SAPF - ECOLI - GREMLIN Contacts

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SAPF - Peptide transport system ATP-binding protein SapF

UniProt:	P0AAH8	Sequences: MIETLLEVRNLSKTFRYRTGWFRRQTVEAVKPLSFTLREGQTLAIIGENGSGKSTLAKMLAGMIEPTSGELLIDDHPLHFGDYSFRSQRIRMIFQDPSTSLNPRQRISQILDFPLRLNTDLEPEQRRKQIIETMRMVGLLPDHVSYYPHMLAPGQKQRLGLARALILRPKVIIADEALASLDMSMRSQLINLMLELQEKQGISYIYVTQHIGMMKHISDQVLVMHQGEVVERGSTADVLASPLHELTKRLIAGHFGEALTADAWRKDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12305
Length:	268 (226)
Sequences:	207290 (119924)
Seq/√Len:	7977.2

ECOLI - SAPF PROV POTG ARAG MALK FBPC POTA DDPD METN CYSA MACB YCJV RBSA YDCT UGPC YEHX OPPF DPPF YADG DPPD MDLA OPPD SAPD FEPC MDLB NIKE HISP MLAF MODC CYDC MSBA DDPF CYDD YTFR FHUC PHNK GSIA FECE TAUB PHNC YECC GLNQ ALSA SSUB YOJI YPHE LIVG YHDZ LPTB LSRA XYLG YHES GLTL LIVF SUFC UUP ARTP LOLD MODF PSTB MGLA BTUD ZNUC THIQ NIKD FTSE FETA YBBA ETTA YEJF PHNL CCMA YDDA YNJD YBHF YBIT YHIH UVRA
BACSU - YVRA OPUCA OPUBA OPUAA TAGH MSMX YDBJ YURJ METN YHEH OPPF YUSV YKFD YFIL OPPD DPPD APPF YVFR RBSA YXLF APPD YHCH YHAQ YCBN YFIC YKNU TCYN BMRA SUFC YGAD YWJA YFMF YFIB YHEI YKNV YKPA ECFA1 FHUC SUNT YCLP CYDC ECSA YLMA CYDD YFMM YXDL YXEO YTRB YKOD BCEA YVCR TCYC ARTM GLNQ NATA MNTB YJKB SKFE YTLC PSTB1 FTSE ECFA2 ALBC PSTB2 YUFO YFMR SSUB YVRO YTHP YDIF YKNY YCLH ZNUC YHCG YYBJ EXPZ YTRE YYDI UVRA
HALSA - Q9HMX3 Q9HMW0 BTUDA Q9HHQ5 Q9HR06 Q9HNZ9 Q9HMX2 Q9HSQ7 Q9HMG1 Q9HMT3 Q9HRJ6 Q9HMU8 Q9HMG6 Q9HNY3 Q9HHM2 Q9HRH8 Q9HRZ9 PSTB2 PHNC Y1631 Q9HRV7 Y2317 PSTB1 Q9HHR7 Q9HR96 Q9HR21 Q9HT03 Q9HS04 Q9HQA8 Q9HMC1 Q9HMW1 Q9HMA2 Q9HMI4
SULSO - Q97UJ9 Q97UF2 Q97UH3 Q97VF5 Q97UY8 Q97YY4 Q7LX64 Q97VK8 Q97YP7 Q97YP3 Q97VF4 Q97VH6 Q97VK9 Q97ZC0 Q97VC1 Q97YP8 Q97YK2 Q97X18 Y2030 Q97YQ7 Y1893 Q7LY07 Q97UD4 Q97UH4 Q97U54 Q97Z03 PSTB Q97W42 Q97V00 Q97VM2 Q97V01 Q7LXM4 Q97VY4 Q980W0 Q7LX80 Q97Z56 Q97YP4 Q97UG5 Q97Z96 Q97UC2 Q97ZU0 Q980K5 Q980E6 Q97ZI2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_Q	220_Q	3.341	1.00
44_A	218_S	3.134	1.00
10_N	32_P	3.094	1.00
7_E	36_T	3.013	1.00
70_E	77_P	2.916	1.00
9_R	70_E	2.905	1.00
28_E	31_K	2.880	1.00
89_R	170_K	2.800	1.00
43_L	222_L	2.656	1.00
143_H	146_Y	2.609	1.00
220_Q	232_R	2.557	1.00
38_R	41_Q	2.553	1.00
31_K	228_E	2.547	1.00
12_S	32_P	2.318	1.00
7_E	72_L	2.315	1.00
8_V	11_L	2.249	1.00
14_T	28_E	2.171	1.00
9_R	72_L	2.015	1.00
12_S	28_E	2.000	1.00
13_K	59_M	1.997	1.00
135_R	141_P	1.984	1.00
234_S	237_D	1.970	1.00
233_G	237_D	1.961	1.00
57_A	207_V	1.901	1.00
222_L	232_R	1.900	1.00
12_S	68_S	1.893	1.00
105_Q	109_Q	1.874	1.00
74_D	170_K	1.859	1.00
168_R	202_I	1.858	1.00
222_L	229_V	1.856	1.00
195_E	199_K	1.842	1.00
57_A	173_I	1.794	1.00
39_E	170_K	1.779	1.00
122_E	125_Q	1.739	1.00
129_Q	168_R	1.686	1.00
134_M	144_V	1.635	1.00
131_I	144_V	1.620	1.00
10_N	34_S	1.617	1.00
194_L	216_H	1.609	1.00
131_I	135_R	1.575	1.00
108_S	145_S	1.567	1.00
136_M	200_Q	1.566	1.00
108_S	112_D	1.529	1.00
208_T	214_M	1.481	1.00
37_L	43_L	1.469	1.00
41_Q	219_D	1.469	1.00
14_T	67_T	1.465	1.00
132_E	136_M	1.463	1.00
16_R	26_T	1.443	1.00
13_K	67_T	1.441	1.00
107_I	151_L	1.441	1.00
129_Q	132_E	1.436	1.00
15_F	29_A	1.432	1.00
35_F	222_L	1.405	1.00
112_D	126_R	1.393	1.00
13_K	64_I	1.391	1.00
5_L	74_D	1.352	1.00
58_K	64_I	1.334	1.00
30_V	59_M	1.324	1.00
146_Y	150_M	1.323	1.00
56_L	224_M	1.321	1.00
108_S	144_V	1.315	1.00
233_G	238_V	1.305	1.00
110_I	163_R	1.301	1.00
12_S	31_K	1.296	1.00
77_P	80_F	1.278	1.00
8_V	35_F	1.277	1.00
127_R	131_I	1.269	1.00
136_M	195_E	1.262	1.00
108_S	130_I	1.244	1.00
62_G	65_E	1.240	1.00
170_K	202_I	1.235	1.00
15_F	55_T	1.211	1.00
59_M	66_P	1.190	1.00
8_V	60_L	1.187	1.00
106_R	109_Q	1.186	1.00
72_L	77_P	1.183	1.00
128_K	132_E	1.175	1.00
38_R	220_Q	1.167	1.00
9_R	36_T	1.165	1.00
197_Q	219_D	1.160	1.00
43_L	220_Q	1.160	1.00
215_K	236_A	1.151	1.00
225_H	230_V	1.141	1.00
108_S	127_R	1.138	1.00
43_L	232_R	1.136	1.00
133_T	166_I	1.132	1.00
42_T	197_Q	1.117	1.00
11_L	66_P	1.113	1.00
197_Q	204_Y	1.113	1.00
181_L	189_L	1.107	1.00
44_A	214_M	1.107	1.00
42_T	218_S	1.102	1.00
91_R	169_P	1.091	1.00
61_A	92_M	1.090	1.00
168_R	200_Q	1.083	1.00
74_D	89_R	1.082	1.00
111_L	166_I	1.078	1.00
42_T	206_Y	1.069	1.00
122_E	126_R	1.065	1.00
172_I	202_I	1.063	1.00
187_S	191_N	1.063	1.00
190_I	213_M	1.037	1.00
196_L	202_I	1.029	1.00
137_V	162_A	1.027	1.00
125_Q	128_K	1.025	1.00
115_L	166_I	1.022	1.00
33_L	56_L	1.021	1.00
174_A	193_M	1.019	1.00
13_K	55_T	1.018	1.00
83_Y	87_S	1.017	1.00
42_T	204_Y	1.008	1.00
9_R	34_S	1.005	1.00
186_R	213_M	1.002	1.00
60_L	205_I	1.002	1.00
231_E	242_P	1.002	1.00
132_E	135_R	1.000	1.00
231_E	243_L	0.994	1.00
131_I	141_P	0.994	1.00
35_F	56_L	0.993	1.00
10_N	68_S	0.989	1.00
108_S	131_I	0.988	1.00
112_D	130_I	0.980	1.00
14_T	29_A	0.979	1.00
45_I	56_L	0.978	1.00
5_L	39_E	0.974	1.00
8_V	71_L	0.970	1.00
124_E	128_K	0.969	1.00
11_L	59_M	0.967	1.00
151_L	159_L	0.967	1.00
61_A	173_I	0.958	1.00
39_E	74_D	0.958	1.00
123_P	127_R	0.957	1.00
237_D	241_S	0.956	1.00
231_E	241_S	0.954	1.00
130_I	133_T	0.947	1.00
192_L	195_E	0.946	1.00
14_T	26_T	0.939	1.00
133_T	162_A	0.937	1.00
186_R	210_H	0.934	1.00
136_M	199_K	0.934	1.00
45_I	222_L	0.932	1.00
221_V	235_T	0.932	1.00
194_L	197_Q	0.930	1.00
176_E	209_Q	0.927	1.00
5_L	38_R	0.921	1.00
115_L	120_D	0.916	1.00
109_Q	112_D	0.914	1.00
93_I	174_A	0.912	1.00
123_P	126_R	0.909	1.00
82_D	85_F	0.906	1.00
59_M	71_L	0.903	1.00
230_V	244_H	0.900	1.00
93_I	161_L	0.900	1.00
37_L	205_I	0.899	1.00
32_P	228_E	0.896	1.00
30_V	33_L	0.891	1.00
5_L	36_T	0.888	1.00
8_V	56_L	0.882	1.00
129_Q	133_T	0.880	1.00
141_P	144_V	0.870	1.00
48_E	225_H	0.865	1.00
37_L	203_S	0.853	1.00
174_A	204_Y	0.852	1.00
118_N	167_L	0.852	1.00
101_L	156_K	0.849	1.00
91_R	164_A	0.849	1.00
172_I	204_Y	0.845	1.00
106_R	147_Y	0.844	1.00
43_L	205_I	0.842	1.00
147_Y	150_M	0.842	1.00
191_N	195_E	0.838	1.00
143_H	151_L	0.823	1.00
76_H	89_R	0.816	1.00
236_A	240_A	0.807	1.00
125_Q	129_Q	0.801	1.00
85_F	88_Q	0.796	1.00
122_E	131_I	0.790	1.00
6_L	73_I	0.789	1.00
188_Q	191_N	0.786	1.00
126_R	131_I	0.784	1.00
45_I	205_I	0.784	1.00
95_Q	153_P	0.783	1.00
107_I	159_L	0.782	1.00
157_Q	180_S	0.779	1.00
191_N	194_L	0.779	1.00
153_P	158_R	0.778	1.00
225_H	244_H	0.774	1.00
139_L	142_D	0.773	1.00
41_Q	232_R	0.771	1.00
115_L	126_R	0.769	1.00
115_L	118_N	0.769	1.00
126_R	130_I	0.769	1.00
138_G	188_Q	0.769	1.00
49_N	185_M	0.760	1.00
51_S	224_M	0.759	1.00
42_T	194_L	0.759	1.00
121_L	126_R	0.758	1.00
65_E	79_H	0.754	1.00
178_L	189_L	0.753	1.00
42_T	217_I	0.753	1.00
143_H	155_Q	0.749	1.00
190_I	216_H	0.746	1.00
46_I	223_V	0.743	1.00
133_T	137_V	0.742	1.00
116_R	126_R	0.741	1.00
77_P	81_G	0.740	1.00
229_V	232_R	0.738	1.00
112_D	127_R	0.736	1.00
102_N	113_F	0.735	1.00
195_E	200_Q	0.733	1.00
93_I	164_A	0.725	1.00
66_P	79_H	0.715	1.00
59_M	64_I	0.710	1.00
173_I	205_I	0.709	1.00
46_I	214_M	0.707	1.00
6_L	171_V	0.703	1.00
106_R	145_S	0.701	1.00
39_E	203_S	0.698	1.00
121_L	125_Q	0.696	1.00
15_F	64_I	0.696	1.00
193_M	204_Y	0.696	1.00
97_P	160_G	0.695	1.00
127_R	130_I	0.694	1.00
231_E	238_V	0.691	1.00
46_I	211_I	0.690	1.00
104_R	149_H	0.690	1.00
28_E	32_P	0.682	1.00
132_E	168_R	0.680	1.00
30_V	56_L	0.679	1.00
191_N	216_H	0.678	1.00
98_S	156_K	0.678	1.00
101_L	148_P	0.676	1.00
5_L	73_I	0.673	1.00
14_T	68_S	0.670	1.00
148_P	159_L	0.670	1.00
72_L	75_D	0.669	1.00
6_L	60_L	0.669	1.00
237_D	240_A	0.668	1.00
106_R	110_I	0.668	1.00
76_H	85_F	0.662	1.00
14_T	31_K	0.661	1.00
10_N	13_K	0.660	1.00
139_L	143_H	0.659	1.00
235_T	239_L	0.656	1.00
32_P	68_S	0.653	1.00
125_Q	134_M	0.652	1.00
151_L	155_Q	0.651	1.00
33_L	229_V	0.646	1.00
7_E	75_D	0.645	1.00
187_S	216_H	0.644	1.00
111_L	134_M	0.644	1.00
39_E	201_G	0.641	1.00
171_V	203_S	0.640	1.00
70_E	79_H	0.640	1.00
73_I	171_V	0.638	1.00
76_H	81_G	0.631	1.00
133_T	165_L	0.627	1.00
60_L	71_L	0.624	1.00
190_I	217_I	0.624	1.00
115_L	167_L	0.621	1.00
108_S	141_P	0.620	1.00
38_R	203_S	0.618	1.00
208_T	213_M	0.613	1.00
218_S	235_T	0.613	1.00
49_N	209_Q	0.611	1.00
185_M	188_Q	0.610	1.00
206_Y	217_I	0.608	1.00
84_S	88_Q	0.606	1.00
36_T	232_R	0.606	1.00
108_S	111_L	0.604	1.00
125_Q	131_I	0.603	1.00
5_L	171_V	0.603	1.00
60_L	173_I	0.603	1.00
5_L	203_S	0.601	1.00
49_N	158_R	0.599	1.00
133_T	136_M	0.598	1.00
85_F	89_R	0.597	1.00
94_F	97_P	0.596	1.00
214_M	218_S	0.595	1.00
96_D	156_K	0.595	1.00
111_L	125_Q	0.593	1.00
182_D	185_M	0.592	1.00
112_D	116_R	0.590	1.00
14_T	27_V	0.588	1.00
110_I	148_P	0.587	1.00
91_R	167_L	0.581	1.00
215_K	239_L	0.580	1.00
59_M	67_T	0.578	1.00
120_D	166_I	0.576	1.00
35_F	43_L	0.575	1.00
53_K	176_E	0.575	1.00
54_S	58_K	0.574	1.00
40_G	203_S	0.572	1.00
152_A	155_Q	0.572	1.00
103_P	156_K	0.571	1.00
45_I	207_V	0.571	1.00
142_D	146_Y	0.570	1.00
90_I	171_V	0.569	1.00
215_K	235_T	0.568	1.00
97_P	156_K	0.566	1.00
13_K	29_A	0.566	1.00
196_L	200_Q	0.562	1.00
213_M	217_I	0.560	1.00
105_Q	113_F	0.559	1.00
53_K	175_D	0.555	1.00
49_N	176_E	0.554	1.00
225_H	228_E	0.550	1.00
223_V	238_V	0.548	1.00
102_N	110_I	0.547	1.00
31_K	226_Q	0.545	1.00
105_Q	110_I	0.539	1.00
197_Q	202_I	0.538	1.00
74_D	171_V	0.536	1.00
13_K	30_V	0.534	1.00
86_R	90_I	0.534	1.00
83_Y	86_R	0.533	1.00
142_D	155_Q	0.533	1.00
53_K	209_Q	0.532	1.00
137_V	192_L	0.531	1.00
28_E	68_S	0.530	1.00
16_R	28_E	0.528	1.00
210_H	213_M	0.527	1.00
231_E	237_D	0.525	1.00
214_M	235_T	0.522	1.00
128_K	131_I	0.521	1.00
6_L	205_I	0.521	1.00
111_L	159_L	0.519	1.00
161_L	189_L	0.518	1.00
54_S	175_D	0.514	1.00
189_L	192_L	0.512	1.00
235_T	238_V	0.511	1.00
165_L	202_I	0.506	1.00
206_Y	218_S	0.506	1.00
13_K	16_R	0.505	1.00
95_Q	179_A	0.505	1.00
214_M	221_V	0.504	1.00
51_S	226_Q	0.502	1.00
158_R	188_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
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	0.9552	100	0.077	Contact Map
4f4cA	1	0.8545	100	0.09	Contact Map
4ry2A	2	0.8881	100	0.093	Contact Map
1g291	4	0.944	100	0.096	Contact Map
2yyzA	1	0.9328	100	0.099	Contact Map
4mkiB	2	0.9664	100	0.1	Contact Map
2it1A	1	0.9366	100	0.1	Contact Map
1v43A	2	0.9142	100	0.101	Contact Map
3rlfA	2	0.9328	100	0.102	Contact Map
3fvqA	2	0.944	100	0.103	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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