YVCP - BACSU - GREMLIN Contacts

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YVCP - Uncharacterized transcriptional regulatory protein YvcP

UniProt:	O06978	Sequences: MYRILLVEDDERIASLLGGHLQKYGYEVKIAEQLNDIKLEFAEMKPDLVLLDINLPFFDGFYWCRQIRTISNAPIIFISARTDELNQVMAIENGGDDYITKPFHLEVVMAKIKSVLRRTYGEYSPSLPQESRIVELGGLTIYPDQNEAEWNSVRILFSQKEFQLLSIFVREHKKIVSRDELLEALWDDVDFVDDNTLTVNVNRLRRKLENAGLTDCISTIRGQGYQFQVNRKDEAEC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	237 (208)
Sequences:	74095 (51623)
Seq/√Len:	3579.4

ECOLI - RSTA KDPE YEDW CPXR ARCA CUSR TORR BAER OMPR PHOP PHOB QSEB CREB BASR UVRY DCUR EVGA YHJB FIMZ UHPA NARL NARP RCSB DPIA YJJQ YGEK BGLJ RCSA CSGD YEHT BARA RSSB TORS RCSC ARCB CHEB YPDB GLRR NTRC ATOC EVGS ZRAR RCSD
BACSU - YVCP YXDJ BCER YYCF YCBL YVRH PHOP YCLJ YRKP CITT YKOG RESD CSSR YFIK CMPA YDFI LIAR MALR YVFU DESR DCTR YXJL DEGU YBDJ YHCZ YESN CHEB LYTT GLNL NATR SP0A CHEV
HALSA - CHEB Q9HR09 Q9HRE5 Q9HNM3 BAT O51970 Q9HP91

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	30_I	3.718	1.00
14_A	32_E	3.191	1.00
18_G	30_I	3.041	1.00
7_V	37_I	2.723	1.00
35_N	57_F	2.632	1.00
29_K	46_P	2.585	1.00
34_L	58_F	2.573	1.00
38_K	66_Q	2.549	1.00
33_Q	57_F	2.524	1.00
42_A	70_I	2.402	1.00
58_F	66_Q	2.343	1.00
3_R	29_K	2.186	1.00
3_R	27_E	2.113	1.00
18_G	22_Q	2.051	1.00
20_H	105_L	2.042	1.00
87_Q	107_V	1.980	1.00
24_Y	109_M	1.961	1.00
31_A	40_E	1.931	1.00
160_K	163_Q	1.928	1.00
195_N	198_T	1.924	1.00
32_E	36_D	1.921	1.00
51_L	63_W	1.886	1.00
54_N	81_R	1.841	1.00
33_Q	36_D	1.814	1.00
84_E	104_H	1.782	1.00
77_F	90_A	1.742	1.00
64_C	75_I	1.729	1.00
5_L	31_A	1.707	1.00
29_K	40_E	1.663	1.00
178_R	198_T	1.649	1.00
59_D	62_Y	1.648	1.00
77_F	95_G	1.645	1.00
68_R	96_D	1.634	1.00
66_Q	70_I	1.618	1.00
166_S	170_R	1.577	1.00
58_F	62_Y	1.563	1.00
138_G	151_N	1.537	1.00
21_L	112_I	1.527	1.00
200_N	203_R	1.522	1.00
34_L	63_W	1.518	1.00
40_E	44_M	1.496	1.00
66_Q	69_T	1.491	1.00
167_I	184_A	1.486	1.00
97_D	111_K	1.485	1.00
135_E	140_T	1.452	1.00
29_K	44_M	1.446	1.00
40_E	43_E	1.442	1.00
64_C	77_F	1.439	1.00
49_V	73_A	1.433	1.00
38_K	63_W	1.421	1.00
81_R	86_N	1.417	1.00
48_L	112_I	1.415	1.00
62_Y	65_R	1.408	1.00
51_L	64_C	1.386	1.00
76_I	115_V	1.384	1.00
41_F	67_I	1.377	1.00
161_E	207_K	1.375	1.00
171_E	174_K	1.369	1.00
176_V	184_A	1.349	1.00
35_N	58_F	1.348	1.00
177_S	180_E	1.345	1.00
65_R	93_N	1.339	1.00
96_D	118_R	1.336	1.00
53_I	77_F	1.326	1.00
8_E	14_A	1.305	1.00
11_E	32_E	1.289	1.00
9_D	52_D	1.281	1.00
7_V	55_L	1.276	1.00
40_E	46_P	1.263	1.00
38_K	58_F	1.260	1.00
39_L	43_E	1.258	1.00
31_A	37_I	1.237	1.00
26_Y	113_K	1.236	1.00
53_I	61_F	1.232	1.00
147_E	154_R	1.232	1.00
92_E	113_K	1.228	1.00
167_I	171_E	1.220	1.00
36_D	39_L	1.196	1.00
96_D	115_V	1.195	1.00
35_N	39_L	1.181	1.00
36_D	40_E	1.178	1.00
3_R	44_M	1.172	1.00
142_Y	145_Q	1.171	1.00
83_D	86_N	1.160	1.00
5_L	46_P	1.155	1.00
162_F	166_S	1.138	1.00
41_F	71_S	1.136	1.00
5_L	37_I	1.132	1.00
24_Y	113_K	1.125	1.00
61_F	89_M	1.125	1.00
48_L	116_L	1.122	1.00
84_E	88_V	1.121	1.00
61_F	90_A	1.104	1.00
65_R	89_M	1.100	1.00
25_G	113_K	1.093	1.00
180_E	184_A	1.085	1.00
210_N	219_T	1.078	1.00
109_M	113_K	1.077	1.00
140_T	149_E	1.068	1.00
4_I	26_Y	1.067	1.00
167_I	176_V	1.055	1.00
141_I	169_V	1.047	1.00
179_D	194_D	1.044	1.00
195_N	199_V	1.039	1.00
107_V	110_A	1.037	1.00
199_V	202_N	1.033	1.00
163_Q	166_S	1.033	1.00
61_F	93_N	1.019	1.00
196_T	200_N	1.016	1.00
89_M	93_N	1.014	1.00
17_L	78_I	1.011	1.00
7_V	49_V	1.011	1.00
37_I	41_F	1.000	1.00
37_I	63_W	0.997	1.00
51_L	75_I	0.995	1.00
85_L	89_M	0.990	1.00
5_L	40_E	0.990	1.00
146_N	223_Q	0.989	1.00
110_A	114_S	0.971	1.00
5_L	41_F	0.970	1.00
201_V	205_R	0.968	1.00
143_P	166_S	0.967	1.00
38_K	42_A	0.945	1.00
15_S	30_I	0.945	1.00
31_A	36_D	0.942	1.00
18_G	28_V	0.941	1.00
49_V	67_I	0.938	1.00
88_V	92_E	0.934	1.00
53_I	59_D	0.933	1.00
45_K	71_S	0.928	1.00
6_L	17_L	0.923	1.00
167_I	181_L	0.922	1.00
6_L	28_V	0.920	1.00
12_R	16_L	0.920	1.00
115_V	118_R	0.919	1.00
11_E	15_S	0.915	1.00
62_Y	66_Q	0.910	1.00
26_Y	109_M	0.907	1.00
64_C	95_G	0.906	1.00
39_L	42_A	0.906	1.00
87_Q	100_T	0.905	1.00
11_E	14_A	0.905	1.00
141_I	162_F	0.901	1.00
7_V	31_A	0.897	1.00
51_L	77_F	0.890	1.00
159_Q	163_Q	0.887	1.00
64_C	93_N	0.884	1.00
176_V	180_E	0.882	1.00
210_N	215_D	0.879	1.00
174_K	180_E	0.878	1.00
50_L	108_V	0.874	1.00
89_M	92_E	0.866	1.00
55_L	63_W	0.861	1.00
149_E	154_R	0.856	1.00
195_N	202_N	0.854	1.00
17_L	108_V	0.852	1.00
88_V	106_E	0.846	1.00
144_D	174_K	0.841	1.00
76_I	111_K	0.841	1.00
3_R	46_P	0.837	1.00
65_R	69_T	0.836	1.00
84_E	87_Q	0.835	1.00
82_T	100_T	0.830	1.00
146_N	163_Q	0.828	1.00
53_I	86_N	0.825	1.00
49_V	75_I	0.821	1.00
179_D	183_E	0.820	1.00
50_L	78_I	0.814	1.00
19_G	23_K	0.811	1.00
194_D	198_T	0.809	1.00
63_W	67_I	0.805	1.00
209_E	215_D	0.805	1.00
107_V	111_K	0.800	1.00
158_S	207_K	0.795	1.00
58_F	63_W	0.795	1.00
54_N	80_A	0.794	1.00
105_L	109_M	0.792	1.00
15_S	18_G	0.787	1.00
91_I	111_K	0.780	1.00
41_F	73_A	0.775	1.00
114_S	117_R	0.773	1.00
76_I	97_D	0.770	1.00
53_I	81_R	0.768	1.00
85_L	106_E	0.768	1.00
74_P	96_D	0.767	1.00
34_L	38_K	0.762	1.00
202_N	206_R	0.756	1.00
203_R	206_R	0.753	1.00
13_I	103_F	0.749	1.00
6_L	18_G	0.747	1.00
103_F	108_V	0.747	1.00
34_L	57_F	0.737	1.00
135_E	138_G	0.735	1.00
219_T	223_Q	0.731	1.00
86_N	89_M	0.720	1.00
38_K	41_F	0.720	1.00
41_F	46_P	0.717	1.00
6_L	30_I	0.714	1.00
212_G	215_D	0.714	1.00
78_I	103_F	0.714	1.00
84_E	106_E	0.708	1.00
178_R	194_D	0.706	1.00
7_V	63_W	0.706	1.00
170_R	184_A	0.704	1.00
8_E	55_L	0.697	1.00
180_E	183_E	0.697	1.00
104_H	107_V	0.695	1.00
149_E	152_S	0.695	1.00
114_S	119_T	0.693	1.00
92_E	110_A	0.689	1.00
167_I	170_R	0.687	1.00
211_A	214_T	0.683	1.00
42_A	71_S	0.680	1.00
116_L	119_T	0.678	1.00
15_S	19_G	0.674	1.00
164_L	168_F	0.663	1.00
138_G	150_W	0.662	1.00
41_F	49_V	0.658	1.00
3_R	47_D	0.656	1.00
22_Q	27_E	0.656	1.00
50_L	112_I	0.654	1.00
42_A	66_Q	0.650	1.00
90_A	95_G	0.650	1.00
205_R	210_N	0.648	1.00
74_P	116_L	0.647	1.00
214_T	217_I	0.642	1.00
21_L	26_Y	0.641	1.00
199_V	203_R	0.639	1.00
106_E	110_A	0.639	1.00
16_L	20_H	0.639	1.00
14_A	18_G	0.638	1.00
209_E	214_T	0.632	1.00
67_I	75_I	0.631	1.00
20_H	109_M	0.631	1.00
192_V	197_L	0.630	1.00
175_I	223_Q	0.624	1.00
139_L	150_W	0.622	1.00
79_S	87_Q	0.621	1.00
111_K	115_V	0.621	1.00
61_F	86_N	0.620	1.00
4_I	21_L	0.619	1.00
201_V	213_L	0.616	1.00
72_N	121_G	0.614	1.00
134_V	143_P	0.606	1.00
34_L	55_L	0.606	1.00
136_L	139_L	0.606	1.00
87_Q	104_H	0.603	1.00
72_N	122_E	0.603	1.00
22_Q	28_V	0.603	1.00
50_L	76_I	0.603	1.00
146_N	162_F	0.600	1.00
168_F	201_V	0.598	1.00
163_Q	167_I	0.598	1.00
119_T	123_Y	0.596	1.00
142_Y	147_E	0.593	1.00
10_D	80_A	0.592	1.00
53_I	90_A	0.592	1.00
97_D	114_S	0.591	1.00
68_R	73_A	0.589	1.00
68_R	74_P	0.586	1.00
143_P	170_R	0.586	1.00
10_D	13_I	0.585	1.00
51_L	55_L	0.585	1.00
4_I	48_L	0.585	1.00
193_D	196_T	0.581	1.00
41_F	63_W	0.579	1.00
52_D	101_K	0.578	1.00
141_I	148_A	0.573	1.00
198_T	201_V	0.572	1.00
38_K	70_I	0.572	1.00
160_K	200_N	0.572	1.00
215_D	218_S	0.567	1.00
103_F	107_V	0.566	1.00
64_C	68_R	0.566	1.00
68_R	71_S	0.565	1.00
136_L	169_V	0.560	1.00
150_W	210_N	0.560	1.00
170_R	176_V	0.559	1.00
154_R	219_T	0.551	1.00
26_Y	116_L	0.550	1.00
9_D	79_S	0.550	1.00
74_P	119_T	0.548	1.00
88_V	91_I	0.548	1.00
150_W	209_E	0.547	1.00
67_I	71_S	0.542	1.00
150_W	153_V	0.541	1.00
110_A	113_K	0.540	1.00
171_E	184_A	0.537	1.00
67_I	73_A	0.535	1.00
134_V	169_V	0.534	1.00
80_A	102_P	0.533	1.00
90_A	98_Y	0.532	1.00
139_L	148_A	0.531	1.00
209_E	212_G	0.531	1.00
113_K	117_R	0.531	1.00
141_I	166_S	0.531	1.00
165_L	216_C	0.530	1.00
135_E	139_L	0.528	1.00
13_I	16_L	0.526	1.00
7_V	51_L	0.525	1.00
51_L	67_I	0.524	1.00
85_L	88_V	0.524	1.00
4_I	112_I	0.520	1.00
6_L	14_A	0.520	1.00
20_H	24_Y	0.519	1.00
112_I	116_L	0.515	1.00
48_L	115_V	0.514	1.00
74_P	118_R	0.512	1.00
7_V	34_L	0.509	1.00
33_Q	55_L	0.508	1.00
211_A	215_D	0.503	1.00
79_S	98_Y	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
1ys7A	2	0.9494	100	0.212	Contact Map
3r0jA	2	0.9241	100	0.214	Contact Map
2gwrA	1	0.9325	100	0.217	Contact Map
4kfcA	2	0.9409	100	0.223	Contact Map
2oqrA	2	0.9494	100	0.225	Contact Map
1kgsA	1	0.9198	100	0.235	Contact Map
4b09A	2	0.8903	100	0.235	Contact Map
2hqrA	2	0.9325	100	0.26	Contact Map
1p2fA	1	0.903	100	0.264	Contact Map
3q9sA	1	0.8861	100	0.267	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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