YRKP - BACSU - GREMLIN Contacts

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YRKP - Uncharacterized transcriptional regulatory protein YrkP

UniProt:	P54443	Sequences: MAYRILVVEDDEDIGDLLEESLTRAGYEVLRAKDGKRALQLVNDSLDLVILDIMMPGISGIETCQHIRKSSNVPILFLTARSSTLDKTEGLLAGGDDYMTKPFSEEELHARVIAQLRRYTIYQEKKEQEETFLIGGKLRVSEEFNEVWKEEKQIKLSDLEYRILKLLMNKRNKIFSAQNIYESVWGQPYFYCSNNTVMVHIRKLRSKIEDDPARPVYIKTEWGRGYRFGAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	231 (202)
Sequences:	73378 (52187)
Seq/√Len:	3671.9

ECOLI - CPXR KDPE TORR BAER RSTA ARCA PHOB YEDW CREB CUSR PHOP OMPR QSEB BASR DPIA UVRY DCUR FIMZ YHJB YJJQ NARP EVGA YGEK RCSB BGLJ NARL UHPA BARA CSGD RCSA TORS CHEB RSSB RCSC YEHT YPDB ARCB EVGS NTRC GLRR ZRAR ATOC RCSD
BACSU - YRKP CSSR YYCF YVRH YCBL PHOP YXDJ YCLJ YVCP RESD BCER YKOG CITT MALR YFIK DCTR CMPA YXJL YBDJ LIAR YDFI DEGU YVFU DESR YHCZ GLNL CHEB YESN SP0A LYTT NATR CHEV
HALSA - CHEB Q9HR09 Q9HNM3 Q9HRE5 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
15_G	31_R	3.717	1.00
15_G	33_K	3.256	1.00
19_E	31_R	3.181	1.00
8_V	38_A	2.743	1.00
39_L	66_H	2.656	1.00
36_K	57_G	2.586	1.00
30_L	46_L	2.519	1.00
35_G	58_I	2.462	1.00
58_I	66_H	2.393	1.00
43_N	70_S	2.392	1.00
34_D	57_G	2.379	1.00
4_R	30_L	2.162	1.00
21_S	105_E	2.054	1.00
19_E	23_T	2.032	1.00
32_A	41_L	2.000	1.00
4_R	28_E	1.990	1.00
25_A	109_H	1.987	1.00
87_K	107_E	1.920	1.00
33_K	37_R	1.882	1.00
54_M	81_R	1.875	1.00
51_L	63_T	1.850	1.00
64_C	75_I	1.811	1.00
195_N	198_M	1.801	1.00
159_L	162_R	1.781	1.00
77_F	90_G	1.776	1.00
34_D	37_R	1.761	1.00
84_T	104_S	1.724	1.00
30_L	41_L	1.708	1.00
77_F	95_G	1.704	1.00
68_R	96_D	1.698	1.00
6_L	32_A	1.680	1.00
66_H	70_S	1.667	1.00
137_K	150_E	1.604	1.00
58_I	62_E	1.596	1.00
177_A	198_M	1.594	1.00
166_L	183_S	1.587	1.00
59_S	62_E	1.560	1.00
3_Y	116_L	1.544	1.00
35_G	63_T	1.532	1.00
165_K	169_N	1.516	1.00
97_D	111_R	1.516	1.00
81_R	86_D	1.507	1.00
22_L	112_V	1.480	1.00
66_H	69_K	1.480	1.00
175_F	183_S	1.449	1.00
42_V	67_I	1.446	1.00
36_K	58_I	1.421	1.00
64_C	77_F	1.404	1.00
200_H	203_K	1.393	1.00
41_L	46_L	1.390	1.00
39_L	63_T	1.386	1.00
65_Q	93_A	1.384	1.00
48_L	112_V	1.379	1.00
49_V	73_V	1.363	1.00
176_S	179_N	1.363	1.00
76_L	115_Q	1.361	1.00
41_L	44_D	1.354	1.00
62_E	65_Q	1.341	1.00
134_I	139_R	1.315	1.00
96_D	118_R	1.313	1.00
53_I	61_I	1.298	1.00
12_E	33_K	1.295	1.00
139_R	148_W	1.292	1.00
51_L	64_C	1.274	1.00
9_E	15_G	1.268	1.00
141_S	144_F	1.261	1.00
166_L	170_K	1.248	1.00
53_I	77_F	1.245	1.00
8_V	55_M	1.242	1.00
10_D	52_D	1.235	1.00
39_L	58_I	1.212	1.00
160_E	207_K	1.211	1.00
37_R	40_Q	1.189	1.00
32_A	38_A	1.183	1.00
27_Y	113_I	1.174	1.00
6_L	46_L	1.170	1.00
37_R	41_L	1.168	1.00
40_Q	44_D	1.166	1.00
83_S	86_D	1.165	1.00
146_E	153_Q	1.165	1.00
36_K	40_Q	1.162	1.00
96_D	115_Q	1.161	1.00
84_T	88_T	1.146	1.00
199_V	202_R	1.146	1.00
109_H	113_I	1.137	1.00
61_I	89_E	1.113	1.00
179_N	183_S	1.111	1.00
61_I	90_G	1.107	1.00
6_L	38_A	1.094	1.00
26_G	113_I	1.083	1.00
25_A	113_I	1.078	1.00
5_I	27_Y	1.077	1.00
6_L	41_L	1.076	1.00
3_Y	27_Y	1.072	1.00
92_L	113_I	1.071	1.00
89_E	93_A	1.063	1.00
166_L	175_F	1.058	1.00
107_E	110_A	1.045	1.00
161_Y	165_K	1.037	1.00
65_Q	89_E	1.029	1.00
110_A	114_A	1.029	1.00
162_R	165_K	1.028	1.00
85_L	89_E	1.027	1.00
38_A	63_T	1.022	1.00
178_Q	194_N	1.021	1.00
48_L	116_L	1.016	1.00
140_V	168_M	1.008	1.00
142_E	165_K	1.005	1.00
38_A	42_V	1.004	1.00
212_P	215_P	1.001	1.00
196_T	200_H	1.001	1.00
211_D	215_P	0.999	1.00
201_I	205_R	0.999	1.00
39_L	43_N	0.991	1.00
16_D	31_R	0.988	1.00
61_I	93_A	0.985	1.00
32_A	37_R	0.985	1.00
6_L	42_V	0.975	1.00
87_K	100_T	0.968	1.00
7_V	18_L	0.968	1.00
88_T	92_L	0.961	1.00
148_W	153_Q	0.961	1.00
8_V	49_V	0.961	1.00
159_L	185_W	0.959	1.00
53_I	59_S	0.956	1.00
19_E	29_V	0.955	1.00
49_V	67_I	0.955	1.00
195_N	199_V	0.953	1.00
51_L	75_I	0.938	1.00
145_N	162_R	0.937	1.00
18_L	78_L	0.933	1.00
13_D	17_L	0.932	1.00
175_F	179_N	0.930	1.00
12_E	16_D	0.929	1.00
158_D	162_R	0.916	1.00
8_V	32_A	0.911	1.00
84_T	87_K	0.903	1.00
132_F	139_R	0.901	1.00
115_Q	118_R	0.900	1.00
51_L	77_F	0.890	1.00
64_C	93_A	0.885	1.00
194_N	198_M	0.885	1.00
62_E	66_H	0.882	1.00
40_Q	43_N	0.874	1.00
3_Y	120_T	0.873	1.00
50_I	108_L	0.867	1.00
64_C	95_G	0.860	1.00
49_V	75_I	0.858	1.00
82_S	100_T	0.855	1.00
7_V	29_V	0.855	1.00
20_E	24_R	0.842	1.00
140_V	161_Y	0.839	1.00
203_K	206_S	0.839	1.00
27_Y	109_H	0.838	1.00
55_M	63_T	0.838	1.00
12_E	15_G	0.836	1.00
74_P	96_D	0.830	1.00
89_E	92_L	0.825	1.00
88_T	106_E	0.825	1.00
195_N	202_R	0.822	1.00
53_I	86_D	0.818	1.00
166_L	180_I	0.811	1.00
105_E	109_H	0.806	1.00
4_R	46_L	0.805	1.00
16_D	19_E	0.803	1.00
50_I	78_L	0.797	1.00
63_T	67_I	0.793	1.00
18_L	108_L	0.793	1.00
65_Q	69_K	0.786	1.00
42_V	73_V	0.785	1.00
58_I	63_T	0.784	1.00
202_R	206_S	0.778	1.00
53_I	81_R	0.766	1.00
67_I	71_S	0.763	1.00
76_L	111_R	0.759	1.00
4_R	47_D	0.757	1.00
107_E	111_R	0.755	1.00
209_E	212_P	0.755	1.00
42_V	46_L	0.755	1.00
210_D	216_V	0.754	1.00
35_G	39_L	0.753	1.00
54_M	80_A	0.752	1.00
86_D	89_E	0.748	1.00
85_L	106_E	0.742	1.00
114_A	119_Y	0.739	1.00
116_L	119_Y	0.734	1.00
177_A	194_N	0.732	1.00
178_Q	182_E	0.727	1.00
114_A	117_R	0.727	1.00
138_L	149_K	0.725	1.00
104_S	107_E	0.723	1.00
91_L	111_R	0.720	1.00
157_S	207_K	0.718	1.00
14_I	103_F	0.713	1.00
39_L	42_V	0.711	1.00
8_V	63_T	0.709	1.00
103_F	108_L	0.708	1.00
78_L	103_F	0.702	1.00
90_G	95_G	0.702	1.00
145_N	161_Y	0.700	1.00
148_W	151_E	0.699	1.00
7_V	19_E	0.693	1.00
76_L	97_D	0.693	1.00
179_N	182_E	0.691	1.00
137_K	149_K	0.690	1.00
84_T	106_E	0.689	1.00
16_D	20_E	0.682	1.00
35_G	57_G	0.682	1.00
17_L	21_S	0.676	1.00
169_N	183_S	0.673	1.00
7_V	31_R	0.672	1.00
92_L	110_A	0.671	1.00
166_L	169_N	0.668	1.00
192_C	197_V	0.662	1.00
42_V	49_V	0.661	1.00
163_I	167_L	0.660	1.00
119_Y	123_Q	0.657	1.00
205_R	210_D	0.655	1.00
106_E	110_A	0.654	1.00
209_E	216_V	0.653	1.00
169_N	175_F	0.652	1.00
43_N	66_H	0.651	1.00
9_E	55_M	0.651	1.00
199_V	203_K	0.648	1.00
131_T	143_E	0.648	1.00
3_Y	47_D	0.647	1.00
87_K	104_S	0.645	1.00
67_I	75_I	0.645	1.00
97_D	114_A	0.644	1.00
182_E	185_W	0.639	1.00
206_S	209_E	0.638	1.00
72_N	122_Y	0.637	1.00
15_G	19_E	0.633	1.00
21_S	109_H	0.629	1.00
74_P	116_L	0.628	1.00
53_I	90_G	0.626	1.00
132_F	141_S	0.625	1.00
68_R	73_V	0.620	1.00
198_M	201_I	0.619	1.00
193_S	196_T	0.617	1.00
72_N	121_I	0.616	1.00
111_R	115_Q	0.615	1.00
61_I	86_D	0.614	1.00
39_L	70_S	0.613	1.00
52_D	101_K	0.612	1.00
50_I	112_V	0.610	1.00
210_D	220_T	0.603	1.00
23_T	29_V	0.600	1.00
11_D	14_I	0.598	1.00
209_E	215_P	0.597	1.00
50_I	76_L	0.595	1.00
5_I	22_L	0.594	1.00
181_Y	185_W	0.593	1.00
35_G	55_M	0.589	1.00
196_T	201_I	0.585	1.00
215_P	218_I	0.585	1.00
68_R	74_P	0.582	1.00
79_T	87_K	0.581	1.00
103_F	107_E	0.580	1.00
11_D	80_A	0.578	1.00
22_L	27_Y	0.578	1.00
140_V	147_V	0.578	1.00
64_C	68_R	0.574	1.00
149_K	211_D	0.570	1.00
142_E	169_N	0.569	1.00
85_L	88_T	0.565	1.00
74_P	122_Y	0.557	1.00
10_D	79_T	0.555	1.00
45_S	71_S	0.554	1.00
5_I	48_L	0.551	1.00
149_K	209_E	0.550	1.00
74_P	118_R	0.550	1.00
134_I	137_K	0.548	1.00
162_R	166_L	0.546	1.00
88_T	91_L	0.543	1.00
23_T	28_E	0.543	1.00
51_L	55_M	0.542	1.00
110_A	113_I	0.537	1.00
37_R	57_G	0.535	1.00
82_S	102_P	0.533	1.00
138_L	147_V	0.529	1.00
167_L	201_I	0.529	1.00
80_A	102_P	0.528	1.00
170_K	183_S	0.527	1.00
14_I	17_L	0.527	1.00
139_R	151_E	0.522	1.00
90_G	98_Y	0.521	1.00
149_K	152_K	0.521	1.00
74_P	119_Y	0.519	1.00
42_V	71_S	0.518	1.00
133_L	142_E	0.516	1.00
7_V	15_G	0.516	1.00
42_V	63_T	0.515	1.00
42_V	70_S	0.515	1.00
149_K	210_D	0.514	1.00
159_L	200_H	0.511	1.00
141_S	146_E	0.511	1.00
140_V	165_K	0.510	1.00
20_E	23_T	0.507	1.00
5_I	112_V	0.505	1.00
21_S	25_A	0.505	1.00
164_L	216_V	0.502	1.00
67_I	73_V	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
2gwrA	1	0.961	100	0.189	Contact Map
2oqrA	2	0.974	100	0.202	Contact Map
4b09A	2	0.9091	100	0.214	Contact Map
3r0jA	2	0.9481	100	0.22	Contact Map
1kgsA	1	0.9394	100	0.226	Contact Map
1ys7A	2	0.9697	100	0.226	Contact Map
1p2fA	1	0.9351	100	0.229	Contact Map
4kfcA	2	0.9654	100	0.23	Contact Map
3q9sA	1	0.9004	100	0.267	Contact Map
2hqrA	2	0.9264	100	0.271	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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