POTH - ECOLI - GREMLIN Contacts

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POTH - Putrescine transport system permease protein PotH

UniProt:	P31135	Sequences: MSTLEPAAQSKPPGGFKLWLSQLQMKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSVGEHG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11631
Length:	317 (258)
Sequences:	69554 (44619)
Seq/√Len:	2777.8

ECOLI - POTH YDCU YCJO UGPA POTB PSTC THIP MALG YCJP PSTA CYSW CYST YNJC MALF POTI YDCV UGPE POTC MODB TAUC YEHY SSUC PHNE YEHW METI PROW
BACSU - ARAP GANP YTEP AMYD YESP LPLB MDXF YURN YESQ YURM YQGH GANQ MDXG LPLC AMYC ARAQ YTCP YQGI YVGM SSUC YTLD OPUAB METP TCYB YXEN TCYL OPUCB OPUBB OPUBD
HALSA - Q9HP01 Q9HMT4 Q9HML6 Q9HHQ7 Q9HR05 Q9HP02 Q9HS11 Q9HHQ6 Q9HPK3 Q9HNI9
SULSO - Q97YY2 Q97UZ0 Q97YY3 Q97UF3 Q97UF4 Q97UY9 Q97ZT7 Q97ZC1 Q97ZC2 Q97VC0 Q97ZT6 Q97Z98

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
227_K	231_T	4.204	1.00
100_L	104_Q	3.210	1.00
55_S	86_F	3.037	1.00
204_Y	208_I	3.010	1.00
219_L	228_T	2.979	1.00
98_A	273_V	2.742	1.00
126_H	215_V	2.647	1.00
97_D	100_L	2.629	1.00
215_V	233_I	2.605	1.00
224_R	227_K	2.556	1.00
218_A	228_T	2.543	1.00
108_I	188_Y	2.471	1.00
112_C	192_V	2.459	1.00
84_G	87_L	2.452	1.00
96_F	100_L	2.387	1.00
268_I	276_Q	2.386	1.00
206_A	240_G	2.386	1.00
110_T	245_S	2.335	1.00
84_G	88_Q	2.315	1.00
226_L	230_F	2.309	1.00
203_I	241_I	2.307	1.00
225_P	228_T	2.272	1.00
118_Y	229_F	2.146	1.00
87_L	91_D	2.132	1.00
129_P	132_R	2.085	1.00
223_A	227_K	2.084	1.00
227_K	230_F	2.068	1.00
283_D	286_V	2.011	1.00
125_A	208_I	2.005	1.00
207_L	237_T	1.997	1.00
199_M	244_G	1.974	1.00
214_L	236_L	1.946	1.00
218_A	223_A	1.858	1.00
53_K	57_A	1.857	1.00
114_L	245_S	1.813	1.00
118_Y	237_T	1.809	1.00
49_L	53_K	1.793	1.00
97_D	101_Q	1.764	1.00
219_L	225_P	1.738	1.00
106_A	249_F	1.734	1.00
117_G	199_M	1.728	1.00
136_L	204_Y	1.721	1.00
215_V	228_T	1.715	1.00
303_M	307_K	1.698	1.00
124_V	200_V	1.650	1.00
104_Q	108_I	1.645	1.00
120_L	200_V	1.622	1.00
109_S	252_A	1.617	1.00
118_Y	203_I	1.617	1.00
88_Q	286_V	1.594	1.00
52_F	292_I	1.575	1.00
128_K	132_R	1.515	1.00
215_V	219_L	1.509	1.00
34_A	38_I	1.487	1.00
105_V	269_M	1.464	1.00
256_F	260_E	1.449	1.00
131_T	134_I	1.446	1.00
184_N	267_S	1.436	1.00
273_V	277_E	1.425	1.00
121_A	203_I	1.422	1.00
212_Y	215_V	1.418	1.00
234_V	241_I	1.415	1.00
46_L	50_I	1.406	1.00
243_A	247_L	1.395	1.00
125_A	204_Y	1.395	1.00
83_L	87_L	1.392	1.00
50_I	54_I	1.372	1.00
207_L	233_I	1.369	1.00
199_M	248_V	1.368	1.00
203_I	244_G	1.351	1.00
126_H	212_Y	1.323	1.00
218_A	232_V	1.314	1.00
82_N	85_N	1.311	1.00
113_C	248_V	1.308	1.00
256_F	275_W	1.302	1.00
190_G	262_L	1.299	1.00
94_L	97_D	1.292	1.00
115_L	119_P	1.286	1.00
212_Y	216_E	1.265	1.00
88_Q	91_D	1.261	1.00
258_I	262_L	1.260	1.00
104_Q	184_N	1.260	1.00
102_S	270_I	1.253	1.00
118_Y	241_I	1.219	1.00
122_W	207_L	1.218	1.00
263_G	267_S	1.217	1.00
277_E	283_D	1.214	1.00
158_L	186_A	1.186	1.00
213_S	216_E	1.183	1.00
108_I	111_F	1.182	1.00
224_R	228_T	1.180	1.00
210_I	236_L	1.172	1.00
29_R	33_I	1.162	1.00
86_F	292_I	1.161	1.00
187_V	259_P	1.158	1.00
38_I	42_L	1.154	1.00
61_R	80_T	1.153	1.00
27_H	31_L	1.139	1.00
51_V	292_I	1.132	1.00
111_F	115_L	1.131	1.00
134_I	137_L	1.130	1.00
203_I	240_G	1.125	1.00
307_K	310_Q	1.115	1.00
101_Q	104_Q	1.114	1.00
90_T	96_F	1.100	1.00
28_G	32_V	1.084	1.00
114_L	241_I	1.082	1.00
268_I	273_V	1.077	1.00
26_K	29_R	1.074	1.00
238_K	242_I	1.072	1.00
31_L	35_L	1.064	1.00
277_E	281_N	1.063	1.00
269_M	272_R	1.062	1.00
185_L	189_I	1.061	1.00
196_V	200_V	1.060	1.00
236_L	239_G	1.056	1.00
122_W	225_P	1.052	1.00
134_I	138_L	1.048	1.00
215_V	225_P	1.047	1.00
58_E	61_R	1.045	1.00
122_W	229_F	1.039	1.00
112_C	188_Y	1.039	1.00
202_P	244_G	1.032	1.00
276_Q	280_N	1.031	1.00
99_Y	270_I	1.031	1.00
125_A	207_L	1.028	1.00
108_I	112_C	1.027	1.00
109_S	191_I	1.023	1.00
156_G	160_N	1.018	1.00
109_S	113_C	1.018	1.00
88_Q	92_D	1.017	1.00
119_P	123_A	1.012	1.00
304_W	308_H	1.010	1.00
273_V	290_V	1.010	1.00
181_L	184_N	1.009	1.00
255_E	259_P	1.009	1.00
28_G	31_L	1.005	1.00
259_P	269_M	0.994	1.00
103_L	107_A	0.993	1.00
307_K	311_K	0.992	1.00
223_A	228_T	0.990	1.00
268_I	272_R	0.990	1.00
255_E	258_I	0.981	1.00
31_L	34_A	0.972	1.00
191_I	252_A	0.966	1.00
50_I	53_K	0.960	1.00
132_R	208_I	0.959	1.00
154_W	262_L	0.957	1.00
228_T	231_T	0.954	1.00
95_Y	290_V	0.948	1.00
188_Y	192_V	0.947	1.00
85_N	285_P	0.944	1.00
60_A	63_I	0.936	1.00
54_I	288_S	0.928	1.00
206_A	237_T	0.927	1.00
278_F	287_A	0.923	1.00
107_A	111_F	0.920	1.00
109_S	188_Y	0.919	1.00
130_S	133_N	0.918	1.00
89_L	293_I	0.903	1.00
121_A	125_A	0.901	1.00
104_Q	107_A	0.889	1.00
99_Y	103_L	0.889	1.00
238_K	241_I	0.888	1.00
104_Q	185_L	0.885	1.00
260_E	272_R	0.882	1.00
111_F	245_S	0.882	1.00
30_K	34_A	0.877	1.00
56_L	81_L	0.876	1.00
229_F	234_V	0.871	1.00
33_I	37_Y	0.870	1.00
154_W	190_G	0.870	1.00
237_T	240_G	0.866	1.00
41_I	45_L	0.863	1.00
113_C	117_G	0.861	1.00
117_G	200_V	0.857	1.00
26_K	30_K	0.856	1.00
199_M	203_I	0.852	1.00
133_N	136_L	0.848	1.00
51_V	288_S	0.847	1.00
151_V	257_V	0.847	1.00
112_C	115_L	0.847	1.00
230_F	234_V	0.845	1.00
140_I	201_L	0.843	1.00
147_F	194_A	0.839	1.00
203_I	237_T	0.839	1.00
277_E	290_V	0.824	1.00
108_I	192_V	0.823	1.00
248_V	252_A	0.817	1.00
124_V	136_L	0.817	1.00
56_L	82_N	0.816	1.00
57_A	61_R	0.816	1.00
121_A	207_L	0.814	1.00
88_Q	283_D	0.810	1.00
214_L	232_V	0.805	1.00
173_V	185_L	0.802	1.00
105_V	184_N	0.802	1.00
121_A	200_V	0.798	1.00
304_W	307_K	0.797	1.00
273_V	276_Q	0.788	1.00
151_V	261_L	0.787	1.00
59_M	63_I	0.787	1.00
51_V	291_A	0.785	1.00
190_G	258_I	0.780	1.00
100_L	103_L	0.780	1.00
46_L	49_L	0.779	1.00
105_V	191_I	0.779	1.00
54_I	57_A	0.778	1.00
228_T	233_I	0.776	1.00
210_I	237_T	0.775	1.00
300_V	304_W	0.775	1.00
123_A	129_P	0.771	1.00
155_M	159_K	0.767	1.00
225_P	229_F	0.765	1.00
182_H	265_P	0.763	1.00
186_A	190_G	0.763	1.00
102_S	271_G	0.762	1.00
275_W	279_F	0.759	1.00
277_E	286_V	0.755	1.00
286_V	290_V	0.753	1.00
25_M	29_R	0.752	1.00
229_F	233_I	0.751	1.00
212_Y	219_L	0.746	1.00
185_L	188_Y	0.746	1.00
113_C	199_M	0.746	1.00
124_V	135_L	0.743	1.00
35_L	38_I	0.742	1.00
120_L	196_V	0.738	1.00
98_A	270_I	0.735	1.00
274_L	290_V	0.734	1.00
288_S	292_I	0.732	1.00
98_A	101_Q	0.729	1.00
106_A	110_T	0.728	1.00
298_L	302_I	0.728	1.00
140_I	143_S	0.724	1.00
113_C	195_Y	0.722	1.00
114_L	203_I	0.722	1.00
203_I	207_L	0.712	1.00
92_D	96_F	0.711	1.00
238_K	308_H	0.710	1.00
186_A	262_L	0.709	1.00
255_E	269_M	0.707	1.00
124_V	204_Y	0.704	1.00
241_I	244_G	0.703	1.00
270_I	294_M	0.703	1.00
259_P	272_R	0.702	1.00
150_R	193_Y	0.700	1.00
32_V	36_P	0.699	1.00
110_T	249_F	0.697	1.00
87_L	90_T	0.692	1.00
58_E	80_T	0.691	1.00
110_T	114_L	0.685	1.00
57_A	78_S	0.684	1.00
223_A	231_T	0.682	1.00
117_G	203_I	0.682	1.00
32_V	35_L	0.682	1.00
55_S	59_M	0.681	1.00
96_F	99_Y	0.677	1.00
58_E	79_I	0.676	1.00
305_F	308_H	0.675	1.00
233_I	236_L	0.674	1.00
240_G	244_G	0.673	1.00
105_V	187_V	0.671	1.00
123_A	127_S	0.669	1.00
86_F	289_A	0.669	1.00
147_F	257_V	0.668	1.00
159_K	181_L	0.668	1.00
116_I	196_V	0.667	1.00
271_G	294_M	0.664	1.00
57_A	80_T	0.664	1.00
81_L	84_G	0.663	1.00
217_A	221_L	0.661	1.00
105_V	188_Y	0.658	1.00
143_S	197_P	0.655	1.00
187_V	191_I	0.654	1.00
89_L	286_V	0.653	1.00
195_Y	248_V	0.650	1.00
83_L	86_F	0.649	1.00
241_I	245_S	0.648	1.00
89_L	290_V	0.647	1.00
27_H	30_K	0.645	1.00
113_C	252_A	0.645	1.00
61_R	79_I	0.643	1.00
41_I	44_F	0.643	1.00
257_V	261_L	0.643	1.00
288_S	291_A	0.633	1.00
101_Q	267_S	0.633	1.00
128_K	133_N	0.632	1.00
93_P	97_D	0.630	1.00
263_G	268_I	0.629	1.00
156_G	159_K	0.629	1.00
40_L	44_F	0.628	1.00
202_P	240_G	0.624	1.00
131_T	135_L	0.624	1.00
116_I	192_V	0.624	1.00
217_A	220_D	0.623	1.00
113_C	192_V	0.620	1.00
37_Y	41_I	0.617	1.00
195_Y	251_P	0.612	1.00
106_A	252_A	0.605	1.00
181_L	185_L	0.605	1.00
120_L	139_V	0.603	1.00
54_I	58_E	0.602	1.00
143_S	198_F	0.599	1.00
129_P	135_L	0.599	1.00
250_I	254_G	0.598	1.00
136_L	201_L	0.597	1.00
55_S	289_A	0.597	1.00
102_S	253_V	0.596	1.00
77_L	80_T	0.594	1.00
121_A	204_Y	0.591	1.00
47_P	59_M	0.589	1.00
272_R	276_Q	0.587	1.00
139_V	197_P	0.586	1.00
284_W	287_A	0.584	1.00
52_F	56_L	0.580	1.00
154_W	157_I	0.579	1.00
274_L	291_A	0.576	1.00
93_P	96_F	0.575	1.00
82_N	86_F	0.574	1.00
294_M	298_L	0.572	1.00
148_L	261_L	0.570	1.00
114_L	118_Y	0.570	1.00
106_A	253_V	0.569	1.00
228_T	232_V	0.568	1.00
187_V	263_G	0.568	1.00
30_K	33_I	0.567	1.00
224_R	230_F	0.566	1.00
155_M	181_L	0.565	1.00
45_L	49_L	0.563	1.00
127_S	130_S	0.562	1.00
194_A	197_P	0.559	1.00
284_W	288_S	0.559	1.00
191_I	255_E	0.559	1.00
183_T	186_A	0.557	1.00
85_N	88_Q	0.555	1.00
285_P	288_S	0.555	1.00
145_T	149_I	0.553	1.00
299_I	303_M	0.552	1.00
135_L	139_V	0.552	1.00
105_V	109_S	0.551	1.00
128_K	212_Y	0.550	1.00
78_S	81_L	0.549	1.00
55_S	292_I	0.548	1.00
210_I	215_V	0.548	1.00
56_L	83_L	0.547	1.00
147_F	151_V	0.546	1.00
133_N	137_L	0.546	1.00
257_V	260_E	0.542	1.00
110_T	252_A	0.542	1.00
151_V	155_M	0.540	1.00
242_I	245_S	0.540	1.00
57_A	79_I	0.540	1.00
25_M	28_G	0.539	1.00
122_W	233_I	0.538	1.00
94_L	273_V	0.536	1.00
245_S	248_V	0.535	1.00
36_P	40_L	0.535	1.00
191_I	259_P	0.527	1.00
251_P	254_G	0.527	1.00
109_S	192_V	0.523	1.00
94_L	268_I	0.522	1.00
130_S	134_I	0.521	1.00
142_P	197_P	0.520	1.00
80_T	83_L	0.518	1.00
92_D	286_V	0.516	1.00
158_L	181_L	0.516	1.00
138_L	142_P	0.515	1.00
259_P	263_G	0.514	1.00
181_L	186_A	0.514	1.00
101_Q	269_M	0.514	1.00
104_Q	188_Y	0.513	1.00
137_L	141_L	0.512	1.00
114_L	119_P	0.512	1.00
282_R	286_V	0.511	1.00
230_F	233_I	0.510	1.00
244_G	248_V	0.509	1.00
80_T	84_G	0.509	1.00
120_L	123_A	0.508	1.00
90_T	293_I	0.507	1.00
184_N	188_Y	0.506	1.00
124_V	129_P	0.505	1.00
42_L	46_L	0.504	1.00
272_R	275_W	0.503	1.00
191_I	194_A	0.502	1.00
34_A	37_Y	0.501	1.00
127_S	132_R	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
2onkC	2	0.795	100	0.333	Contact Map
3d31C	2	0.7823	100	0.355	Contact Map
4tquM	1	0.8612	100	0.359	Contact Map
3rlfG	1	0.8454	100	0.409	Contact Map
3rlfF	1	0.9148	100	0.416	Contact Map
4tquN	1	0.8423	100	0.417	Contact Map
4ymuD	2	0.6782	100	0.54	Contact Map
3tuiA	2	0.6593	99.9	0.566	Contact Map
2kogA	1	0.1703	16.5	0.951	Contact Map
1pw4A	1	0.6688	12.9	0.953	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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