YKFD - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YKFD - Putative oligopeptide transport ATP-binding protein YkfD

UniProt:	C0SP98	Sequences: MRRLPLLEVSQLKMHFDAGKKRTVKAVDGVTFQIREGETFGLVGESGCGKSTLGRVLMRLYQPTEGSVTYRGTNLHALSEKEQFAFNRKLQMIFQDPYASLNPRMTVREIILEPMEIHNLYNTHKARLLVVDELLEAVGLHPDFGSRYPHEFSGGQRQRIGIARALSLNPEFIVADEPISALDVSVQAQVVNLLKRLQKEKGLTFLFIAHDLSMVKHISDRIGVMYLGHMMEITESGTLYREPLHPYTKALLSSIPIPDPELEDKRERILLKGELPSPVNPPSGCVFRTRCPEAMPECGESRPQLQEIEPGRFVACHLYRNAETKEKVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	329 (270)
Sequences:	53548 (33916)
Seq/√Len:	2064.1

ECOLI - FBPC POTG PROV CYSA METN YCJV OPPF POTA MALK YDCT DPPF UGPC SAPD DPPD YEHX OPPD DDPD MODC YADG GSIA UUP YHES DDPF ARAG FEPC RBSA MLAF SAPF MACB MDLA MDLB CYDC NIKE FECE CYDD MSBA TAUB FHUC ETTA HISP LSRA YTFR SSUB PHNC YECC GLNQ YOJI PHNK YHDZ GLTL LPTB YPHE ZNUC SUFC LIVG XYLG MODF LIVF LOLD FTSE ALSA MGLA BTUD ARTP PSTB YBBA THIQ FETA NIKD YEJF PHNL CCMA YBHF YDDA YNJD YBIT YHIH
BACSU - YKFD OPUCA OPUBA OPPD OPUAA MSMX APPF YVRA YURJ DPPD METN APPD YHCH OPPF YFIL YVFR YCBN YXLF YDBJ YHAQ TAGH YKPA YFMM YDIF ECFA1 YUSV YHEH YFMR RBSA YTRB FHUC SUNT YFMF YFIB YFIC YCLP BMRA YKNV TCYN YGAD YLMA YWJA YHEI YKNU SUFC BCEA CYDD YTLC ECFA2 YXDL ECSA SKFE YKOD YXEO YVCR CYDC FTSE TCYC GLNQ YJKB NATA SSUB ARTM MNTB PSTB1 ALBC YVRO YTHP PSTB2 YKNY EXPZ YUFO YCLH YHCG ZNUC YYBJ YTRE YYDI
HALSA - Q9HMX3 Q9HMW0 BTUDA Q9HMX2 Q9HHQ5 Q9HR06 Q9HNZ9 Q9HMT3 Q9HRJ6 Q9HMG1 Q9HMU8 Q9HRH8 Q9HSQ7 Q9HHM2 PSTB2 PHNC Q9HMG6 Q9HNY3 Q9HRV7 Q9HRZ9 Y1631 PSTB1 Y2317 Q9HR96 Q9HHR7 Q9HS04 Q9HQA8 Q9HT03 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q97UF2 Q97UY8 Q97VK8 Q97UH3 Q97VC1 Q97YY4 Q97YP7 Q97ZC0 Q97YP3 Q97VF5 Q7LX64 Q97VF4 Q97YP8 Q97VK9 Q97VH6 Q97UJ9 Q97YK2 Q97UD4 Q97X18 Q97YQ7 Q97Z03 Q97U54 Q97UH4 Q980W0 Y1893 Q97W42 PSTB Y2030 Q7LY07 Q97V01 Q97V00 Q97VM2 Q7LXM4 Q7LX80 Q97VY4 Q97UG5 Q97YP4 Q97Z56 Q97Z96 Q97UC2 Q980K5 Q97ZU0 Q980E6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_E	221_R	4.369	1.00
89_K	171_E	3.681	1.00
11_Q	29_G	3.604	1.00
8_E	33_Q	3.415	1.00
10_S	67_S	3.357	1.00
25_K	28_D	3.033	1.00
14_M	56_V	2.998	1.00
40_F	223_G	2.894	1.00
67_S	74_N	2.697	1.00
235_E	238_T	2.630	1.00
137_A	201_K	2.621	1.00
41_G	219_S	2.621	1.00
35_R	38_E	2.574	1.00
28_D	229_H	2.539	1.00
221_R	233_I	2.472	1.00
223_G	230_M	2.438	1.00
9_V	12_L	2.428	1.00
71_R	171_E	2.425	1.00
8_E	69_T	2.357	1.00
15_H	25_K	2.354	1.00
144_F	147_R	2.343	1.00
13_K	29_G	2.267	1.00
216_K	237_G	2.201	1.00
54_G	208_I	2.193	1.00
36_E	171_E	2.192	1.00
13_K	65_E	2.182	1.00
74_N	77_A	2.152	1.00
134_L	167_S	2.139	1.00
234_T	239_L	2.089	1.00
209_A	215_V	1.953	1.00
10_S	69_T	1.939	1.00
16_F	52_T	1.927	1.00
41_G	215_V	1.858	1.00
130_V	133_E	1.858	1.00
105_M	109_E	1.819	1.00
130_V	169_N	1.789	1.00
54_G	174_V	1.787	1.00
132_D	145_G	1.745	1.00
13_K	25_K	1.720	1.00
14_M	61_Y	1.703	1.00
112_L	131_V	1.659	1.00
16_F	26_A	1.659	1.00
197_L	203_L	1.631	1.00
147_R	151_E	1.630	1.00
223_G	233_I	1.627	1.00
5_P	35_R	1.624	1.00
11_Q	31_T	1.623	1.00
112_L	127_R	1.618	1.00
15_H	64_T	1.617	1.00
144_F	152_F	1.616	1.00
14_M	64_T	1.608	1.00
9_V	32_F	1.585	1.00
195_K	217_H	1.574	1.00
5_P	8_E	1.565	1.00
108_R	146_S	1.532	1.00
12_L	63_P	1.521	1.00
238_T	242_E	1.515	1.00
133_E	137_A	1.512	1.00
169_N	201_K	1.496	1.00
234_T	238_T	1.495	1.00
108_R	145_G	1.485	1.00
71_R	89_K	1.445	1.00
106_T	109_E	1.427	1.00
13_K	28_D	1.424	1.00
175_A	205_F	1.418	1.00
9_V	57_L	1.414	1.00
191_V	214_M	1.407	1.00
122_N	126_A	1.366	1.00
116_E	127_R	1.364	1.00
38_E	220_D	1.362	1.00
93_I	175_A	1.356	1.00
152_F	160_I	1.355	1.00
10_S	33_Q	1.328	1.00
34_I	40_F	1.325	1.00
108_R	112_L	1.312	1.00
128_L	132_D	1.300	1.00
39_T	198_Q	1.299	1.00
111_I	135_L	1.281	1.00
98_Y	157_R	1.278	1.00
32_F	223_G	1.275	1.00
59_R	62_Q	1.270	1.00
58_M	92_M	1.262	1.00
39_T	205_F	1.250	1.00
125_K	129_L	1.248	1.00
10_S	31_T	1.243	1.00
109_E	112_L	1.238	1.00
42_L	206_L	1.220	1.00
32_F	53_L	1.210	1.00
195_K	198_Q	1.195	1.00
40_F	221_R	1.192	1.00
73_T	78_L	1.183	1.00
194_L	205_F	1.174	1.00
249_K	253_S	1.171	1.00
104_R	150_H	1.170	1.00
127_R	131_V	1.166	1.00
136_E	142_P	1.159	1.00
246_P	249_K	1.153	1.00
128_L	145_G	1.151	1.00
236_S	240_Y	1.150	1.00
69_T	74_N	1.149	1.00
182_L	190_V	1.144	1.00
237_G	241_R	1.138	1.00
135_L	145_G	1.134	1.00
126_A	129_L	1.126	1.00
143_D	147_R	1.122	1.00
110_I	164_R	1.116	1.00
39_T	219_S	1.113	1.00
30_V	53_L	1.112	1.00
106_T	146_S	1.111	1.00
40_F	233_I	1.105	1.00
173_I	203_L	1.100	1.00
11_Q	65_E	1.092	1.00
86_F	90_L	1.091	1.00
108_R	131_V	1.088	1.00
36_E	71_R	1.079	1.00
56_V	63_P	1.078	1.00
5_P	33_Q	1.074	1.00
27_V	56_V	1.067	1.00
111_I	167_S	1.066	1.00
141_H	144_F	1.052	1.00
53_L	225_M	1.035	1.00
132_D	142_P	1.030	1.00
108_R	128_L	1.029	1.00
35_R	221_R	1.024	1.00
222_I	236_S	1.020	1.00
34_I	172_F	1.016	1.00
169_N	203_L	1.015	1.00
238_T	241_R	1.005	1.00
124_H	127_R	1.003	1.00
14_M	52_T	1.001	1.00
15_H	28_D	1.000	1.00
105_M	113_E	0.993	1.00
91_Q	165_A	0.990	1.00
91_Q	170_P	0.989	1.00
240_Y	243_P	0.982	1.00
58_M	174_V	0.980	1.00
133_E	136_E	0.979	1.00
207_F	218_I	0.978	1.00
173_I	205_F	0.976	1.00
129_L	133_E	0.974	1.00
132_D	136_E	0.973	1.00
137_A	196_R	0.956	1.00
57_L	206_L	0.954	1.00
115_M	167_S	0.954	1.00
119_N	122_N	0.953	1.00
55_R	60_L	0.949	1.00
112_L	116_E	0.949	1.00
56_V	68_V	0.948	1.00
9_V	68_V	0.938	1.00
90_L	172_F	0.935	1.00
35_R	204_T	0.932	1.00
139_G	196_R	0.930	1.00
42_L	53_L	0.924	1.00
132_D	140_L	0.922	1.00
18_A	24_V	0.921	1.00
275_L	278_P	0.918	1.00
48_C	225_M	0.916	1.00
121_Y	127_R	0.905	1.00
246_P	250_A	0.902	1.00
230_M	233_I	0.897	1.00
134_L	137_A	0.894	1.00
281_P	284_G	0.891	1.00
6_L	71_R	0.889	1.00
198_Q	205_F	0.885	1.00
12_L	56_V	0.884	1.00
55_R	61_Y	0.884	1.00
42_L	223_G	0.884	1.00
248_T	252_L	0.880	1.00
124_H	128_L	0.879	1.00
257_I	260_P	0.877	1.00
187_Q	214_M	0.877	1.00
36_E	202_G	0.873	1.00
187_Q	211_D	0.869	1.00
27_V	30_V	0.863	1.00
5_P	36_E	0.858	1.00
106_T	148_Y	0.856	1.00
128_L	146_S	0.851	1.00
101_L	157_R	0.851	1.00
237_G	240_Y	0.843	1.00
119_N	130_V	0.841	1.00
70_Y	89_K	0.839	1.00
56_V	61_Y	0.837	1.00
121_Y	124_H	0.837	1.00
236_S	239_L	0.835	1.00
115_M	119_N	0.831	1.00
198_Q	220_D	0.830	1.00
105_M	110_I	0.824	1.00
195_K	218_I	0.817	1.00
177_E	210_H	0.817	1.00
81_K	85_A	0.816	1.00
139_G	189_Q	0.813	1.00
175_A	194_L	0.813	1.00
107_V	152_F	0.812	1.00
280_N	283_S	0.812	1.00
29_G	229_H	0.809	1.00
6_L	70_Y	0.805	1.00
93_I	162_I	0.805	1.00
34_I	204_T	0.805	1.00
192_N	217_H	0.801	1.00
214_M	218_I	0.797	1.00
121_Y	126_A	0.796	1.00
39_T	195_K	0.795	1.00
219_S	222_I	0.790	1.00
7_L	57_L	0.789	1.00
126_A	130_V	0.787	1.00
130_V	134_L	0.786	1.00
74_N	78_L	0.784	1.00
239_L	243_P	0.782	1.00
26_A	52_T	0.781	1.00
276_P	280_N	0.779	1.00
278_P	281_P	0.778	1.00
236_S	247_Y	0.774	1.00
102_N	105_M	0.774	1.00
131_V	145_G	0.774	1.00
207_F	219_S	0.773	1.00
268_R	271_L	0.772	1.00
239_L	248_T	0.772	1.00
107_V	160_I	0.772	1.00
148_Y	151_E	0.770	1.00
14_M	27_V	0.768	1.00
134_L	163_A	0.767	1.00
174_V	206_L	0.766	1.00
11_Q	14_M	0.763	1.00
30_V	230_M	0.762	1.00
73_T	89_K	0.760	1.00
188_A	192_N	0.759	1.00
172_F	206_L	0.757	1.00
93_I	165_A	0.756	1.00
272_K	275_L	0.753	1.00
138_V	163_A	0.753	1.00
273_G	278_P	0.753	1.00
226_Y	231_M	0.752	1.00
277_S	281_P	0.745	1.00
193_L	196_R	0.744	1.00
136_E	141_H	0.743	1.00
266_R	270_L	0.741	1.00
276_P	282_P	0.741	1.00
43_V	215_V	0.741	1.00
39_T	218_I	0.735	1.00
75_L	86_F	0.731	1.00
191_V	217_H	0.729	1.00
224_V	243_P	0.727	1.00
118_H	168_L	0.726	1.00
80_E	85_A	0.726	1.00
277_S	280_N	0.726	1.00
280_N	284_G	0.725	1.00
152_F	156_Q	0.720	1.00
245_H	248_T	0.719	1.00
149_P	160_I	0.717	1.00
172_F	204_T	0.716	1.00
40_F	206_L	0.713	1.00
112_L	128_L	0.710	1.00
144_F	156_Q	0.710	1.00
114_P	117_I	0.709	1.00
59_R	87_N	0.709	1.00
34_I	206_L	0.706	1.00
279_V	282_P	0.706	1.00
259_D	262_L	0.703	1.00
39_T	220_D	0.700	1.00
219_S	236_S	0.698	1.00
114_P	168_L	0.698	1.00
273_G	277_S	0.697	1.00
250_A	254_S	0.695	1.00
114_P	164_R	0.694	1.00
275_L	281_P	0.691	1.00
15_H	65_E	0.690	1.00
276_P	284_G	0.682	1.00
125_K	128_L	0.682	1.00
37_G	204_T	0.682	1.00
221_R	232_E	0.681	1.00
140_L	144_F	0.678	1.00
179_I	214_M	0.677	1.00
43_V	224_V	0.676	1.00
70_Y	172_F	0.676	1.00
255_I	258_P	0.675	1.00
134_L	166_L	0.675	1.00
70_Y	75_L	0.675	1.00
55_R	92_M	0.674	1.00
253_S	269_I	0.674	1.00
57_L	68_V	0.672	1.00
101_L	160_I	0.671	1.00
192_N	195_K	0.671	1.00
212_L	240_Y	0.668	1.00
78_L	86_F	0.665	1.00
115_M	121_Y	0.665	1.00
273_G	276_P	0.664	1.00
60_L	94_F	0.663	1.00
250_A	253_S	0.657	1.00
56_V	64_T	0.653	1.00
6_L	172_F	0.652	1.00
118_H	121_Y	0.652	1.00
19_G	24_V	0.651	1.00
226_Y	229_H	0.651	1.00
27_V	53_L	0.651	1.00
278_P	282_P	0.649	1.00
255_I	259_D	0.648	1.00
58_M	90_L	0.648	1.00
192_N	196_R	0.647	1.00
270_L	274_E	0.645	1.00
120_L	127_R	0.640	1.00
274_E	278_P	0.638	1.00
154_G	159_R	0.638	1.00
106_T	110_I	0.637	1.00
7_L	70_Y	0.636	1.00
29_G	65_E	0.635	1.00
278_P	284_G	0.635	1.00
117_I	121_Y	0.634	1.00
16_F	61_Y	0.633	1.00
70_Y	86_F	0.631	1.00
67_S	76_H	0.630	1.00
7_L	172_F	0.627	1.00
51_S	55_R	0.627	1.00
99_A	157_R	0.624	1.00
276_P	281_P	0.622	1.00
268_R	272_K	0.622	1.00
231_M	245_H	0.621	1.00
247_Y	251_L	0.609	1.00
75_L	90_L	0.608	1.00
277_S	282_P	0.608	1.00
226_Y	250_A	0.607	1.00
131_V	134_L	0.604	1.00
111_I	131_V	0.603	1.00
247_Y	250_A	0.603	1.00
85_A	88_R	0.600	1.00
67_S	77_A	0.599	1.00
234_T	240_Y	0.587	1.00
234_T	243_P	0.587	1.00
45_E	48_C	0.584	1.00
129_L	136_E	0.579	1.00
108_R	111_I	0.579	1.00
100_S	161_G	0.578	1.00
224_V	239_L	0.577	1.00
115_M	122_N	0.573	1.00
36_E	204_T	0.573	1.00
96_D	99_A	0.573	1.00
15_H	26_A	0.568	1.00
179_I	190_V	0.566	1.00
6_L	204_T	0.566	1.00
110_I	149_P	0.566	1.00
38_E	233_I	0.565	1.00
215_V	222_I	0.565	1.00
88_R	119_N	0.565	1.00
101_L	110_I	0.563	1.00
261_E	265_K	0.561	1.00
147_R	152_F	0.559	1.00
276_P	279_V	0.559	1.00
122_N	127_R	0.557	1.00
238_T	244_L	0.555	1.00
268_R	273_G	0.554	1.00
275_L	280_N	0.554	1.00
15_H	18_A	0.553	1.00
235_E	239_L	0.551	1.00
271_L	275_L	0.551	1.00
162_I	190_V	0.550	1.00
140_L	156_Q	0.550	1.00
276_P	283_S	0.549	1.00
271_L	276_P	0.548	1.00
128_L	131_V	0.546	1.00
116_E	124_H	0.545	1.00
118_H	122_N	0.544	1.00
272_K	278_P	0.542	1.00
166_L	203_L	0.541	1.00
46_S	177_E	0.539	1.00
5_P	71_R	0.537	1.00
111_I	114_P	0.537	1.00
158_Q	181_A	0.537	1.00
267_E	271_L	0.535	1.00
68_V	76_H	0.534	1.00
236_S	243_P	0.534	1.00
115_M	120_L	0.532	1.00
69_T	72_G	0.532	1.00
116_E	122_N	0.531	1.00
25_K	29_G	0.530	1.00
268_R	275_L	0.529	1.00
6_L	35_R	0.528	1.00
275_L	279_V	0.528	1.00
135_L	144_F	0.524	1.00
95_Q	154_G	0.522	1.00
243_P	248_T	0.521	1.00
277_S	284_G	0.520	1.00
278_P	283_S	0.520	1.00
215_V	219_S	0.519	1.00
119_N	169_N	0.518	1.00
279_V	283_S	0.518	1.00
267_E	270_L	0.518	1.00
107_V	111_I	0.517	1.00
252_L	256_P	0.516	1.00
268_R	276_P	0.515	1.00
33_Q	233_I	0.513	1.00
260_P	263_E	0.512	1.00
115_M	118_H	0.512	1.00
271_L	274_E	0.510	1.00
9_V	53_L	0.510	1.00
274_E	279_V	0.508	1.00
45_E	247_Y	0.508	1.00
59_R	76_H	0.506	1.00
198_Q	201_K	0.505	1.00
45_E	226_Y	0.505	1.00
275_L	284_G	0.503	1.00
113_E	117_I	0.503	1.00
244_L	249_K	0.502	1.00
115_M	168_L	0.502	1.00
75_L	78_L	0.501	1.00
131_V	167_S	0.501	1.00
191_V	209_A	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
3tuiC	2	0.9696	100	0.218	Contact Map
4ry2A	2	0.7234	100	0.234	Contact Map
4mkiB	2	0.8693	100	0.236	Contact Map
1b0uA	2	0.7477	100	0.237	Contact Map
4u00A	1	0.7295	100	0.238	Contact Map
2oljA	2	0.7356	100	0.239	Contact Map
4fwiB	1	0.924	100	0.24	Contact Map
4f4cA	1	0.7021	100	0.24	Contact Map
4ymuJ	2	0.7295	100	0.241	Contact Map
4yerA	2	0.845	100	0.245	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.

Page generated in 0.0126 seconds.