PHOP - BACSU - GREMLIN Contacts

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PHOP - Alkaline phosphatase synthesis transcriptional regulatory protein PhoP

UniProt:	P13792	Sequences: MNKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRRSEIAAPSSEMKNDEMEGQIVIGDLKILPDHYEAYFKESQLELTPKEFELLLYLGRHKGRVLTRDLLLSAVWNYDFAGDTRIVDVHISHLRDKIENNTKKPIYIKTIRGLGYKLEEPKMNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	240 (205)
Sequences:	76471 (54188)
Seq/√Len:	3784.7

ECOLI - PHOB CUSR CREB QSEB OMPR PHOP YEDW BASR RSTA BAER TORR CPXR KDPE ARCA EVGA YHJB DPIA UVRY FIMZ DCUR RCSB NARP NARL YJJQ YGEK BGLJ RCSA TORS CSGD BARA UHPA RSSB RCSC YPDB ARCB CHEB YEHT EVGS NTRC GLRR ATOC ZRAR RCSD
BACSU - PHOP YYCF CSSR YVRH YVCP YRKP YCBL YXDJ YCLJ YKOG CITT RESD BCER YFIK DCTR DEGU YXJL MALR CMPA LIAR YHCZ YVFU YBDJ YDFI DESR YESN LYTT GLNL CHEB SP0A NATR CHEV CHEY
HALSA - Q9HR09 CHEB Q9HNM3 Q9HRE5 BAT O51970 F2Z6H5

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_V	31_T	3.731	1.00
15_V	33_S	3.220	1.00
19_Q	31_T	3.120	1.00
8_V	38_A	2.750	1.00
39_L	67_Q	2.611	1.00
36_E	58_K	2.585	1.00
30_I	47_P	2.485	1.00
35_G	59_L	2.469	1.00
34_D	58_K	2.388	1.00
43_E	71_Q	2.372	1.00
59_L	67_Q	2.332	1.00
4_K	30_I	2.200	1.00
4_K	28_D	2.091	1.00
19_Q	23_E	2.036	1.00
21_N	107_P	2.034	1.00
25_S	111_N	2.017	1.00
32_A	41_K	1.951	1.00
89_K	109_E	1.892	1.00
33_S	37_E	1.889	1.00
200_R	203_D	1.860	1.00
55_M	83_K	1.854	1.00
52_L	64_V	1.836	1.00
165_K	168_E	1.790	1.00
34_D	37_E	1.771	1.00
30_I	41_K	1.728	1.00
6_L	32_A	1.726	1.00
79_M	92_G	1.725	1.00
65_C	77_I	1.715	1.00
183_R	203_D	1.708	1.00
86_E	106_S	1.705	1.00
69_R	98_D	1.662	1.00
67_Q	71_Q	1.657	1.00
41_K	45_E	1.648	1.00
79_M	97_A	1.622	1.00
143_D	156_K	1.592	1.00
30_I	45_E	1.571	1.00
171_L	175_R	1.566	1.00
59_L	63_E	1.562	1.00
35_G	64_V	1.555	1.00
60_D	63_E	1.553	1.00
22_L	114_V	1.526	1.00
205_H	208_H	1.511	1.00
99_D	113_R	1.507	1.00
66_K	95_L	1.493	1.00
83_K	88_D	1.469	1.00
67_Q	70_Q	1.459	1.00
172_Y	189_A	1.455	1.00
41_K	44_T	1.438	1.00
42_A	68_L	1.417	1.00
65_C	79_M	1.389	1.00
50_I	75_F	1.378	1.00
166_E	212_K	1.376	1.00
182_T	185_L	1.369	1.00
78_L	117_I	1.360	1.00
39_L	64_V	1.360	1.00
181_L	189_A	1.355	1.00
49_L	114_V	1.354	1.00
63_E	66_K	1.349	1.00
140_V	145_K	1.346	1.00
36_E	59_L	1.342	1.00
12_E	33_S	1.322	1.00
98_D	120_R	1.300	1.00
176_H	179_R	1.290	1.00
4_K	45_E	1.288	1.00
52_L	65_C	1.278	1.00
9_D	15_V	1.268	1.00
41_K	47_P	1.258	1.00
27_Y	115_K	1.257	1.00
10_D	53_D	1.248	1.00
8_V	56_L	1.246	1.00
54_V	62_I	1.228	1.00
54_V	79_M	1.225	1.00
98_D	117_I	1.224	1.00
39_L	59_L	1.215	1.00
172_Y	176_H	1.203	1.00
32_A	38_A	1.201	1.00
40_K	44_T	1.201	1.00
167_F	171_L	1.181	1.00
85_E	88_D	1.168	1.00
145_K	154_Y	1.165	1.00
37_E	40_K	1.160	1.00
6_L	47_P	1.155	1.00
37_E	41_K	1.150	1.00
62_I	92_G	1.146	1.00
36_E	40_K	1.135	1.00
6_L	38_A	1.130	1.00
62_I	91_L	1.126	1.00
72_K	75_F	1.122	1.00
49_L	118_L	1.121	1.00
147_L	150_H	1.118	1.00
94_E	115_K	1.116	1.00
26_G	115_K	1.109	1.00
184_D	199_T	1.105	1.00
111_N	115_K	1.093	1.00
185_L	189_A	1.089	1.00
152_E	159_Q	1.087	1.00
86_E	90_V	1.083	1.00
25_S	115_K	1.083	1.00
200_R	204_V	1.078	1.00
146_I	174_G	1.059	1.00
91_L	95_L	1.056	1.00
204_V	207_S	1.047	1.00
172_Y	181_L	1.045	1.00
5_I	27_Y	1.036	1.00
66_K	91_L	1.026	1.00
168_E	171_L	1.022	1.00
201_I	205_H	1.022	1.00
6_L	41_K	1.008	1.00
112_A	116_A	1.001	1.00
109_E	112_A	0.992	1.00
32_A	37_E	0.981	1.00
38_A	42_A	0.979	1.00
38_A	64_V	0.976	1.00
52_L	77_I	0.972	1.00
87_F	91_L	0.965	1.00
62_I	95_L	0.960	1.00
8_V	50_I	0.952	1.00
39_L	43_E	0.952	1.00
50_I	68_L	0.949	1.00
181_L	185_L	0.949	1.00
18_L	80_L	0.945	1.00
90_V	94_E	0.939	1.00
148_P	171_L	0.937	1.00
12_E	16_T	0.937	1.00
7_V	18_L	0.936	1.00
19_Q	29_V	0.933	1.00
54_V	60_D	0.932	1.00
89_K	102_T	0.932	1.00
42_A	72_K	0.931	1.00
16_T	31_T	0.928	1.00
164_P	168_E	0.927	1.00
6_L	42_A	0.926	1.00
8_V	32_A	0.925	1.00
215_N	225_T	0.913	1.00
217_T	220_P	0.909	1.00
52_L	79_M	0.897	1.00
172_Y	186_L	0.896	1.00
12_E	15_V	0.883	1.00
7_V	29_V	0.878	1.00
117_I	120_R	0.877	1.00
13_S	17_L	0.877	1.00
63_E	67_Q	0.875	1.00
78_L	113_R	0.870	1.00
65_C	95_L	0.870	1.00
65_C	97_A	0.869	1.00
40_K	43_E	0.867	1.00
51_V	110_V	0.863	1.00
146_I	167_F	0.860	1.00
169_L	173_L	0.859	1.00
27_Y	111_N	0.857	1.00
149_D	179_R	0.851	1.00
91_L	94_E	0.847	1.00
154_Y	159_Q	0.845	1.00
199_T	203_D	0.841	1.00
54_V	88_D	0.840	1.00
18_L	110_V	0.838	1.00
86_E	89_K	0.832	1.00
215_N	221_I	0.831	1.00
64_V	68_L	0.830	1.00
206_I	210_R	0.823	1.00
84_D	102_T	0.822	1.00
50_I	77_I	0.819	1.00
184_D	188_S	0.816	1.00
4_K	47_P	0.815	1.00
220_P	223_I	0.812	1.00
107_P	111_N	0.809	1.00
16_T	19_Q	0.809	1.00
163_T	212_K	0.809	1.00
46_K	72_K	0.807	1.00
200_R	207_S	0.805	1.00
56_L	64_V	0.805	1.00
4_K	48_D	0.795	1.00
179_R	185_L	0.795	1.00
68_L	73_L	0.793	1.00
151_Y	168_E	0.792	1.00
14_I	105_F	0.785	1.00
90_V	108_R	0.781	1.00
109_E	113_R	0.779	1.00
20_Y	24_R	0.778	1.00
208_H	211_D	0.777	1.00
216_N	220_P	0.777	1.00
185_L	188_S	0.770	1.00
51_V	80_L	0.770	1.00
59_L	64_V	0.765	1.00
66_K	70_Q	0.764	1.00
35_G	39_L	0.760	1.00
116_A	119_R	0.758	1.00
54_V	83_K	0.758	1.00
88_D	91_L	0.755	1.00
207_S	211_D	0.755	1.00
42_A	75_F	0.754	1.00
183_R	199_T	0.753	1.00
172_Y	175_R	0.750	1.00
76_P	98_D	0.748	1.00
78_L	99_D	0.743	1.00
87_F	108_R	0.742	1.00
204_V	208_H	0.739	1.00
51_V	114_V	0.737	1.00
55_M	82_A	0.737	1.00
42_A	47_P	0.733	1.00
116_A	121_S	0.724	1.00
106_S	109_E	0.722	1.00
35_G	58_K	0.715	1.00
80_L	105_F	0.712	1.00
21_N	111_N	0.709	1.00
93_L	113_R	0.706	1.00
16_T	20_Y	0.705	1.00
8_V	64_V	0.705	1.00
168_E	172_Y	0.704	1.00
7_V	19_Q	0.689	1.00
203_D	206_I	0.687	1.00
39_L	42_A	0.684	1.00
214_E	217_T	0.684	1.00
7_V	31_T	0.682	1.00
154_Y	157_E	0.682	1.00
175_R	189_A	0.681	1.00
105_F	110_V	0.678	1.00
140_V	143_D	0.677	1.00
197_G	202_V	0.677	1.00
210_R	215_N	0.672	1.00
43_E	67_Q	0.668	1.00
118_L	121_S	0.662	1.00
92_G	97_A	0.661	1.00
121_S	125_A	0.656	1.00
76_P	118_L	0.656	1.00
9_D	56_L	0.655	1.00
146_I	153_A	0.654	1.00
143_D	155_F	0.651	1.00
35_G	56_L	0.647	1.00
5_I	22_L	0.646	1.00
144_L	155_F	0.645	1.00
94_E	112_A	0.642	1.00
17_L	21_N	0.641	1.00
42_A	50_I	0.640	1.00
214_E	221_I	0.637	1.00
15_V	19_Q	0.637	1.00
86_E	108_R	0.637	1.00
22_L	27_Y	0.635	1.00
216_N	221_I	0.630	1.00
68_L	77_I	0.628	1.00
108_R	112_A	0.626	1.00
23_E	29_V	0.623	1.00
155_F	158_S	0.623	1.00
151_Y	167_F	0.622	1.00
43_E	72_K	0.621	1.00
53_D	103_K	0.615	1.00
173_L	206_I	0.614	1.00
81_T	89_K	0.610	1.00
5_I	49_L	0.607	1.00
74_M	124_A	0.605	1.00
74_M	123_I	0.600	1.00
69_R	76_P	0.596	1.00
99_D	116_A	0.594	1.00
221_I	224_K	0.593	1.00
139_I	148_P	0.592	1.00
89_K	106_S	0.588	1.00
69_R	75_F	0.588	1.00
39_L	71_Q	0.587	1.00
214_E	220_P	0.585	1.00
198_D	201_I	0.583	1.00
23_E	28_D	0.579	1.00
144_L	153_A	0.577	1.00
165_K	205_H	0.577	1.00
11_E	82_A	0.576	1.00
113_R	117_I	0.575	1.00
62_I	88_D	0.573	1.00
112_A	115_K	0.573	1.00
147_L	152_E	0.570	1.00
51_V	78_L	0.568	1.00
148_P	175_R	0.567	1.00
105_F	109_E	0.564	1.00
115_K	119_R	0.564	1.00
139_I	174_G	0.563	1.00
146_I	171_L	0.563	1.00
54_V	92_G	0.558	1.00
52_L	56_L	0.552	1.00
155_F	216_N	0.547	1.00
10_D	81_T	0.546	1.00
176_H	189_A	0.545	1.00
175_R	181_L	0.543	1.00
179_R	189_A	0.539	1.00
87_F	90_V	0.539	1.00
65_C	69_R	0.537	1.00
76_P	120_R	0.536	1.00
145_K	157_E	0.535	1.00
68_L	75_F	0.534	1.00
220_P	224_K	0.533	1.00
27_Y	118_L	0.531	1.00
84_D	104_P	0.530	1.00
90_V	93_L	0.528	1.00
155_F	215_N	0.525	1.00
11_E	14_I	0.525	1.00
49_L	117_I	0.523	1.00
42_A	64_V	0.523	1.00
217_T	221_I	0.520	1.00
163_T	166_E	0.519	1.00
21_N	25_S	0.518	1.00
17_L	20_Y	0.514	1.00
52_L	68_L	0.513	1.00
141_I	174_G	0.512	1.00
14_I	17_L	0.511	1.00
201_I	204_V	0.509	1.00
92_G	100_Y	0.509	1.00
155_F	214_E	0.506	1.00
143_D	147_L	0.505	1.00
183_R	206_I	0.504	1.00
5_I	114_V	0.500	1.00
8_V	35_G	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
3r0jA	2	0.9208	100	0.249	Contact Map
1ys7A	2	0.9417	100	0.25	Contact Map
2gwrA	1	0.9292	100	0.252	Contact Map
1kgsA	1	0.9125	100	0.252	Contact Map
2oqrA	2	0.9417	100	0.259	Contact Map
4b09A	2	0.8958	100	0.265	Contact Map
4kfcA	2	0.9333	100	0.278	Contact Map
1p2fA	1	0.9042	100	0.287	Contact Map
2hqrA	2	0.9167	100	0.297	Contact Map
3q9sA	1	0.8708	100	0.302	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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