Seq/√Len:	767.2

ECOLI - HISM ARTQ GLTJ HISQ GLTK ARTM YHDY YECS GLNP YHDX YEHY METI
BACSU - YCKA TCYM GLNM GLNP ARTQ YXEN TCYL TCYB METP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_A	104_S	3.267	1.00
158_A	215_Q	3.258	1.00
192_D	195_T	3.178	1.00
130_A	140_T	3.040	1.00
99_A	171_A	2.936	1.00
28_G	32_L	2.727	1.00
136_S	139_Q	2.702	1.00
183_A	200_T	2.670	1.00
51_A	63_A	2.553	1.00
48_I	112_A	2.300	1.00
127_W	140_T	2.233	1.00
138_W	142_R	2.225	1.00
131_S	140_T	2.224	1.00
213_V	217_I	2.163	1.00
126_Q	148_Q	2.138	1.00
73_V	78_I	2.111	1.00
58_L	62_P	2.080	1.00
58_L	61_W	1.984	1.00
127_W	131_S	1.980	1.00
181_Q	185_I	1.966	1.00
48_I	108_A	1.964	1.00
52_R	64_K	1.902	1.00
44_I	108_A	1.867	1.00
29_Y	32_L	1.832	1.00
36_V	100_L	1.810	1.00
57_A	61_W	1.780	1.00
24_I	28_G	1.778	1.00
94_S	97_T	1.763	1.00
49_S	115_N	1.742	1.00
32_L	96_V	1.707	1.00
121_S	152_I	1.696	1.00
27_I	207_I	1.692	1.00
183_A	196_M	1.672	1.00
53_M	120_S	1.656	1.00
217_I	220_K	1.644	1.00
25_K	28_G	1.642	1.00
34_S	165_I	1.642	1.00
118_A	153_A	1.638	1.00
209_S	213_V	1.631	1.00
205_W	209_S	1.620	1.00
187_G	193_Y	1.603	1.00
213_V	216_N	1.588	1.00
136_S	140_T	1.586	1.00
33_I	171_A	1.578	1.00
82_L	102_G	1.569	1.00
22_Y	25_K	1.555	1.00
29_Y	176_V	1.541	1.00
139_Q	143_G	1.521	1.00
67_I	112_A	1.519	1.00
38_M	161_L	1.502	1.00
137_Y	141_M	1.497	1.00
41_G	107_S	1.486	1.00
113_E	116_R	1.439	1.00
48_I	63_A	1.419	1.00
111_I	157_L	1.414	1.00
46_L	115_N	1.410	1.00
214_F	217_I	1.380	1.00
131_S	137_Y	1.324	1.00
182_H	185_I	1.306	1.00
56_L	61_W	1.304	1.00
34_S	168_S	1.303	1.00
135_L	139_Q	1.297	1.00
139_Q	142_R	1.294	1.00
47_F	51_A	1.255	1.00
57_A	60_R	1.246	1.00
32_L	36_V	1.241	1.00
115_N	153_A	1.238	1.00
96_V	100_L	1.232	1.00
56_L	59_L	1.230	1.00
36_V	104_S	1.225	1.00
20_F	24_I	1.217	1.00
111_I	160_V	1.200	1.00
78_I	106_N	1.199	1.00
60_R	64_K	1.196	1.00
79_L	102_G	1.195	1.00
61_W	65_L	1.189	1.00
177_P	181_Q	1.185	1.00
70_M	105_L	1.184	1.00
22_Y	182_H	1.183	1.00
43_V	47_F	1.182	1.00
127_W	145_I	1.164	1.00
95_A	175_T	1.163	1.00
25_K	29_Y	1.158	1.00
116_R	120_S	1.155	1.00
62_P	65_L	1.150	1.00
40_A	100_L	1.146	1.00
181_Q	184_K	1.123	1.00
45_G	111_I	1.123	1.00
21_P	25_K	1.113	1.00
130_A	144_I	1.113	1.00
73_V	106_N	1.101	1.00
119_I	145_I	1.097	1.00
52_R	113_E	1.096	1.00
217_I	221_K	1.088	1.00
114_I	160_V	1.085	1.00
68_S	209_S	1.076	1.00
97_T	100_L	1.067	1.00
187_G	197_Y	1.063	1.00
137_Y	140_T	1.057	1.00
165_I	207_I	1.053	1.00
63_A	112_A	1.048	1.00
114_I	156_P	1.045	1.00
53_M	119_I	1.033	1.00
100_L	104_S	1.032	1.00
34_S	161_L	1.018	1.00
79_L	171_A	1.017	1.00
51_A	54_S	1.016	1.00
62_P	66_Y	1.012	1.00
184_K	187_G	1.011	1.00
141_M	146_L	1.001	1.00
38_M	164_L	0.989	1.00
195_T	198_I	0.988	1.00
96_V	176_V	0.978	1.00
122_V	149_S	0.977	1.00
185_I	189_R	0.971	1.00
171_A	178_E	0.968	1.00
216_N	220_K	0.965	1.00
66_Y	108_A	0.954	1.00
82_L	98_A	0.951	1.00
186_I	196_M	0.951	1.00
214_F	218_L	0.950	1.00
165_I	211_A	0.949	1.00
78_I	82_L	0.948	1.00
70_M	109_A	0.941	1.00
65_L	68_S	0.932	1.00
135_L	143_G	0.931	1.00
68_S	205_W	0.921	1.00
27_I	203_I	0.913	1.00
37_S	104_S	0.900	1.00
163_D	167_A	0.894	1.00
56_L	62_P	0.893	1.00
55_K	60_R	0.885	1.00
85_G	89_I	0.884	1.00
30_T	165_I	0.883	1.00
216_N	219_E	0.880	1.00
75_I	167_A	0.875	1.00
169_S	204_Y	0.873	1.00
80_F	84_F	0.871	1.00
79_L	170_L	0.870	1.00
39_F	43_V	0.868	1.00
141_M	145_I	0.856	1.00
61_W	64_K	0.853	1.00
51_A	59_L	0.851	1.00
36_V	40_A	0.845	1.00
124_K	128_E	0.844	1.00
42_T	157_L	0.840	1.00
97_T	101_I	0.838	1.00
56_L	60_R	0.836	1.00
27_I	179_L	0.836	1.00
49_S	119_I	0.834	1.00
66_Y	70_M	0.831	1.00
173_M	177_P	0.831	1.00
107_S	160_V	0.827	1.00
122_V	152_I	0.826	1.00
190_E	193_Y	0.823	1.00
210_I	214_F	0.820	1.00
127_W	137_Y	0.819	1.00
75_I	106_N	0.808	1.00
125_G	129_A	0.804	1.00
21_P	24_I	0.798	1.00
171_A	176_V	0.796	1.00
83_Y	174_I	0.792	1.00
54_S	63_A	0.791	1.00
198_I	202_L	0.786	1.00
152_I	156_P	0.782	1.00
37_S	164_L	0.781	1.00
49_S	53_M	0.781	1.00
165_I	208_C	0.777	1.00
107_S	167_A	0.775	1.00
26_G	182_H	0.773	1.00
50_L	141_M	0.772	1.00
95_A	176_V	0.771	1.00
103_F	168_S	0.768	1.00
64_K	68_S	0.766	1.00
81_I	85_G	0.765	1.00
177_P	182_H	0.762	1.00
66_Y	109_A	0.761	1.00
124_K	127_W	0.756	1.00
206_A	210_I	0.754	1.00
79_L	174_I	0.753	1.00
54_S	137_Y	0.746	1.00
78_I	102_G	0.744	1.00
31_L	35_F	0.743	1.00
46_L	146_L	0.738	1.00
189_R	192_D	0.738	1.00
35_F	39_F	0.734	1.00
41_G	111_I	0.731	1.00
37_S	103_F	0.730	1.00
81_I	198_I	0.730	1.00
44_I	104_S	0.726	1.00
44_I	48_I	0.722	1.00
83_Y	98_A	0.717	1.00
85_G	88_Y	0.717	1.00
76_L	173_M	0.714	1.00
33_I	37_S	0.711	1.00
119_I	149_S	0.710	1.00
99_A	174_I	0.707	1.00
30_T	34_S	0.707	1.00
48_I	51_A	0.704	1.00
59_L	62_P	0.703	1.00
183_A	187_G	0.701	1.00
29_Y	178_E	0.700	1.00
180_L	197_Y	0.697	1.00
33_I	176_V	0.697	1.00
172_A	181_Q	0.696	1.00
187_G	196_M	0.691	1.00
115_N	119_I	0.688	1.00
111_I	115_N	0.687	1.00
52_R	67_I	0.681	1.00
199_L	203_I	0.680	1.00
130_A	135_L	0.671	1.00
118_A	152_I	0.670	1.00
202_L	206_A	0.666	1.00
33_I	99_A	0.662	1.00
107_S	164_L	0.661	1.00
29_Y	96_V	0.658	1.00
179_L	203_I	0.656	1.00
36_V	39_F	0.648	1.00
212_A	216_N	0.647	1.00
30_T	204_Y	0.647	1.00
83_Y	93_F	0.646	1.00
103_F	164_L	0.644	1.00
23_V	203_I	0.643	1.00
52_R	55_K	0.643	1.00
107_S	111_I	0.640	1.00
36_V	96_V	0.635	1.00
70_M	78_I	0.635	1.00
211_A	215_Q	0.634	1.00
124_K	131_S	0.634	1.00
218_L	222_Y	0.633	1.00
19_S	186_I	0.633	1.00
104_S	108_A	0.632	1.00
169_S	172_A	0.631	1.00
160_V	163_D	0.625	1.00
69_F	73_V	0.622	1.00
154_L	222_Y	0.620	1.00
52_R	60_R	0.617	1.00
156_P	159_N	0.615	1.00
155_P	219_E	0.610	1.00
197_Y	200_T	0.606	1.00
24_I	27_I	0.605	1.00
40_A	43_V	0.603	1.00
180_L	200_T	0.602	1.00
40_A	44_I	0.601	1.00
95_A	174_I	0.601	1.00
122_V	145_I	0.601	1.00
119_I	141_M	0.596	1.00
42_T	115_N	0.594	1.00
136_S	143_G	0.592	1.00
125_G	128_E	0.588	1.00
200_T	203_I	0.587	1.00
46_L	150_I	0.585	1.00
51_A	62_P	0.583	1.00
106_N	167_A	0.582	1.00
210_I	217_I	0.575	1.00
52_R	112_A	0.571	1.00
169_S	180_L	0.570	1.00
154_L	218_L	0.570	1.00
180_L	204_Y	0.569	1.00
43_V	46_L	0.567	1.00
83_Y	95_A	0.566	1.00
161_L	211_A	0.566	1.00
28_G	31_L	0.562	1.00
128_E	143_G	0.562	1.00
99_A	176_V	0.561	1.00
198_I	201_A	0.560	1.00
32_L	97_T	0.558	1.00
23_V	183_A	0.558	1.00
162_L	208_C	0.548	1.00
103_F	171_A	0.548	1.00
205_W	208_C	0.546	1.00
95_A	98_A	0.546	1.00
48_I	66_Y	0.540	1.00
215_Q	218_L	0.539	1.00
118_A	156_P	0.539	1.00
65_L	69_F	0.538	1.00
34_S	38_M	0.537	1.00
80_F	173_M	0.536	1.00
64_K	67_I	0.535	1.00
145_I	148_Q	0.534	1.00
90_G	93_F	0.534	1.00
43_V	104_S	0.534	1.00
26_G	29_Y	0.532	1.00
151_R	222_Y	0.530	1.00
76_L	170_L	0.530	1.00
194_M	198_I	0.530	1.00
93_F	97_T	0.524	1.00
33_I	168_S	0.524	1.00
210_I	213_V	0.524	1.00
23_V	186_I	0.522	1.00
186_I	190_E	0.521	1.00
45_G	49_S	0.520	1.00
86_F	91_I	0.520	1.00
76_L	80_F	0.519	1.00
51_A	56_L	0.519	1.00
22_Y	185_I	0.518	1.00
55_K	137_Y	0.518	1.00
123_E	152_I	0.518	1.00
55_K	59_L	0.516	1.00
55_K	58_L	0.511	1.00
44_I	47_F	0.509	1.00
117_S	156_P	0.507	1.00
25_K	32_L	0.505	1.00
209_S	212_A	0.504	1.00
33_I	96_V	0.503	1.00
38_M	42_T	0.503	1.00
29_Y	33_I	0.503	1.00
45_G	112_A	0.501	1.00
24_I	203_I	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
4ymuD	2	0.9513	100	0.466	Contact Map
3tuiA	2	0.9248	99.9	0.52	Contact Map
3rlfF	1	0.9381	99.9	0.551	Contact Map
3d31C	2	0.9469	99.9	0.552	Contact Map
2onkC	2	0.9602	99.9	0.554	Contact Map
4tquM	1	0.9646	99.9	0.579	Contact Map
3rlfG	1	0.9956	99.9	0.592	Contact Map
4tquN	1	0.969	99.8	0.628	Contact Map
2kv5A	1	0.146	4.6	0.959	Contact Map
5a63B	1	0.3097	4.1	0.96	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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