SAPD - ECOLI - GREMLIN Contacts

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SAPD - Peptide transport system ATP-binding protein SapD

UniProt:	P0AAH4	Sequences: MPLLDIRNLTIEFKTGDEWVKAVDRVSMTLTEGEIRGLVGESGSGKSLIAKAICGVNKDNWRVTADRMRFDDIDLLRLSARERRKLVGHNVSMIFQEPQSCLDPSERVGRQLMQNIPAWTYKGRWWQRFGWRKRRAIELLHRVGIKDHKDAMRSFPYELTEGECQKVMIAIALANQPRLLIADEPTNSMEPTTQAQIFRLLTRLNQNSNTTILLISHDLQMLSQWADKINVLYCGQTVETAPSKELVTMPHHPYTQALIRAIPDFGSAMPHKSRLNTLPGAIPLLEQLPIGCRLGPRCPYAQRECIVTPRLTGAKNHLYACHFPLNMEKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12304
Length:	330 (266)
Sequences:	51007 (31444)
Seq/√Len:	1928.0

ECOLI - SAPD YCJV DPPD UGPC MALK CYSA POTG PROV OPPF METN POTA FBPC OPPD DDPD YDCT DPPF YEHX DDPF YADG MODC YHES GSIA ARAG UUP RBSA MACB FEPC MLAF YECC SAPF MDLA MDLB TAUB NIKE FHUC ETTA YTFR FECE LPTB HISP CYDC SSUB CYDD LSRA MSBA PHNC GLNQ YOJI GLTL PHNK YHDZ YPHE ZNUC XYLG SUFC ARTP MODF BTUD THIQ ALSA FTSE LIVG LIVF PSTB LOLD MGLA NIKD FETA YBBA YEJF CCMA PHNL YBHF YDDA YNJD YBIT YHIH
BACSU - OPUCA OPUBA MSMX YURJ OPUAA APPF OPPD YVRA YKFD DPPD APPD METN YFMM YHCH YKPA OPPF YXLF YDBJ YCBN YVFR YHAQ YDIF YFIL TAGH FHUC YUSV ECFA1 YTRB YFMF RBSA YFMR YHEH SUNT BCEA YCLP YTLC TCYN YVCR YFIC ECSA YKNV YLMA SKFE BMRA YFIB YGAD YKNU ECFA2 SUFC YHEI YXDL YWJA MNTB YXEO ALBC CYDC YKOD CYDD NATA ARTM GLNQ TCYC FTSE YJKB SSUB YCLH YVRO YKNY ZNUC YTHP PSTB1 YUFO EXPZ PSTB2 YHCG YYBJ YYDI YTRE
HALSA - Q9HMX3 Q9HHQ5 Q9HMW0 BTUDA Q9HMT3 Q9HMX2 Q9HNZ9 Q9HR06 Q9HMU8 Q9HRJ6 Q9HMG1 PHNC Q9HRH8 Q9HSQ7 PSTB2 Q9HMG6 Q9HHM2 Q9HRV7 Q9HNY3 Y1631 Q9HRZ9 Y2317 PSTB1 Q9HHR7 Q9HR96 Q9HT03 Q9HS04 Q9HR21 Q9HQA8 Q9HMC1 Q9HMW1
SULSO - Q97UF2 Q97YY4 Q97UY8 Q97VK8 Q97YP3 Q97VF5 Q97ZC0 Q97UH3 Q97VC1 Q97YP7 Q97VK9 Q97YP8 Q97VF4 Q97UD4 Q97VH6 Q7LX64 Q97YK2 Q97X18 Q97UJ9 Q97YQ7 Q97Z03 Y1893 Q97U54 Y2030 Q980W0 Q97UH4 Q97V01 Q97W42 PSTB Q7LY07 Q97V00 Q7LXM4 Q97VM2 Q7LX80 Q97VY4 Q97Z56 Q97UG5 Q97Z96 Q97UC2 Q97YP4 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
34_E	228_K	4.208	1.00
90_N	178_R	3.519	1.00
8_N	25_R	3.266	1.00
5_D	29_T	3.201	1.00
7_R	67_R	3.133	1.00
21_K	24_D	2.922	1.00
11_I	52_A	2.872	1.00
36_R	230_N	2.865	1.00
67_R	74_D	2.603	1.00
37_G	226_A	2.567	1.00
242_P	245_E	2.508	1.00
71_D	178_R	2.503	1.00
31_T	34_E	2.483	1.00
228_K	240_T	2.462	1.00
230_N	237_T	2.411	1.00
12_E	21_K	2.402	1.00
128_R	131_W	2.378	1.00
151_A	154_S	2.374	1.00
5_D	69_R	2.325	1.00
24_D	236_Q	2.257	1.00
10_T	65_A	2.246	1.00
6_I	9_L	2.190	1.00
10_T	25_R	2.134	1.00
223_S	244_K	2.096	1.00
50_A	215_I	2.095	1.00
135_R	138_E	2.093	1.00
32_E	178_R	2.058	1.00
135_R	176_Q	2.051	1.00
74_D	77_R	2.042	1.00
139_L	174_A	1.988	1.00
7_R	69_R	1.976	1.00
241_A	246_L	1.961	1.00
79_S	82_E	1.937	1.00
13_F	48_L	1.931	1.00
137_I	152_M	1.847	1.00
106_E	110_R	1.838	1.00
14_K	19_W	1.819	1.00
10_T	21_K	1.755	1.00
216_S	222_L	1.737	1.00
50_A	181_I	1.734	1.00
55_G	83_R	1.731	1.00
230_N	240_T	1.711	1.00
73_I	82_E	1.709	1.00
37_G	222_L	1.701	1.00
154_S	158_E	1.678	1.00
13_F	22_A	1.677	1.00
58_K	63_V	1.664	1.00
113_M	136_A	1.628	1.00
11_I	57_N	1.626	1.00
12_E	64_T	1.610	1.00
138_E	142_R	1.609	1.00
241_A	245_E	1.597	1.00
71_D	90_N	1.591	1.00
6_I	28_M	1.559	1.00
8_N	27_S	1.552	1.00
12_E	19_W	1.551	1.00
109_G	153_R	1.548	1.00
113_M	132_R	1.541	1.00
147_D	150_D	1.528	1.00
245_E	249_M	1.510	1.00
109_G	152_M	1.499	1.00
9_L	63_V	1.494	1.00
151_A	159_L	1.491	1.00
137_I	147_D	1.489	1.00
11_I	64_T	1.478	1.00
202_T	224_Q	1.454	1.00
117_P	132_R	1.437	1.00
10_T	24_D	1.411	1.00
78_L	82_E	1.388	1.00
107_R	110_R	1.369	1.00
146_K	150_D	1.369	1.00
182_A	212_I	1.359	1.00
133_K	137_I	1.349	1.00
112_L	140_L	1.334	1.00
109_G	113_M	1.312	1.00
6_I	53_I	1.303	1.00
35_I	205_N	1.284	1.00
198_F	221_M	1.281	1.00
99_Q	164_C	1.276	1.00
34_E	227_D	1.274	1.00
94_I	182_A	1.269	1.00
28_M	49_I	1.263	1.00
30_L	36_R	1.255	1.00
7_R	27_S	1.253	1.00
150_D	154_S	1.251	1.00
73_I	78_L	1.233	1.00
7_R	29_T	1.229	1.00
28_M	230_N	1.223	1.00
52_A	63_V	1.207	1.00
110_R	113_M	1.204	1.00
35_I	212_I	1.204	1.00
134_R	138_E	1.201	1.00
256_Q	260_R	1.199	1.00
202_T	205_N	1.195	1.00
201_L	212_I	1.192	1.00
54_C	93_M	1.187	1.00
38_L	213_L	1.183	1.00
244_K	248_T	1.176	1.00
133_K	152_M	1.176	1.00
36_R	240_T	1.175	1.00
159_L	167_V	1.173	1.00
55_G	58_K	1.170	1.00
121_Y	127_Q	1.168	1.00
107_R	153_R	1.166	1.00
69_R	74_D	1.161	1.00
105_S	157_Y	1.159	1.00
26_V	49_I	1.152	1.00
140_L	152_M	1.145	1.00
78_L	83_R	1.144	1.00
36_R	228_K	1.139	1.00
32_E	71_D	1.104	1.00
129_F	132_R	1.103	1.00
109_G	133_K	1.096	1.00
109_G	136_A	1.093	1.00
111_Q	171_I	1.090	1.00
35_I	226_A	1.082	1.00
31_T	228_K	1.075	1.00
180_L	210_T	1.070	1.00
112_L	174_A	1.060	1.00
130_G	134_R	1.055	1.00
131_W	134_R	1.053	1.00
14_K	18_E	1.022	1.00
138_E	141_H	1.021	1.00
253_P	256_Q	1.014	1.00
229_I	243_S	1.011	1.00
113_M	117_P	1.010	1.00
146_K	151_A	1.005	1.00
189_M	197_I	0.998	1.00
120_T	127_Q	0.987	1.00
8_N	65_A	0.987	1.00
132_R	136_A	0.986	1.00
30_L	179_L	0.974	1.00
144_G	203_R	0.973	1.00
205_N	212_I	0.972	1.00
176_Q	210_T	0.971	1.00
245_E	248_T	0.971	1.00
141_H	147_D	0.969	1.00
106_E	114_Q	0.967	1.00
116_I	174_A	0.961	1.00
214_L	225_W	0.961	1.00
12_E	24_D	0.957	1.00
49_I	232_L	0.955	1.00
137_I	141_H	0.950	1.00
23_V	52_A	0.949	1.00
237_T	240_T	0.947	1.00
53_I	213_L	0.943	1.00
180_L	212_I	0.943	1.00
32_E	209_N	0.938	1.00
51_K	56_V	0.933	1.00
92_S	172_A	0.928	1.00
139_L	142_R	0.922	1.00
141_H	146_K	0.922	1.00
38_L	230_N	0.922	1.00
264_D	267_S	0.912	1.00
228_K	239_E	0.911	1.00
6_I	68_M	0.910	1.00
142_R	203_R	0.909	1.00
31_T	211_T	0.908	1.00
194_Q	218_D	0.898	1.00
54_C	181_I	0.897	1.00
128_R	132_R	0.896	1.00
38_L	49_I	0.891	1.00
11_I	48_L	0.889	1.00
129_F	133_K	0.888	1.00
44_S	232_L	0.885	1.00
22_A	48_L	0.883	1.00
120_T	135_R	0.881	1.00
91_V	179_L	0.873	1.00
135_R	139_L	0.873	1.00
3_L	71_D	0.871	1.00
255_T	259_I	0.867	1.00
92_S	177_P	0.867	1.00
74_D	78_L	0.860	1.00
247_V	250_P	0.858	1.00
194_Q	221_M	0.855	1.00
80_A	83_R	0.854	1.00
253_P	257_A	0.848	1.00
35_I	202_T	0.845	1.00
202_T	225_W	0.840	1.00
51_K	57_N	0.839	1.00
102_L	164_C	0.838	1.00
182_A	201_L	0.837	1.00
246_L	255_T	0.836	1.00
113_M	133_K	0.833	1.00
106_E	111_Q	0.833	1.00
116_I	120_T	0.828	1.00
52_A	68_M	0.826	1.00
108_V	159_L	0.825	1.00
260_R	276_N	0.824	1.00
3_L	70_F	0.820	1.00
108_V	167_V	0.819	1.00
119_W	175_N	0.817	1.00
73_I	90_N	0.816	1.00
94_I	169_I	0.815	1.00
107_R	155_F	0.815	1.00
155_F	158_E	0.814	1.00
70_F	90_N	0.810	1.00
23_V	26_V	0.810	1.00
11_I	23_V	0.810	1.00
275_L	278_L	0.805	1.00
288_L	291_G	0.805	1.00
280_G	284_L	0.804	1.00
221_M	225_W	0.804	1.00
133_K	153_R	0.800	1.00
9_L	52_A	0.799	1.00
139_L	170_A	0.797	1.00
200_L	203_R	0.797	1.00
52_A	57_N	0.793	1.00
144_G	196_Q	0.789	1.00
226_A	229_I	0.788	1.00
39_V	222_L	0.788	1.00
205_N	227_D	0.787	1.00
233_Y	238_V	0.784	1.00
8_N	11_I	0.777	1.00
282_I	285_L	0.773	1.00
159_L	163_E	0.772	1.00
252_H	255_T	0.772	1.00
284_L	287_Q	0.771	1.00
243_S	247_V	0.770	1.00
198_F	224_Q	0.769	1.00
30_L	211_T	0.769	1.00
136_A	152_M	0.767	1.00
115_N	171_I	0.767	1.00
83_R	88_G	0.765	1.00
26_V	237_T	0.763	1.00
25_R	236_Q	0.760	1.00
184_E	217_H	0.756	1.00
231_V	250_P	0.754	1.00
147_D	152_M	0.752	1.00
145_I	151_A	0.742	1.00
257_A	261_A	0.739	1.00
287_Q	290_I	0.736	1.00
214_L	226_A	0.733	1.00
103_D	106_E	0.733	1.00
143_V	170_A	0.732	1.00
115_N	175_N	0.729	1.00
35_I	225_W	0.729	1.00
289_P	292_C	0.728	1.00
156_P	167_V	0.725	1.00
4_L	53_I	0.724	1.00
195_A	199_R	0.724	1.00
30_L	213_L	0.718	1.00
147_D	151_A	0.714	1.00
272_K	276_N	0.713	1.00
181_I	213_L	0.707	1.00
219_L	247_V	0.706	1.00
51_K	93_M	0.705	1.00
130_G	133_K	0.704	1.00
121_Y	128_R	0.704	1.00
75_L	91_V	0.704	1.00
139_L	173_L	0.701	1.00
285_L	288_L	0.700	1.00
199_R	202_T	0.699	1.00
199_R	224_Q	0.696	1.00
112_L	136_A	0.696	1.00
94_I	172_A	0.694	1.00
179_L	211_T	0.685	1.00
204_L	210_T	0.685	1.00
13_F	57_N	0.684	1.00
280_G	283_P	0.684	1.00
36_R	213_L	0.683	1.00
117_P	129_F	0.682	1.00
23_V	49_I	0.682	1.00
67_R	76_L	0.681	1.00
89_H	120_T	0.679	1.00
274_R	278_L	0.678	1.00
35_I	227_D	0.672	1.00
281_A	284_L	0.670	1.00
233_Y	236_Q	0.668	1.00
179_L	213_L	0.667	1.00
56_V	95_F	0.666	1.00
151_A	163_E	0.664	1.00
226_A	243_S	0.656	1.00
266_G	269_M	0.653	1.00
107_R	111_Q	0.652	1.00
238_V	252_H	0.652	1.00
69_R	72_D	0.647	1.00
261_A	264_D	0.647	1.00
70_F	75_L	0.646	1.00
63_V	76_L	0.645	1.00
286_E	289_P	0.643	1.00
39_V	231_V	0.643	1.00
4_L	179_L	0.640	1.00
186_T	221_M	0.640	1.00
243_S	254_Y	0.640	1.00
285_L	289_P	0.640	1.00
54_C	91_V	0.638	1.00
12_E	65_A	0.637	1.00
115_N	118_A	0.636	1.00
121_Y	132_R	0.634	1.00
257_A	260_R	0.630	1.00
233_Y	257_A	0.629	1.00
283_P	289_P	0.627	1.00
8_N	66_D	0.623	1.00
254_Y	258_L	0.623	1.00
173_L	210_T	0.622	1.00
67_R	77_R	0.620	1.00
278_L	281_A	0.614	1.00
6_I	49_I	0.612	1.00
131_W	135_R	0.611	1.00
282_I	286_E	0.611	1.00
25_R	65_A	0.610	1.00
249_M	252_H	0.609	1.00
3_L	179_L	0.609	1.00
278_L	282_I	0.609	1.00
202_T	206_Q	0.608	1.00
102_L	167_V	0.606	1.00
279_P	292_C	0.606	1.00
280_G	285_L	0.605	1.00
199_R	203_R	0.605	1.00
231_V	246_L	0.604	1.00
287_Q	291_G	0.604	1.00
283_P	291_G	0.603	1.00
53_I	68_M	0.603	1.00
79_S	83_R	0.602	1.00
120_T	176_Q	0.597	1.00
47_S	51_K	0.597	1.00
284_L	288_L	0.597	1.00
254_Y	257_A	0.595	1.00
109_G	112_L	0.588	1.00
275_L	279_P	0.587	1.00
245_E	251_H	0.586	1.00
283_P	287_Q	0.586	1.00
154_S	159_L	0.585	1.00
57_N	63_V	0.585	1.00
41_E	233_Y	0.584	1.00
277_T	281_A	0.583	1.00
102_L	111_Q	0.580	1.00
111_Q	156_P	0.579	1.00
68_M	76_L	0.578	1.00
256_Q	259_I	0.578	1.00
33_G	211_T	0.576	1.00
169_I	197_I	0.575	1.00
145_I	163_E	0.573	1.00
281_A	285_L	0.572	1.00
135_R	142_R	0.570	1.00
134_R	141_H	0.568	1.00
41_E	44_S	0.566	1.00
52_A	64_T	0.566	1.00
246_L	250_P	0.565	1.00
113_M	152_M	0.564	1.00
134_R	137_I	0.562	1.00
261_A	265_F	0.562	1.00
32_E	211_T	0.561	1.00
281_A	286_E	0.559	1.00
109_G	137_I	0.559	1.00
70_F	179_L	0.556	1.00
283_P	288_L	0.555	1.00
116_I	127_Q	0.555	1.00
273_S	276_N	0.553	1.00
288_L	292_C	0.551	1.00
285_L	291_G	0.551	1.00
284_L	289_P	0.549	1.00
116_I	121_Y	0.546	1.00
4_L	70_F	0.541	1.00
165_Q	188_S	0.541	1.00
3_L	211_T	0.541	1.00
10_T	64_T	0.540	1.00
275_L	282_I	0.540	1.00
75_L	78_L	0.538	1.00
113_M	121_Y	0.537	1.00
278_L	285_L	0.536	1.00
243_S	246_L	0.536	1.00
279_P	282_I	0.536	1.00
276_N	291_G	0.536	1.00
265_F	269_M	0.535	1.00
121_Y	131_W	0.532	1.00
284_L	291_G	0.532	1.00
127_Q	131_W	0.531	1.00
282_I	288_L	0.528	1.00
262_I	265_F	0.528	1.00
222_L	229_I	0.527	1.00
282_I	291_G	0.527	1.00
11_I	63_V	0.523	1.00
178_R	210_T	0.523	1.00
272_K	275_L	0.522	1.00
186_T	197_I	0.520	1.00
127_Q	132_R	0.519	1.00
255_T	258_L	0.519	1.00
241_A	250_P	0.516	1.00
116_I	175_N	0.515	1.00
161_E	166_K	0.514	1.00
35_I	214_L	0.514	1.00
238_V	253_P	0.514	1.00
285_L	290_I	0.512	1.00
29_T	240_T	0.511	1.00
264_D	269_M	0.511	1.00
12_E	22_A	0.510	1.00
140_L	151_A	0.509	1.00
116_I	119_W	0.508	1.00
241_A	247_V	0.507	1.00
34_E	240_T	0.506	1.00
114_Q	118_A	0.505	1.00
283_P	290_I	0.505	1.00
285_L	292_C	0.504	1.00
198_F	225_W	0.503	1.00
222_L	226_A	0.502	1.00
286_E	290_I	0.501	1.00
220_Q	224_Q	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
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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	0.9485	100	0.227	Contact Map
4fwiB	1	0.9212	100	0.233	Contact Map
2yyzA	1	0.9212	100	0.247	Contact Map
2it1A	1	0.9242	100	0.247	Contact Map
1g291	4	0.8667	100	0.248	Contact Map
1v43A	2	0.8121	100	0.251	Contact Map
4u00A	1	0.7273	100	0.252	Contact Map
4ry2A	2	0.7303	100	0.253	Contact Map
2oljA	2	0.7273	100	0.253	Contact Map
1oxxK	1	0.9152	100	0.254	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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