YTBQ - BACSU - GREMLIN Contacts

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YTBQ - Uncharacterized protein YtbQ

UniProt:	P53560	Sequences: MKKVLIAGGNGVIGRLLAEGLISDYEVTVLDKDHFDGKASSIQADAANYEELLKKIPKDTDAILNLLAVKIKYDIMDIAEFEKMTDVFYRASYYLCRAAAELGIQKLVFASSNHVTDVYEKDGRSLLGREITTSDYPLSKNLYGVLKLTSEQIGHLFYLENKLSVINLRIGTVVTDEMDTLHEKERTKKTLLSHPDLLSIFKAAIETNIRYGTYYAVSDNPGRPWSIESAVNELGFSPQINTAELLNEEENGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	253 (232)
Sequences:	53314 (35905)
Seq/√Len:	2357.3

ECOLI - RMLB2 RMLB1 GM4D GALE HLDD YBJS FCL YFCH RMLD YEEZ ARNA YRAR QOR2
BACSU - YTBQ RMLB YFNG GALE YTCB SPSK YFHF YHEG YWNB YHFK YESF
HALSA - Q9HSQ3 Q9HSU9 Q9HSV1 Q9HRD1 Q9HSE7 Q9HS50 Q9HML4 Q9HNV3 Q9HPF1 Q9HR86
SULSO - Q97VN5 Q980W1 Q97UM3 Q7LXG5 Q7LXE8 Q97XG1 Q97XJ9 Q7LX44 Q7LXE6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_G	29_V	3.228	1.00
3_K	26_E	2.824	1.00
20_G	199_S	2.749	1.00
86_D	90_R	2.639	1.00
241_N	244_E	2.395	1.00
62_A	205_I	2.289	1.00
80_E	83_K	2.276	1.00
106_K	164_S	2.204	1.00
110_A	201_F	2.179	1.00
231_V	237_S	2.171	1.00
30_L	44_A	2.095	1.00
65_N	109_F	2.092	1.00
132_T	135_D	2.079	1.00
20_G	24_D	2.064	1.00
44_A	51_E	2.020	1.00
20_G	202_K	2.009	1.00
199_S	239_Q	1.998	1.00
64_L	205_I	1.995	1.00
170_I	201_F	1.973	1.00
48_N	51_E	1.969	1.00
7_A	65_N	1.953	1.00
28_T	60_T	1.919	1.00
5_L	60_T	1.910	1.00
154_G	165_V	1.896	1.00
6_I	18_A	1.869	1.00
3_K	28_T	1.861	1.00
174_V	245_L	1.850	1.00
24_D	206_E	1.824	1.00
199_S	203_A	1.820	1.00
28_T	40_S	1.813	1.00
228_E	232_N	1.769	1.00
168_L	204_A	1.766	1.00
26_E	40_S	1.763	1.00
28_T	42_I	1.712	1.00
111_S	115_V	1.710	1.00
49_Y	97_R	1.695	1.00
47_A	86_D	1.694	1.00
93_Y	153_I	1.643	1.00
92_S	150_S	1.620	1.00
17_L	198_L	1.615	1.00
17_L	64_L	1.613	1.00
202_K	206_E	1.611	1.00
90_R	93_Y	1.598	1.00
93_Y	97_R	1.594	1.00
24_D	202_K	1.577	1.00
137_P	148_L	1.554	1.00
33_D	41_S	1.551	1.00
66_L	110_A	1.539	1.00
85_T	149_T	1.534	1.00
100_A	161_N	1.533	1.00
148_L	152_Q	1.524	1.00
61_D	105_Q	1.496	1.00
17_L	66_L	1.465	1.00
20_G	23_S	1.462	1.00
63_I	99_A	1.448	1.00
49_Y	94_Y	1.445	1.00
4_V	25_Y	1.442	1.00
88_F	146_L	1.434	1.00
13_I	173_V	1.412	1.00
230_A	234_L	1.404	1.00
82_E	86_D	1.391	1.00
20_G	198_L	1.379	1.00
203_A	207_T	1.378	1.00
18_A	29_V	1.356	1.00
133_T	229_S	1.354	1.00
19_E	177_E	1.352	1.00
96_C	157_F	1.322	1.00
106_K	166_I	1.321	1.00
95_L	107_L	1.319	1.00
46_A	91_A	1.318	1.00
9_G	18_A	1.315	1.00
131_I	135_D	1.310	1.00
244_E	247_N	1.308	1.00
64_L	201_F	1.305	1.00
143_Y	147_K	1.303	1.00
25_Y	206_E	1.300	1.00
152_Q	155_H	1.299	1.00
193_S	245_L	1.294	1.00
99_A	107_L	1.277	1.00
192_L	197_L	1.265	1.00
10_N	31_D	1.262	1.00
170_I	197_L	1.261	1.00
171_G	225_W	1.251	1.00
110_A	170_I	1.247	1.00
28_T	58_K	1.234	1.00
227_I	231_V	1.229	1.00
65_N	92_S	1.227	1.00
97_R	100_A	1.221	1.00
158_Y	165_V	1.218	1.00
227_I	238_P	1.212	1.00
5_L	30_L	1.209	1.00
22_I	39_A	1.208	1.00
109_F	150_S	1.205	1.00
145_V	149_T	1.204	1.00
109_F	154_G	1.201	1.00
20_G	195_P	1.193	1.00
29_V	39_A	1.179	1.00
96_C	107_L	1.177	1.00
155_H	167_N	1.173	1.00
168_L	201_F	1.152	1.00
57_P	60_T	1.137	1.00
16_L	195_P	1.137	1.00
109_F	167_N	1.135	1.00
21_L	202_K	1.128	1.00
194_H	198_L	1.128	1.00
57_P	63_I	1.110	1.00
97_R	101_E	1.110	1.00
69_V	87_V	1.107	1.00
99_A	104_I	1.106	1.00
46_A	67_L	1.105	1.00
19_E	23_S	1.101	1.00
4_V	62_A	1.090	1.00
108_V	168_L	1.070	1.00
66_L	201_F	1.069	1.00
106_K	208_N	1.061	1.00
98_A	102_L	1.055	1.00
229_S	233_E	1.054	1.00
100_A	163_L	1.054	1.00
16_L	194_H	1.053	1.00
35_F	39_A	1.051	1.00
107_L	154_G	1.042	1.00
122_D	130_E	1.039	1.00
52_L	98_A	1.033	1.00
96_C	154_G	1.022	1.00
40_S	58_K	1.012	1.00
4_V	21_L	1.010	1.00
22_I	38_K	1.004	1.00
87_V	91_A	1.003	1.00
173_V	197_L	0.997	1.00
15_R	177_E	0.996	1.00
54_K	101_E	0.994	1.00
90_R	94_Y	0.989	1.00
3_K	61_D	0.984	1.00
156_L	160_E	0.983	1.00
153_I	156_L	0.981	1.00
30_L	52_L	0.981	1.00
155_H	165_V	0.980	1.00
3_K	60_T	0.975	1.00
94_Y	97_R	0.967	1.00
151_E	169_R	0.963	1.00
132_T	226_S	0.960	1.00
3_K	25_Y	0.956	1.00
57_P	102_L	0.953	1.00
193_S	196_D	0.952	1.00
174_V	193_S	0.945	1.00
111_S	151_E	0.942	1.00
57_P	98_A	0.937	1.00
12_V	194_H	0.935	1.00
85_T	89_Y	0.925	1.00
34_H	43_Q	0.925	1.00
89_Y	149_T	0.920	1.00
33_D	43_Q	0.911	1.00
22_I	27_V	0.911	1.00
18_A	27_V	0.908	1.00
98_A	101_E	0.899	1.00
51_E	56_I	0.898	1.00
155_H	159_L	0.898	1.00
4_V	64_L	0.895	1.00
47_A	87_V	0.894	1.00
7_A	67_L	0.893	1.00
17_L	21_L	0.890	1.00
50_E	54_K	0.886	1.00
166_I	204_A	0.884	1.00
85_T	90_R	0.881	1.00
113_N	171_G	0.880	1.00
30_L	51_E	0.879	1.00
121_K	132_T	0.876	1.00
32_K	45_D	0.874	1.00
84_M	146_L	0.873	1.00
243_A	247_N	0.872	1.00
42_I	56_I	0.870	1.00
166_I	208_N	0.870	1.00
12_V	175_T	0.866	1.00
30_L	56_I	0.865	1.00
49_Y	101_E	0.859	1.00
134_S	229_S	0.853	1.00
203_A	206_E	0.848	1.00
7_A	95_L	0.847	1.00
16_L	19_E	0.837	1.00
200_I	230_A	0.835	1.00
31_D	41_S	0.832	1.00
92_S	154_G	0.831	1.00
28_T	59_D	0.829	1.00
96_C	153_I	0.821	1.00
121_K	135_D	0.817	1.00
115_V	137_P	0.816	1.00
199_S	202_K	0.815	1.00
94_Y	98_A	0.812	1.00
69_V	83_K	0.811	1.00
188_K	222_G	0.808	1.00
149_T	152_Q	0.807	1.00
62_A	106_K	0.806	1.00
63_I	95_L	0.805	1.00
97_R	157_F	0.797	1.00
16_L	20_G	0.797	1.00
77_D	84_M	0.797	1.00
81_F	145_V	0.793	1.00
173_V	192_L	0.791	1.00
199_S	236_F	0.790	1.00
69_V	84_M	0.788	1.00
78_I	142_L	0.776	1.00
105_Q	164_S	0.772	1.00
25_Y	61_D	0.769	1.00
57_P	99_A	0.766	1.00
204_A	234_L	0.764	1.00
52_L	94_Y	0.761	1.00
168_L	200_I	0.760	1.00
157_F	161_N	0.759	1.00
91_A	94_Y	0.754	1.00
145_V	156_L	0.750	1.00
214_Y	217_V	0.750	1.00
4_V	205_I	0.749	1.00
115_V	151_E	0.741	1.00
145_V	152_Q	0.740	1.00
48_N	52_L	0.738	1.00
42_I	58_K	0.738	1.00
83_K	86_D	0.737	1.00
85_T	146_L	0.732	1.00
92_S	96_C	0.732	1.00
176_D	193_S	0.731	1.00
16_L	198_L	0.729	1.00
152_Q	156_L	0.728	1.00
228_E	231_V	0.726	1.00
150_S	154_G	0.724	1.00
56_I	60_T	0.723	1.00
171_G	190_T	0.721	1.00
198_L	202_K	0.720	1.00
114_H	144_G	0.718	1.00
36_D	39_A	0.716	1.00
120_E	135_D	0.715	1.00
51_E	54_K	0.714	1.00
100_A	157_F	0.712	1.00
65_N	95_L	0.705	1.00
5_L	44_A	0.699	1.00
83_K	87_V	0.698	1.00
10_N	33_D	0.694	1.00
149_T	153_I	0.690	1.00
45_D	48_N	0.684	1.00
3_K	58_K	0.683	1.00
133_T	230_A	0.681	1.00
170_I	173_V	0.673	1.00
211_Y	214_Y	0.672	1.00
35_F	38_K	0.672	1.00
81_F	142_L	0.667	1.00
229_S	232_N	0.667	1.00
63_I	107_L	0.665	1.00
26_E	38_K	0.665	1.00
172_T	189_K	0.661	1.00
5_L	63_I	0.661	1.00
141_N	144_G	0.660	1.00
3_K	59_D	0.659	1.00
21_L	205_I	0.655	1.00
164_S	209_I	0.655	1.00
16_L	177_E	0.655	1.00
5_L	57_P	0.653	1.00
100_A	162_K	0.653	1.00
204_A	230_A	0.650	1.00
164_S	210_R	0.648	1.00
203_A	235_G	0.644	1.00
68_A	88_F	0.643	1.00
209_I	233_E	0.643	1.00
58_K	102_L	0.643	1.00
6_I	21_L	0.642	1.00
137_P	152_Q	0.641	1.00
227_I	236_F	0.637	1.00
139_S	144_G	0.637	1.00
85_T	145_V	0.631	1.00
15_R	19_E	0.631	1.00
24_D	199_S	0.625	1.00
216_A	219_D	0.624	1.00
119_Y	131_I	0.624	1.00
154_G	167_N	0.618	1.00
200_I	236_F	0.618	1.00
62_A	105_Q	0.616	1.00
13_I	197_L	0.615	1.00
108_V	201_F	0.614	1.00
196_D	199_S	0.614	1.00
182_H	211_Y	0.611	1.00
155_H	158_Y	0.609	1.00
69_V	88_F	0.608	1.00
220_N	223_R	0.607	1.00
108_V	204_A	0.605	1.00
203_A	234_L	0.605	1.00
230_A	233_E	0.604	1.00
17_L	201_F	0.603	1.00
156_L	159_L	0.603	1.00
214_Y	218_S	0.595	1.00
16_L	176_D	0.589	1.00
213_T	216_A	0.589	1.00
207_T	210_R	0.589	1.00
115_V	169_R	0.587	1.00
25_Y	62_A	0.587	1.00
142_L	145_V	0.585	1.00
146_L	150_S	0.582	1.00
215_Y	218_S	0.580	1.00
5_L	56_I	0.578	1.00
139_S	148_L	0.576	1.00
153_I	157_F	0.573	1.00
31_D	34_H	0.571	1.00
117_D	138_L	0.570	1.00
63_I	104_I	0.568	1.00
54_K	98_A	0.568	1.00
106_K	209_I	0.566	1.00
49_Y	98_A	0.565	1.00
113_N	225_W	0.565	1.00
196_D	239_Q	0.565	1.00
66_L	170_I	0.565	1.00
239_Q	244_E	0.561	1.00
212_G	215_Y	0.559	1.00
176_D	195_P	0.559	1.00
29_V	41_S	0.558	1.00
108_V	205_I	0.557	1.00
19_E	195_P	0.557	1.00
203_A	236_F	0.556	1.00
157_F	163_L	0.555	1.00
112_S	115_V	0.554	1.00
18_A	22_I	0.548	1.00
122_D	222_G	0.547	1.00
6_I	29_V	0.546	1.00
164_S	208_N	0.543	1.00
88_F	143_Y	0.540	1.00
12_V	16_L	0.537	1.00
214_Y	219_D	0.535	1.00
172_T	191_L	0.532	1.00
28_T	56_I	0.530	1.00
215_Y	219_D	0.530	1.00
17_L	202_K	0.527	1.00
202_K	205_I	0.526	1.00
25_Y	202_K	0.526	1.00
24_D	203_A	0.524	1.00
215_Y	221_P	0.523	1.00
18_A	39_A	0.522	1.00
116_T	169_R	0.522	1.00
158_Y	163_L	0.522	1.00
130_E	135_D	0.516	1.00
62_A	108_V	0.516	1.00
207_T	233_E	0.513	1.00
99_A	102_L	0.512	1.00
142_L	146_L	0.508	1.00
42_I	51_E	0.506	1.00
143_Y	146_L	0.505	1.00
92_S	109_F	0.504	1.00
21_L	25_Y	0.504	1.00
6_I	9_G	0.502	1.00
59_D	102_L	0.502	1.00
178_M	181_L	0.502	1.00
44_A	56_I	0.501	1.00
89_Y	146_L	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
1sb8A	2	0.9605	100	0.24	Contact Map
4wkgA	5	0.9605	100	0.244	Contact Map
3rufA	2	0.9605	100	0.244	Contact Map
2yy7A	2	0.9605	100	0.246	Contact Map
3wmwA	2	0.8458	100	0.252	Contact Map
1orrA	3	0.9842	100	0.255	Contact Map
3slgA	4	0.9447	100	0.256	Contact Map
1gy8A	2	0.9723	100	0.258	Contact Map
2c20A	2	0.9565	100	0.258	Contact Map
2z1mA	4	0.9565	100	0.261	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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