YJNA - BACSU - GREMLIN Contacts

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YJNA - UPF0721 transmembrane protein YjnA

UniProt:	O34578	Sequences: MSVSIILMGLFVGALVGLTGVGGAALLTPLLIVLGINPSIAVGTDLVYNSITKLFGVASHWRQKTINFKLVKYLAIGSIPSASLAIGILHLFPAFHQHQEEIIKHALGYVLTLVAISIIVRLFLDRKLRPNRWQLMPLENKRALTILIGVVFGFIVGLTSIGSGSLFAIAMIYLFNMKASQIVGTDIAHAFLLVTAAGILNASFGSVDYMLAANLLLGSIPGVLIGSHLSPRFSPRPLQFIMASIILVSGLKLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (237)
Sequences:	9621 (6532)
Seq/√Len:	424.3

ECOLI - YFCA
BACSU - YJNA YDHB YUNE YRKJ YTNM
HALSA - O54662
SULSO - Q981D0 Q97WF4 Q97UT0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_A	229_L	3.671	1.00
81_S	150_V	3.599	1.00
88_I	154_F	3.117	1.00
67_N	181_Q	2.889	1.00
6_I	218_G	2.729	1.00
61_W	68_F	2.511	1.00
236_R	240_F	2.493	1.00
51_I	216_L	2.485	1.00
148_I	170_A	2.432	1.00
237_P	240_F	2.410	1.00
75_A	192_L	2.399	1.00
55_F	220_I	2.352	1.00
8_M	30_L	2.345	1.00
116_I	120_V	2.342	1.00
71_V	188_A	2.204	1.00
178_K	181_Q	2.203	1.00
77_G	146_I	2.195	1.00
46_L	197_A	2.171	1.00
228_H	232_R	2.111	1.00
55_F	224_L	2.031	1.00
115_A	250_G	2.014	1.00
83_S	200_L	1.945	1.00
40_I	43_G	1.937	1.00
44_T	212_A	1.932	1.00
108_G	250_G	1.922	1.00
67_N	70_L	1.851	1.00
70_L	177_M	1.792	1.00
234_S	237_P	1.790	1.00
47_V	212_A	1.788	1.00
115_A	247_L	1.783	1.00
59_S	227_S	1.773	1.00
112_T	250_G	1.733	1.00
60_H	65_T	1.698	1.00
10_L	221_P	1.679	1.00
10_L	222_G	1.671	1.00
69_K	72_K	1.667	1.00
208_D	211_L	1.653	1.00
12_V	26_L	1.650	1.00
109_Y	113_L	1.649	1.00
152_F	166_L	1.646	1.00
87_G	91_L	1.631	1.00
9_G	215_L	1.620	1.00
119_I	243_A	1.615	1.00
31_L	215_L	1.609	1.00
79_I	196_A	1.590	1.00
115_A	243_A	1.573	1.00
150_V	154_F	1.572	1.00
72_K	76_I	1.532	1.00
63_Q	231_P	1.528	1.00
93_P	101_E	1.522	1.00
240_F	244_S	1.518	1.00
247_L	251_L	1.510	1.00
14_A	225_I	1.504	1.00
69_K	73_Y	1.471	1.00
213_A	217_L	1.444	1.00
84_L	150_V	1.442	1.00
60_H	230_S	1.438	1.00
72_K	75_A	1.436	1.00
57_V	188_A	1.432	1.00
54_L	191_F	1.429	1.00
202_A	209_Y	1.413	1.00
71_V	185_T	1.398	1.00
7_L	11_F	1.368	1.00
50_S	195_T	1.365	1.00
143_A	147_L	1.360	1.00
224_L	228_H	1.345	1.00
210_M	214_N	1.343	1.00
36_I	211_L	1.340	1.00
167_F	189_H	1.338	1.00
102_I	106_A	1.330	1.00
32_I	38_P	1.329	1.00
81_S	85_A	1.324	1.00
168_A	182_I	1.319	1.00
58_A	62_R	1.315	1.00
200_L	204_F	1.314	1.00
82_A	197_A	1.314	1.00
56_G	187_I	1.312	1.00
199_I	203_S	1.299	1.00
217_L	221_P	1.291	1.00
123_F	126_R	1.274	1.00
6_I	214_N	1.267	1.00
110_V	159_T	1.265	1.00
37_N	40_I	1.259	1.00
68_F	72_K	1.247	1.00
65_T	231_P	1.242	1.00
65_T	184_G	1.230	1.00
86_I	200_L	1.227	1.00
40_I	208_D	1.226	1.00
145_T	175_F	1.224	1.00
78_S	193_L	1.221	1.00
83_S	87_G	1.219	1.00
244_S	248_V	1.215	1.00
222_G	225_I	1.193	1.00
206_S	210_M	1.181	1.00
57_V	61_W	1.172	1.00
56_G	223_V	1.158	1.00
108_G	112_T	1.154	1.00
120_V	123_F	1.153	1.00
222_G	226_G	1.134	1.00
92_F	158_L	1.132	1.00
218_G	222_G	1.125	1.00
9_G	218_G	1.124	1.00
172_I	182_I	1.123	1.00
86_I	197_A	1.112	1.00
68_F	71_V	1.109	1.00
190_A	193_L	1.105	1.00
54_L	58_A	1.101	1.00
123_F	127_K	1.099	1.00
19_T	241_I	1.093	1.00
77_G	149_G	1.088	1.00
141_K	144_L	1.074	1.00
42_V	201_N	1.066	1.00
118_I	242_M	1.056	1.00
237_P	241_I	1.052	1.00
61_W	66_I	1.050	1.00
60_H	227_S	1.045	1.00
163_S	167_F	1.043	1.00
52_T	219_S	1.042	1.00
102_I	105_H	1.042	1.00
172_I	179_A	1.040	1.00
94_A	101_E	1.037	1.00
143_A	146_I	1.037	1.00
101_E	105_H	1.034	1.00
74_L	189_H	1.025	1.00
59_S	63_Q	1.020	1.00
57_V	68_F	1.017	1.00
84_L	87_G	1.006	1.00
77_G	81_S	1.006	1.00
57_V	191_F	1.000	1.00
180_S	230_S	0.992	1.00
81_S	154_F	0.982	1.00
27_L	215_L	0.981	1.00
45_D	49_N	0.978	1.00
168_A	186_D	0.971	1.00
78_S	189_H	0.971	1.00
35_G	41_A	0.963	1.00
147_L	151_V	0.963	1.00
74_L	171_M	0.962	1.00
163_S	169_I	0.959	1.00
179_A	183_V	0.957	1.00
59_S	224_L	0.954	1.00
55_F	223_V	0.953	1.00
4_S	7_L	0.949	1.00
89_L	201_N	0.948	1.00
6_I	217_L	0.948	1.00
87_G	90_H	0.941	1.00
6_I	10_L	0.940	1.00
113_L	117_S	0.939	1.00
76_I	80_P	0.938	1.00
149_G	167_F	0.931	1.00
213_A	216_L	0.929	1.00
230_S	238_L	0.924	1.00
161_I	165_S	0.922	1.00
105_H	109_Y	0.915	1.00
60_H	184_G	0.911	1.00
59_S	228_H	0.910	1.00
12_V	27_L	0.900	1.00
248_V	251_L	0.893	1.00
86_I	196_A	0.892	1.00
5_I	214_N	0.888	1.00
112_T	247_L	0.886	1.00
228_H	231_P	0.885	1.00
5_I	211_L	0.872	1.00
43_G	207_V	0.871	1.00
242_M	246_I	0.854	1.00
168_A	183_V	0.852	1.00
116_I	247_L	0.848	1.00
85_A	154_F	0.846	1.00
28_T	45_D	0.844	1.00
82_A	86_I	0.840	1.00
10_L	218_G	0.839	1.00
88_I	91_L	0.839	1.00
50_S	198_G	0.833	1.00
80_P	84_L	0.829	1.00
112_T	116_I	0.829	1.00
214_N	218_G	0.828	1.00
221_P	224_L	0.827	1.00
47_V	198_G	0.826	1.00
121_R	124_L	0.826	1.00
61_W	64_K	0.825	1.00
66_I	185_T	0.821	1.00
44_T	207_V	0.821	1.00
84_L	154_F	0.818	1.00
40_I	44_T	0.816	1.00
144_L	147_L	0.816	1.00
101_E	104_K	0.813	1.00
24_A	157_G	0.801	1.00
156_V	193_L	0.799	1.00
17_G	56_G	0.797	1.00
63_Q	228_H	0.786	1.00
43_G	198_G	0.779	1.00
10_L	225_I	0.770	1.00
9_G	27_L	0.770	1.00
233_F	237_P	0.768	1.00
59_S	62_R	0.760	1.00
84_L	88_I	0.760	1.00
77_G	80_P	0.759	1.00
167_F	171_M	0.759	1.00
223_V	227_S	0.758	1.00
51_I	220_I	0.758	1.00
188_A	192_L	0.756	1.00
32_I	41_A	0.750	1.00
53_K	190_A	0.749	1.00
106_A	159_T	0.748	1.00
36_I	40_I	0.746	1.00
152_F	163_S	0.743	1.00
18_L	226_G	0.742	1.00
55_F	59_S	0.741	1.00
16_V	24_A	0.738	1.00
73_Y	142_R	0.736	1.00
149_G	153_G	0.736	1.00
201_N	206_S	0.736	1.00
94_A	104_K	0.734	1.00
90_H	204_F	0.728	1.00
105_H	108_G	0.721	1.00
73_Y	76_I	0.720	1.00
125_D	128_L	0.719	1.00
39_S	43_G	0.718	1.00
5_I	215_L	0.718	1.00
87_G	204_F	0.717	1.00
86_I	201_N	0.714	1.00
58_A	61_W	0.714	1.00
121_R	239_Q	0.713	1.00
27_L	31_L	0.711	1.00
4_S	8_M	0.709	1.00
156_V	163_S	0.705	1.00
210_M	213_A	0.702	1.00
10_L	14_A	0.701	1.00
18_L	233_F	0.698	1.00
71_V	189_H	0.696	1.00
17_G	227_S	0.696	1.00
127_K	130_P	0.694	1.00
78_S	167_F	0.694	1.00
114_V	165_S	0.684	1.00
139_E	143_A	0.684	1.00
176_N	182_I	0.682	1.00
15_L	26_L	0.681	1.00
18_L	238_L	0.676	1.00
74_L	149_G	0.675	1.00
234_S	238_L	0.675	1.00
225_I	228_H	0.674	1.00
53_K	191_F	0.665	1.00
12_V	30_L	0.664	0.99
36_I	208_D	0.664	0.99
87_G	200_L	0.662	0.99
144_L	170_A	0.662	0.99
198_G	212_A	0.659	0.99
115_A	246_I	0.658	0.99
93_P	102_I	0.658	0.99
160_S	163_S	0.656	0.99
14_A	222_G	0.654	0.99
138_L	141_K	0.653	0.99
66_I	71_V	0.653	0.99
6_I	9_G	0.652	0.99
48_Y	219_S	0.650	0.99
88_I	92_F	0.648	0.99
170_A	174_L	0.646	0.99
69_K	142_R	0.645	0.99
49_N	53_K	0.641	0.99
65_T	181_Q	0.639	0.99
229_L	233_F	0.638	0.99
166_L	169_I	0.636	0.99
27_L	48_Y	0.633	0.99
9_G	13_G	0.632	0.99
180_S	235_P	0.628	0.99
24_A	49_N	0.627	0.99
179_A	242_M	0.626	0.99
220_I	224_L	0.625	0.99
54_L	57_V	0.623	0.99
163_S	190_A	0.623	0.99
209_Y	213_A	0.623	0.99
68_F	188_A	0.621	0.99
46_L	49_N	0.616	0.99
92_F	102_I	0.616	0.99
137_P	140_N	0.615	0.99
235_P	239_Q	0.613	0.99
115_A	119_I	0.612	0.99
42_V	89_L	0.612	0.99
181_Q	184_G	0.610	0.99
207_V	212_A	0.610	0.99
67_N	72_K	0.608	0.99
152_F	167_F	0.607	0.99
212_A	216_L	0.606	0.99
13_G	23_G	0.605	0.99
16_V	156_V	0.602	0.99
49_N	163_S	0.602	0.99
187_I	190_A	0.601	0.99
195_T	199_I	0.596	0.99
236_R	239_Q	0.593	0.99
44_T	208_D	0.593	0.99
18_L	229_L	0.591	0.99
229_L	232_R	0.589	0.99
198_G	202_A	0.588	0.99
38_P	42_V	0.586	0.99
38_P	103_I	0.584	0.99
39_S	42_V	0.584	0.99
42_V	46_L	0.580	0.99
16_V	26_L	0.579	0.99
118_I	243_A	0.579	0.99
177_M	181_Q	0.578	0.99
46_L	160_S	0.578	0.99
25_A	111_L	0.577	0.99
170_A	175_F	0.576	0.99
6_I	221_P	0.573	0.99
83_S	203_S	0.568	0.98
53_K	160_S	0.566	0.98
49_N	156_V	0.566	0.98
75_A	78_S	0.566	0.98
42_V	103_I	0.557	0.98
147_L	150_V	0.556	0.98
16_V	21_V	0.555	0.98
182_I	186_D	0.555	0.98
240_F	243_A	0.555	0.98
82_A	196_A	0.555	0.98
47_V	216_L	0.552	0.98
112_T	251_L	0.551	0.98
19_T	245_I	0.550	0.98
22_G	50_S	0.549	0.98
164_G	223_V	0.546	0.98
139_E	142_R	0.545	0.98
14_A	18_L	0.545	0.98
36_I	44_T	0.542	0.98
90_H	206_S	0.541	0.98
39_S	103_I	0.538	0.98
145_T	171_M	0.538	0.98
70_L	74_L	0.535	0.98
20_G	162_G	0.534	0.98
13_G	219_S	0.532	0.98
27_L	45_D	0.529	0.98
94_A	158_L	0.528	0.98
197_A	200_L	0.526	0.97
33_V	252_K	0.526	0.97
221_P	225_I	0.526	0.97
202_A	207_V	0.525	0.97
19_T	223_V	0.524	0.97
67_N	185_T	0.524	0.97
16_V	52_T	0.523	0.97
30_L	34_L	0.522	0.97
160_S	186_D	0.522	0.97
46_L	156_V	0.521	0.97
36_I	41_A	0.520	0.97
167_F	190_A	0.518	0.97
74_L	196_A	0.514	0.97
186_D	190_A	0.511	0.97
16_V	190_A	0.510	0.97
177_M	182_I	0.509	0.97
53_K	194_V	0.509	0.97
17_G	223_V	0.508	0.97
38_P	104_K	0.507	0.97
171_M	189_H	0.505	0.97
248_V	252_K	0.502	0.97
117_S	121_R	0.501	0.97
57_V	184_G	0.501	0.97
123_F	240_F	0.500	0.97
164_G	186_D	0.500	0.97
17_G	183_V	0.500	0.97

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
3o7qA	1	0.874	84.3	0.901	Contact Map
2gfpA	2	0.8346	83.1	0.903	Contact Map
1pw4A	1	0.8425	79.2	0.907	Contact Map
4j05A	3	0.8465	74.3	0.911	Contact Map
3wdoA	1	0.8346	61.8	0.918	Contact Map
4m64A	1	0.878	60.5	0.918	Contact Map
2cfqA	1	0.8386	59.9	0.919	Contact Map
4pypA	1	0.8425	56.7	0.92	Contact Map
4xnjA	1	0.9331	40.1	0.928	Contact Map
4rp9A	2	0.4724	34.4	0.93	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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