YURM - BACSU - GREMLIN Contacts

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YURM - Probable ABC transporter permease protein YurM

UniProt:	O32154	Sequences: MLPQKKTDSFRLEPVPDQHIEVKDKPRRKWYIGETSVWVFLFLYLIAIAYPLLWMVMSAFKNSDDIFEHSWSLPSSWHPENFVSAWNQGISSYFMNSVIVTALTCVITVFISAWAAYGLSRFEFKGKGFFLVLCLGGLMLTPQVSLVPLYSIIQSLGLYNTYWALILPYAAYRIPFTIILIRSYFLSISKELEEAAYLDGCTSFGVFFRIFLPMSVPILVTSGILTAYHTWNEFMFAIIFIDDENLRTIPAGLMQFRDALQTDWGVLLAGLTISAAPIIILFLLMQKYFVRGIASGSVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	300 (255)
Sequences:	69713 (46004)
Seq/√Len:	2880.9

ECOLI - YCJP POTH MALG YDCU UGPA UGPE PSTA YCJO PSTC POTB YDCV THIP POTI POTC MALF CYSW CYST YNJC MODB TAUC SSUC PHNE YEHY METI YEHW PROW
BACSU - YURM YESQ GANQ ARAP MDXG ARAQ GANP AMYC LPLC YTEP AMYD MDXF YTCP LPLB YESP YQGH YURN YQGI YTLD YVGM SSUC OPUAB TCYB TCYL YXEN METP OPUCB OPUBB OPUBD OPUCD
HALSA - Q9HHQ6 Q9HML6 Q9HP01 Q9HMT4 Q9HP02 Q9HHQ7 Q9HS11 Q9HR05 Q9HPK3 Q9HNI9
SULSO - Q97UF3 Q97UY9 Q97YY3 Q97ZC1 Q97YY2 Q97VC0 Q97UZ0 Q97ZT6 Q97UF4 Q97ZC2 Q97ZT7 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
205_G	209_R	3.913	1.00
95_M	99_I	3.273	1.00
197_Y	206_V	3.135	1.00
182_R	186_L	3.010	1.00
92_S	95_M	2.657	1.00
93_Y	252_G	2.543	1.00
121_R	193_E	2.512	1.00
184_Y	218_I	2.507	1.00
59_A	82_F	2.507	1.00
202_T	205_G	2.493	1.00
196_A	206_V	2.489	1.00
83_V	87_N	2.465	1.00
103_L	166_I	2.448	1.00
107_I	170_A	2.420	1.00
193_E	211_F	2.412	1.00
247_R	255_Q	2.403	1.00
91_S	95_M	2.399	1.00
203_S	206_V	2.328	1.00
80_E	83_V	2.312	1.00
105_C	223_G	2.258	1.00
80_E	84_S	2.207	1.00
181_I	219_L	2.188	1.00
204_F	208_F	2.179	1.00
263_D	266_V	2.155	1.00
124_F	127_K	2.118	1.00
201_C	205_G	2.041	1.00
205_G	208_F	1.998	1.00
177_T	222_S	1.965	1.00
113_A	207_F	1.951	1.00
196_A	201_C	1.925	1.00
53_L	57_M	1.918	1.00
192_L	214_M	1.909	1.00
185_F	215_S	1.904	1.00
120_S	186_L	1.897	1.00
57_M	61_K	1.894	1.00
160_N	164_A	1.871	1.00
113_A	215_S	1.853	1.00
131_L	182_R	1.840	1.00
92_S	96_N	1.773	1.00
109_V	223_G	1.753	1.00
197_Y	203_S	1.730	1.00
99_I	103_L	1.696	1.00
193_E	206_V	1.691	1.00
104_T	230_T	1.667	1.00
101_T	227_A	1.644	1.00
252_G	256_F	1.642	1.00
113_A	181_I	1.620	1.00
112_S	177_T	1.611	1.00
115_A	178_I	1.611	1.00
193_E	197_Y	1.595	1.00
84_S	266_V	1.565	1.00
119_L	178_I	1.517	1.00
84_S	87_N	1.517	1.00
190_K	193_E	1.512	1.00
38_W	42_F	1.488	1.00
126_G	129_F	1.463	1.00
89_G	92_S	1.453	1.00
177_T	226_T	1.434	1.00
123_E	127_K	1.426	1.00
56_V	272_T	1.420	1.00
54_W	58_S	1.410	1.00
50_Y	54_W	1.403	1.00
234_F	238_I	1.381	1.00
79_P	83_V	1.372	1.00
221_T	225_L	1.363	1.00
120_S	182_R	1.361	1.00
162_Y	246_L	1.355	1.00
236_F	240_F	1.341	1.00
247_R	252_G	1.340	1.00
110_F	114_W	1.335	1.00
108_T	226_T	1.331	1.00
116_A	181_I	1.321	1.00
212_L	219_L	1.318	1.00
100_V	248_T	1.313	1.00
181_I	222_S	1.309	1.00
185_F	211_F	1.302	1.00
160_N	163_W	1.293	1.00
190_K	194_E	1.289	1.00
121_R	190_K	1.280	1.00
78_H	81_N	1.280	1.00
196_A	210_I	1.266	1.00
191_E	194_E	1.254	1.00
129_F	132_V	1.244	1.00
113_A	219_L	1.229	1.00
65_D	76_S	1.209	1.00
234_F	254_M	1.205	1.00
109_V	219_L	1.202	1.00
96_N	99_I	1.201	1.00
32_I	36_S	1.201	1.00
106_V	110_F	1.200	1.00
31_Y	35_T	1.194	1.00
117_Y	185_F	1.193	1.00
255_Q	259_A	1.175	1.00
103_L	106_V	1.175	1.00
168_P	240_F	1.171	1.00
42_F	46_I	1.170	1.00
188_I	214_M	1.167	1.00
161_T	164_A	1.165	1.00
33_G	37_V	1.161	1.00
97_S	249_I	1.155	1.00
283_L	287_K	1.147	1.00
202_T	206_V	1.146	1.00
35_T	39_V	1.135	1.00
243_D	246_L	1.132	1.00
256_F	261_Q	1.132	1.00
241_I	246_L	1.131	1.00
55_M	272_T	1.122	1.00
216_V	220_V	1.122	1.00
62_N	65_D	1.118	1.00
84_S	88_Q	1.100	1.00
30_W	33_G	1.094	1.00
166_I	170_A	1.093	1.00
287_K	290_V	1.089	1.00
32_I	35_T	1.063	1.00
129_F	133_L	1.061	1.00
256_F	263_D	1.061	1.00
181_I	218_I	1.057	1.00
233_E	236_F	1.057	1.00
54_W	57_M	1.051	1.00
174_I	178_I	1.050	1.00
86_W	91_S	1.049	1.00
107_I	166_I	1.045	1.00
103_L	107_I	1.039	1.00
35_T	38_W	1.037	1.00
193_E	203_S	1.031	1.00
117_Y	203_S	1.030	1.00
120_S	185_F	1.024	1.00
247_R	251_A	1.022	1.00
99_I	162_Y	1.021	1.00
104_T	108_T	1.013	1.00
104_T	169_Y	1.012	1.00
117_Y	207_F	1.010	1.00
180_L	222_S	1.006	1.00
248_T	251_A	1.005	1.00
214_M	217_P	0.999	1.00
114_W	118_G	0.993	1.00
252_G	255_Q	0.978	1.00
98_V	102_A	0.976	1.00
64_D	67_F	0.960	1.00
106_V	223_G	0.960	1.00
158_L	163_W	0.955	1.00
206_V	209_R	0.947	1.00
201_C	206_V	0.943	1.00
30_W	34_E	0.941	1.00
34_E	38_W	0.934	1.00
37_V	41_L	0.934	1.00
127_K	186_L	0.928	1.00
165_L	237_A	0.923	1.00
99_I	102_A	0.920	1.00
82_F	272_T	0.907	1.00
151_S	155_S	0.902	1.00
58_S	61_K	0.898	1.00
85_A	273_I	0.897	1.00
128_G	131_L	0.895	1.00
252_G	270_G	0.894	1.00
284_L	288_Y	0.889	1.00
238_I	251_A	0.889	1.00
116_A	120_S	0.889	1.00
45_L	49_A	0.883	1.00
102_A	106_V	0.879	1.00
104_T	166_I	0.875	1.00
149_L	240_F	0.875	1.00
94_F	249_I	0.871	1.00
169_Y	230_T	0.871	1.00
184_Y	215_S	0.871	1.00
125_K	128_G	0.862	1.00
233_E	237_A	0.860	1.00
108_T	112_S	0.857	1.00
94_F	98_V	0.856	1.00
215_S	218_I	0.855	1.00
112_S	178_I	0.848	1.00
61_K	65_D	0.845	1.00
119_L	131_L	0.841	1.00
149_L	168_P	0.840	1.00
107_I	110_F	0.838	1.00
208_F	212_L	0.837	1.00
63_S	67_F	0.832	1.00
216_V	219_L	0.832	1.00
206_V	211_F	0.830	1.00
244_E	247_R	0.828	1.00
254_M	258_D	0.827	1.00
226_T	230_T	0.826	1.00
135_L	179_I	0.826	1.00
257_R	267_L	0.826	1.00
251_A	255_Q	0.826	1.00
237_A	248_T	0.823	1.00
150_Y	154_Q	0.823	1.00
177_T	181_I	0.822	1.00
118_G	124_F	0.822	1.00
181_I	215_S	0.818	1.00
168_P	236_F	0.814	1.00
47_A	51_P	0.814	1.00
207_F	212_L	0.811	1.00
95_M	98_V	0.803	1.00
142_P	172_Y	0.803	1.00
100_V	169_Y	0.800	1.00
278_I	282_F	0.799	1.00
280_I	284_L	0.796	1.00
90_I	270_G	0.796	1.00
59_A	63_S	0.794	1.00
81_N	265_G	0.791	1.00
216_V	288_Y	0.790	1.00
160_N	243_D	0.786	1.00
201_C	209_R	0.786	1.00
58_S	62_N	0.785	1.00
58_S	268_L	0.784	1.00
203_S	207_F	0.780	1.00
116_A	178_I	0.769	1.00
108_T	177_T	0.768	1.00
268_L	272_T	0.763	1.00
73_L	76_S	0.763	1.00
154_Q	159_Y	0.761	1.00
192_L	210_I	0.760	1.00
55_M	268_L	0.756	1.00
103_L	170_A	0.751	1.00
60_F	77_W	0.750	1.00
116_A	185_F	0.749	1.00
146_L	239_I	0.748	1.00
109_V	181_I	0.738	1.00
108_T	230_T	0.738	1.00
84_S	263_D	0.735	1.00
142_P	235_M	0.734	1.00
108_T	173_R	0.727	1.00
62_N	76_S	0.725	1.00
256_F	270_G	0.721	1.00
219_L	222_S	0.721	1.00
93_Y	96_N	0.720	1.00
115_A	174_I	0.716	1.00
279_I	283_L	0.715	1.00
101_T	105_C	0.715	1.00
88_Q	91_S	0.714	1.00
207_F	211_F	0.714	1.00
79_P	82_F	0.712	1.00
256_F	266_V	0.708	1.00
146_L	235_M	0.708	1.00
188_I	215_S	0.708	1.00
119_L	182_R	0.707	1.00
274_S	278_I	0.704	1.00
60_F	78_H	0.701	1.00
50_Y	53_L	0.698	1.00
266_V	270_G	0.697	1.00
36_S	39_V	0.695	1.00
195_A	199_D	0.693	1.00
119_L	130_F	0.693	1.00
190_K	197_Y	0.692	1.00
181_I	185_F	0.688	1.00
155_S	159_Y	0.686	1.00
105_C	227_A	0.685	1.00
211_F	214_M	0.679	1.00
218_I	222_S	0.679	1.00
265_G	268_L	0.679	1.00
100_V	165_L	0.678	1.00
135_L	138_L	0.678	1.00
55_M	271_L	0.675	1.00
83_V	86_W	0.674	1.00
112_S	181_I	0.673	1.00
249_I	274_S	0.672	1.00
285_M	288_Y	0.670	1.00
91_S	94_F	0.668	1.00
173_R	226_T	0.668	1.00
45_L	48_I	0.667	1.00
61_K	74_P	0.666	1.00
169_Y	172_Y	0.665	1.00
145_S	171_A	0.663	1.00
36_S	40_F	0.660	1.00
173_R	229_H	0.659	1.00
100_V	166_I	0.658	1.00
268_L	271_L	0.658	1.00
100_V	162_Y	0.654	1.00
77_W	80_E	0.653	1.00
81_N	84_S	0.649	1.00
105_C	109_V	0.647	1.00
151_S	154_Q	0.647	1.00
111_I	174_I	0.646	1.00
233_E	248_T	0.645	1.00
34_E	37_V	0.645	1.00
195_A	198_L	0.639	1.00
124_F	130_F	0.639	1.00
283_L	286_Q	0.638	1.00
65_D	75_S	0.632	1.00
149_L	152_I	0.631	1.00
165_L	169_Y	0.631	1.00
41_L	45_L	0.630	1.00
85_A	270_G	0.629	1.00
115_A	134_C	0.629	1.00
44_Y	48_I	0.628	1.00
219_L	223_G	0.628	1.00
111_I	170_A	0.628	1.00
96_N	246_L	0.627	1.00
235_M	238_I	0.623	1.00
125_K	129_F	0.621	1.00
85_A	266_V	0.617	1.00
118_G	122_F	0.616	1.00
39_V	42_F	0.615	1.00
156_L	159_Y	0.614	1.00
62_N	75_S	0.613	1.00
93_Y	249_I	0.612	1.00
165_L	241_I	0.611	1.00
134_C	175_P	0.610	1.00
100_V	104_T	0.608	1.00
78_H	82_F	0.607	1.00
180_L	218_I	0.606	1.00
97_S	250_P	0.605	1.00
132_V	136_G	0.604	1.00
126_G	130_F	0.603	1.00
250_P	253_L	0.603	1.00
255_Q	258_D	0.603	1.00
31_Y	34_E	0.602	1.00
131_L	179_I	0.600	1.00
253_L	270_G	0.597	1.00
74_P	77_W	0.594	1.00
62_N	66_I	0.593	1.00
284_L	287_K	0.590	1.00
76_S	79_P	0.589	1.00
108_T	170_A	0.587	1.00
264_W	267_L	0.586	1.00
229_H	232_N	0.586	1.00
82_F	269_A	0.585	1.00
89_G	252_G	0.585	1.00
250_P	274_S	0.584	1.00
208_F	211_F	0.583	1.00
230_T	233_E	0.582	1.00
123_E	128_G	0.582	1.00
223_G	226_T	0.582	1.00
220_V	223_G	0.582	1.00
101_T	231_W	0.581	1.00
117_Y	211_F	0.580	1.00
40_F	44_Y	0.580	1.00
142_P	146_L	0.579	1.00
206_V	210_I	0.579	1.00
49_A	53_L	0.577	1.00
280_I	283_L	0.575	1.00
138_L	175_P	0.574	1.00
101_T	230_T	0.574	1.00
97_S	231_W	0.573	1.00
116_A	182_R	0.572	1.00
122_F	203_S	0.571	1.00
146_L	150_Y	0.571	1.00
128_G	132_V	0.568	1.00
282_F	286_Q	0.568	1.00
59_A	269_A	0.566	1.00
264_W	268_L	0.565	1.00
76_S	80_E	0.564	1.00
143_Q	239_I	0.564	1.00
130_F	134_C	0.563	1.00
235_M	239_I	0.563	1.00
46_I	50_Y	0.559	1.00
241_I	245_N	0.559	1.00
228_Y	232_N	0.553	1.00
131_L	186_L	0.550	1.00
271_L	274_S	0.549	1.00
138_L	176_F	0.547	1.00
51_P	55_M	0.546	1.00
109_V	113_A	0.546	1.00
104_T	170_A	0.544	1.00
277_P	280_I	0.542	1.00
133_L	137_G	0.540	1.00
169_Y	233_E	0.540	1.00
123_E	190_K	0.538	1.00
172_Y	175_P	0.535	1.00
137_G	175_P	0.534	1.00
153_I	159_Y	0.532	1.00
194_E	197_Y	0.529	1.00
251_A	254_M	0.526	1.00
115_A	118_G	0.526	1.00
202_T	208_F	0.525	1.00
38_W	41_L	0.523	1.00
127_K	131_L	0.522	1.00
188_I	193_E	0.520	1.00
61_K	76_S	0.519	1.00
89_G	93_Y	0.515	1.00
43_L	47_A	0.515	1.00
153_I	164_A	0.514	1.00
58_S	63_S	0.514	1.00
123_E	126_G	0.510	1.00
57_M	60_F	0.510	1.00
110_F	113_A	0.508	1.00
226_T	229_H	0.507	1.00
105_C	230_T	0.507	1.00
92_S	99_I	0.503	1.00
82_F	86_W	0.500	1.00
109_V	114_W	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
3rlfG	1	0.8867	100	0.323	Contact Map
4tquN	1	0.89	100	0.333	Contact Map
2onkC	2	0.8067	100	0.351	Contact Map
3d31C	2	0.7867	100	0.375	Contact Map
4tquM	1	0.86	100	0.394	Contact Map
3rlfF	1	0.9267	100	0.423	Contact Map
4ymuD	2	0.7133	99.9	0.532	Contact Map
3tuiA	2	0.6933	99.9	0.551	Contact Map
3fymA	1	0.03	12.9	0.95	Contact Map
2m8rA	1	0.1767	12	0.95	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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