SAPB - ECOLI - GREMLIN Contacts

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SAPB - Peptide transport system permease protein SapB

UniProt:	P0AGH3	Sequences: MIIFTLRRILLLIVTLFLLTFVGFSLSYFTPHAPLQGASLWNAWVFWFNGLIHWDFGVSSINGQPIAEQLKEVFPATMELCILAFGFALIVGIPVGMIAGITRHKWQDNLINAIALLGFSIPVFWLALLLTLFCSLTLGWLPVSGRFDLLYEVKPITGFALIDAWLSDSPWRDEMIMSAIRHMILPVITLSVAPTTEVIRLMRISTIEVYDQNYVKAAATRGLSRFTILRRHVLHNALPPVIPRLGLQFSTMLTLAMITEMVFSWPGLGRWLINAIRQQDYAAISAGVMVCGSLVIIVNVISDILGAMANPLKHKEWYALR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG20255
Length:	321 (259)
Sequences:	28307 (18194)
Seq/√Len:	1130.5

ECOLI - SAPB DDPB YEJB DPPB NIKB OPPB GSIC YEJE DPPC NIKC SAPC DDPC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMX0 Q9HMI2 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97VK6 Q97VF8 Q97YQ0 Q97UH1 Q97UG4 Q97YP1 Q97UG3 Q97UH2 Q97VK7 Q97VF6 Q97YP2 Q97YP9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
206_T	233_V	2.819	1.00
28_Y	43_A	2.624	1.00
108_D	203_R	2.582	1.00
49_N	53_H	2.562	1.00
219_A	225_R	2.477	1.00
209_V	214_Y	2.468	1.00
223_L	227_T	2.435	1.00
83_L	187_V	2.415	1.00
45_V	49_N	2.405	1.00
95_V	111_I	2.400	1.00
227_T	231_R	2.380	1.00
76_A	265_W	2.346	1.00
209_V	212_Q	2.317	1.00
270_R	274_N	2.284	1.00
87_F	191_S	2.270	1.00
224_S	227_T	2.262	1.00
226_F	230_R	2.250	1.00
215_V	233_V	2.084	1.00
213_N	216_K	2.027	1.00
246_G	302_S	2.018	1.00
20_T	44_W	1.989	1.00
102_T	105_K	1.959	1.00
97_M	206_T	1.954	1.00
102_T	225_R	1.935	1.00
215_V	228_I	1.921	1.00
65_P	68_E	1.912	1.00
69_Q	271_W	1.900	1.00
41_W	45_V	1.899	1.00
98_I	102_T	1.891	1.00
90_I	94_P	1.874	1.00
198_V	248_Q	1.816	1.00
101_I	225_R	1.811	1.00
42_N	45_V	1.810	1.00
102_T	107_Q	1.768	1.00
100_G	206_T	1.739	1.00
106_W	110_L	1.737	1.00
214_Y	236_N	1.729	1.00
59_S	64_Q	1.700	1.00
33_A	36_Q	1.697	1.00
210_Y	233_V	1.688	1.00
62_N	69_Q	1.674	1.00
209_V	237_A	1.648	1.00
56_F	286_A	1.641	1.00
52_I	55_D	1.639	1.00
67_A	71_K	1.631	1.00
66_I	286_A	1.607	1.00
48_F	51_L	1.599	1.00
21_F	44_W	1.599	1.00
42_N	46_F	1.595	1.00
91_V	195_T	1.586	1.00
79_E	83_L	1.586	1.00
98_I	107_Q	1.577	1.00
107_Q	111_I	1.575	1.00
91_V	94_P	1.556	1.00
101_I	229_L	1.548	1.00
72_E	75_P	1.526	1.00
50_G	55_D	1.512	1.00
89_L	245_L	1.505	1.00
88_A	194_P	1.504	1.00
187_V	191_S	1.499	1.00
54_W	65_P	1.481	1.00
115_A	199_I	1.477	1.00
205_S	208_E	1.462	1.00
272_L	287_G	1.461	1.00
64_Q	68_E	1.454	1.00
111_I	199_I	1.453	1.00
46_F	49_N	1.448	1.00
61_I	274_N	1.424	1.00
275_A	283_A	1.402	1.00
217_A	221_R	1.401	1.00
85_F	245_L	1.400	1.00
96_G	100_G	1.391	1.00
92_G	198_V	1.388	1.00
208_E	212_Q	1.380	1.00
92_G	202_M	1.361	1.00
209_V	233_V	1.357	1.00
25_S	28_Y	1.345	1.00
113_A	116_L	1.342	1.00
45_V	48_F	1.338	1.00
6_L	10_L	1.333	1.00
106_W	109_N	1.333	1.00
17_F	21_F	1.326	1.00
46_F	50_G	1.323	1.00
243_P	306_G	1.295	1.00
95_V	199_I	1.288	1.00
209_V	215_V	1.288	1.00
125_W	129_L	1.286	1.00
56_F	67_A	1.285	1.00
250_S	295_V	1.282	1.00
100_G	210_Y	1.281	1.00
19_L	292_G	1.279	1.00
130_L	189_T	1.279	1.00
76_A	79_E	1.276	1.00
281_Y	285_S	1.271	1.00
201_L	244_R	1.266	1.00
97_M	229_L	1.265	1.00
203_R	207_I	1.256	1.00
39_S	42_N	1.254	1.00
132_L	137_T	1.245	1.00
23_G	74_F	1.238	1.00
61_I	278_Q	1.236	1.00
305_L	308_M	1.235	1.00
191_S	195_T	1.226	1.00
306_G	310_N	1.224	1.00
96_G	202_M	1.218	1.00
104_H	108_D	1.208	1.00
99_A	111_I	1.205	1.00
184_I	188_I	1.202	1.00
10_L	14_V	1.195	1.00
242_I	309_A	1.191	1.00
206_T	237_A	1.177	1.00
51_L	56_F	1.173	1.00
218_A	228_I	1.166	1.00
64_Q	69_Q	1.164	1.00
70_L	290_V	1.158	1.00
118_G	196_T	1.149	1.00
64_Q	72_E	1.145	1.00
218_A	223_L	1.123	1.00
202_M	206_T	1.104	1.00
218_A	232_H	1.102	1.00
97_M	234_L	1.101	1.00
202_M	241_V	1.101	1.00
16_L	293_S	1.091	1.00
114_I	118_G	1.072	1.00
109_N	113_A	1.068	1.00
273_I	277_R	1.067	1.00
24_F	28_Y	1.067	1.00
189_T	193_A	1.059	1.00
80_L	260_E	1.059	1.00
287_G	291_C	1.046	1.00
17_F	44_W	1.041	1.00
221_R	232_H	1.041	1.00
58_V	65_P	1.040	1.00
93_I	202_M	1.039	1.00
94_P	97_M	1.036	1.00
216_K	219_A	1.035	1.00
205_S	209_V	1.035	1.00
56_F	70_L	1.034	1.00
304_I	308_M	1.026	1.00
66_I	283_A	1.018	1.00
121_I	126_L	1.014	1.00
195_T	199_I	1.009	1.00
227_T	230_R	1.003	1.00
66_I	271_W	1.000	1.00
12_L	296_I	0.988	1.00
271_W	283_A	0.985	1.00
18_L	22_V	0.982	1.00
21_F	25_S	0.980	1.00
219_A	228_I	0.973	1.00
68_E	72_E	0.969	1.00
84_A	191_S	0.965	1.00
249_F	298_V	0.963	1.00
79_E	183_M	0.960	1.00
202_M	237_A	0.953	1.00
75_P	79_E	0.944	1.00
12_L	15_T	0.943	1.00
26_L	72_E	0.942	1.00
112_N	199_I	0.942	1.00
69_Q	283_A	0.937	1.00
84_A	190_L	0.937	1.00
218_A	221_R	0.931	1.00
133_F	137_T	0.928	1.00
127_A	189_T	0.925	1.00
275_A	284_I	0.924	1.00
14_V	17_F	0.921	1.00
239_P	306_G	0.920	1.00
110_L	114_I	0.916	1.00
108_D	207_I	0.915	1.00
286_A	289_M	0.915	1.00
84_A	88_A	0.911	1.00
282_A	286_A	0.907	1.00
184_I	187_V	0.904	1.00
73_V	271_W	0.898	1.00
242_I	302_S	0.893	1.00
7_R	10_L	0.891	1.00
79_E	82_I	0.889	1.00
223_L	228_I	0.888	1.00
20_T	47_W	0.872	1.00
70_L	286_A	0.871	1.00
297_I	301_I	0.870	1.00
123_V	259_T	0.866	1.00
93_I	241_V	0.860	1.00
298_V	302_S	0.860	1.00
109_N	112_N	0.860	1.00
225_R	228_I	0.858	1.00
13_I	17_F	0.856	1.00
96_G	206_T	0.856	1.00
107_Q	110_L	0.845	1.00
108_D	112_N	0.843	1.00
69_Q	72_E	0.839	1.00
137_T	185_L	0.835	1.00
123_V	127_A	0.833	1.00
37_G	42_N	0.826	1.00
273_I	276_I	0.817	1.00
244_R	248_Q	0.812	1.00
90_I	93_I	0.811	1.00
89_L	198_V	0.809	1.00
190_L	259_T	0.808	1.00
134_C	185_L	0.808	1.00
71_K	75_P	0.804	1.00
50_G	53_H	0.804	1.00
37_G	43_A	0.798	1.00
58_V	63_G	0.798	1.00
71_K	74_F	0.797	1.00
21_F	40_L	0.796	1.00
89_L	93_I	0.795	1.00
274_N	277_R	0.794	1.00
237_A	240_P	0.794	1.00
94_P	98_I	0.789	1.00
84_A	256_A	0.788	1.00
100_G	207_I	0.787	1.00
115_A	196_T	0.781	1.00
9_I	13_I	0.780	1.00
188_I	191_S	0.779	1.00
216_K	220_T	0.776	1.00
49_N	52_I	0.775	1.00
225_R	229_L	0.774	1.00
230_R	233_V	0.772	1.00
30_T	68_E	0.772	1.00
68_E	71_K	0.769	1.00
183_M	187_V	0.768	1.00
271_W	287_G	0.768	1.00
5_T	304_I	0.766	1.00
89_L	94_P	0.764	1.00
285_S	289_M	0.763	1.00
104_H	210_Y	0.761	1.00
83_L	265_W	0.761	1.00
43_A	46_F	0.757	1.00
95_V	195_T	0.749	1.00
28_Y	40_L	0.747	1.00
223_L	232_H	0.743	1.00
77_T	81_C	0.741	1.00
44_W	48_F	0.739	1.00
87_F	187_V	0.738	1.00
104_H	109_N	0.737	1.00
204_I	207_I	0.737	1.00
83_L	86_G	0.734	1.00
209_V	236_N	0.731	1.00
274_N	278_Q	0.731	1.00
212_Q	216_K	0.730	1.00
26_L	29_F	0.728	1.00
74_F	294_L	0.726	1.00
286_A	290_V	0.726	1.00
20_T	289_M	0.726	1.00
185_L	188_I	0.725	1.00
14_V	18_L	0.716	1.00
291_C	295_V	0.714	1.00
307_A	313_K	0.714	1.00
202_M	205_S	0.712	1.00
119_F	196_T	0.711	1.00
130_L	185_L	0.710	1.00
59_S	280_D	0.707	1.00
12_L	300_V	0.704	1.00
293_S	297_I	0.704	1.00
25_S	40_L	0.703	1.00
55_D	67_A	0.703	1.00
228_I	233_V	0.702	1.00
206_T	210_Y	0.701	1.00
306_G	313_K	0.700	1.00
32_H	53_H	0.700	1.00
82_I	86_G	0.697	1.00
99_A	108_D	0.694	1.00
12_L	297_I	0.687	1.00
285_S	288_V	0.686	1.00
250_S	298_V	0.685	1.00
246_G	298_V	0.683	1.00
226_F	229_L	0.682	1.00
27_S	31_P	0.681	1.00
54_W	58_V	0.679	1.00
25_S	29_F	0.677	1.00
258_I	261_M	0.675	1.00
23_G	27_S	0.675	1.00
205_S	237_A	0.674	1.00
10_L	304_I	0.674	1.00
272_L	275_A	0.670	1.00
45_V	50_G	0.669	1.00
205_S	240_P	0.668	1.00
91_V	191_S	0.665	1.00
19_L	294_L	0.665	1.00
92_G	96_G	0.662	1.00
301_I	305_L	0.659	1.00
88_A	191_S	0.657	1.00
28_Y	281_Y	0.651	1.00
23_G	288_V	0.651	1.00
40_L	43_A	0.650	1.00
16_L	296_I	0.641	1.00
194_P	197_E	0.639	1.00
70_L	287_G	0.639	1.00
135_S	185_L	0.633	1.00
47_W	50_G	0.632	1.00
193_A	196_T	0.628	1.00
9_I	300_V	0.621	1.00
207_I	210_Y	0.620	1.00
110_L	113_A	0.620	1.00
81_C	256_A	0.619	1.00
99_A	112_N	0.618	1.00
51_L	289_M	0.618	1.00
27_S	30_T	0.612	1.00
271_W	275_A	0.612	1.00
111_I	115_A	0.610	1.00
129_L	133_F	0.607	1.00
102_T	229_L	0.607	1.00
85_F	249_F	0.604	1.00
32_H	68_E	0.604	1.00
112_N	115_A	0.603	1.00
198_V	244_R	0.600	1.00
101_I	230_R	0.599	1.00
48_F	52_I	0.598	1.00
32_H	54_W	0.597	1.00
101_I	210_Y	0.596	1.00
295_V	299_N	0.594	1.00
260_E	264_S	0.593	1.00
59_S	62_N	0.593	1.00
284_I	288_V	0.593	1.00
197_E	248_Q	0.593	1.00
123_V	126_L	0.592	1.00
248_Q	251_T	0.592	1.00
223_L	226_F	0.588	1.00
23_G	28_Y	0.587	1.00
92_G	199_I	0.586	1.00
51_L	55_D	0.585	1.00
43_A	50_G	0.584	1.00
55_D	65_P	0.583	1.00
85_F	248_Q	0.582	1.00
10_L	13_I	0.579	1.00
44_W	47_W	0.576	1.00
83_L	184_I	0.574	1.00
7_R	11_L	0.573	1.00
5_T	11_L	0.573	1.00
194_P	251_T	0.571	1.00
115_A	195_T	0.569	1.00
21_F	41_W	0.568	1.00
132_L	136_L	0.563	1.00
12_L	18_L	0.562	1.00
86_G	90_I	0.561	1.00
78_M	82_I	0.560	1.00
91_V	95_V	0.556	1.00
186_P	260_E	0.556	1.00
196_T	199_I	0.556	1.00
307_A	314_H	0.552	1.00
32_H	35_L	0.551	1.00
69_Q	73_V	0.549	1.00
51_L	54_W	0.546	1.00
257_M	261_M	0.546	1.00
22_V	26_L	0.545	1.00
17_F	48_F	0.544	1.00
22_V	74_F	0.544	1.00
24_F	27_S	0.544	1.00
258_I	262_V	0.543	1.00
11_L	15_T	0.542	1.00
194_P	248_Q	0.542	1.00
215_V	219_A	0.542	1.00
47_W	51_L	0.540	1.00
261_M	270_R	0.539	1.00
256_A	259_T	0.539	1.00
80_L	187_V	0.539	1.00
126_L	193_A	0.537	1.00
230_R	235_H	0.535	1.00
99_A	203_R	0.535	1.00
197_E	244_R	0.534	1.00
271_W	274_N	0.532	1.00
201_L	205_S	0.527	1.00
123_V	192_V	0.526	1.00
300_V	304_I	0.525	1.00
49_N	54_W	0.525	1.00
105_K	108_D	0.525	1.00
259_T	262_V	0.524	1.00
22_V	71_K	0.519	1.00
74_F	78_M	0.518	1.00
198_V	202_M	0.518	1.00
191_S	194_P	0.517	1.00
16_L	297_I	0.516	1.00
81_C	249_F	0.515	1.00
113_A	117_L	0.515	1.00
224_S	228_I	0.514	1.00
100_G	108_D	0.514	1.00
89_L	241_V	0.513	1.00
250_S	302_S	0.513	1.00
8_R	11_L	0.512	1.00
31_P	67_A	0.511	1.00
127_A	131_T	0.511	1.00
188_I	192_V	0.510	1.00
31_P	68_E	0.509	1.00
32_H	279_Q	0.504	1.00
134_C	137_T	0.503	1.00
95_V	98_I	0.501	1.00
261_M	273_I	0.501	1.00
20_T	24_F	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
3tuiA	2	0.6511	99.9	0.662	Contact Map
4tquM	1	0.838	99.9	0.671	Contact Map
3rlfF	1	0.8318	99.9	0.676	Contact Map
3d31C	2	0.7632	99.8	0.692	Contact Map
2onkC	2	0.7757	99.8	0.697	Contact Map
4ymuD	2	0.6542	99.8	0.699	Contact Map
4tquN	1	0.7975	99.8	0.715	Contact Map
3rlfG	1	0.8224	99.8	0.722	Contact Map
2yevC	1	0.1059	7.8	0.963	Contact Map
1q16C	2	0.3863	5.1	0.966	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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