PHNK - ECOLI - GREMLIN Contacts

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PHNK - Putative phosphonates utilization ATP-binding protein PhnK

UniProt:	P16678	Sequences: MNQPLLSVNNLTHLYAPGKGFSDVSFDLWPGEVLGIVGESGSGKTTLLKSISARLTPQQGEIHYENRSLYAMSEADRRRLLRTEWGVVHQHPLDGLRRQVSAGGNIGERLMATGARHYGDIRATAQKWLEEVEIPANRIDDLPTTFSGGMQQRLQIARNLVTHPKLVFMDEPTGGLDVSVQARLLDLLRGLVVELNLAVVIVTHDLGVARLLADRLLVMKQGQVVESGLTDRVLDDPHHPYTQLLVSSVLQN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10720
Length:	252 (221)
Sequences:	211506 (124199)
Seq/√Len:	8354.5

ECOLI - PHNK FBPC PROV POTG MALK ARAG CYSA POTA DDPD YCJV MACB UGPC METN SAPF YDCT YADG HISP YEHX DPPD OPPD RBSA OPPF DPPF SAPD GLNQ FEPC YECC YHDZ MLAF MDLA GLTL PHNC YTFR GSIA FHUC CYDC MODC MSBA TAUB LIVG LPTB MDLB FECE ALSA DDPF NIKE CYDD MODF YOJI YPHE LIVF SUFC XYLG ARTP SSUB YHES LOLD PSTB LSRA UUP MGLA THIQ BTUD FTSE FETA NIKD ZNUC YBBA YEJF ETTA CCMA PHNL YNJD YDDA YBHF YBIT YHIH UVRA
BACSU - YVRA OPUCA OPUAA OPUBA MSMX OPPF YURJ YDBJ YVFR TAGH METN YKFD YFIL YUSV YHCH DPPD OPPD APPF YHAQ YHEH APPD YXLF SUFC YCBN RBSA TCYN YKPA YGAD ECFA1 YFMF YFIB FHUC YFIC YXEO YHEI GLNQ TCYC YWJA YCLP ARTM YKNV ECSA YXDL YKOD PSTB1 NATA YTRB SUNT BMRA YKNU SKFE YFMM YLMA CYDD BCEA YVCR CYDC PSTB2 YJKB FTSE ALBC MNTB YTLC ECFA2 YTHP YUFO YVRO YKNY YFMR SSUB ZNUC YHCG YDIF YYBJ YCLH EXPZ YYDI YTRE UVRA
HALSA - Q9HMX3 Q9HMW0 BTUDA Q9HHQ5 Q9HR06 Q9HNZ9 Q9HMX2 Q9HMT3 Q9HRJ6 Q9HNY3 Q9HMU8 Q9HSQ7 Q9HMG1 Q9HMG6 PSTB2 Q9HRZ9 Q9HHM2 Q9HRH8 Y1631 PHNC Y2317 PSTB1 Q9HHR7 Q9HRV7 Q9HR96 Q9HT03 Q9HQA8 Q9HR21 Q9HS04 Q9HMC1 Q9HMW1 Q9HMA2 Q9HMI4
SULSO - Q97UF2 Q97UH3 Q97UJ9 Q7LX64 Q97YY4 Q97VF5 Q97UY8 Q97VK8 Q97VH6 Q97YP7 Q97VC1 Q97YP3 Q97ZC0 Q97YK2 Q97YP8 Q97VK9 Q97VF4 Q97YQ7 Q97X18 Q97UH4 Y2030 Y1893 Q7LY07 Q97UD4 Q97W42 PSTB Q97U54 Q97V00 Q97V01 Q97Z03 Q97VM2 Q7LXM4 Q980W0 Q97VY4 Q97Z56 Q97UG5 Q7LX80 Q97YP4 Q97Z96 Q97ZU0 Q97UC2 Q980E6 Q980K5 Q97ZI2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_E	215_R	3.292	1.00
35_G	213_A	3.144	1.00
7_S	27_D	2.911	1.00
19_K	22_S	2.909	1.00
61_E	68_S	2.869	1.00
10_N	23_D	2.822	1.00
138_R	141_D	2.801	1.00
34_L	217_L	2.800	1.00
9_N	61_E	2.755	1.00
84_E	165_K	2.733	1.00
215_R	227_S	2.647	1.00
29_W	32_E	2.498	1.00
7_S	63_H	2.379	1.00
14_L	19_K	2.331	1.00
22_S	223_Q	2.302	1.00
9_N	63_H	2.137	1.00
12_T	23_D	2.123	1.00
12_T	19_K	2.122	1.00
12_T	59_Q	2.075	1.00
229_L	232_R	2.044	1.00
8_V	11_L	2.030	1.00
217_L	227_S	2.027	1.00
228_G	232_R	2.012	1.00
100_V	104_G	1.996	1.00
13_H	50_S	1.994	1.00
65_E	165_K	1.984	1.00
130_E	135_P	1.840	1.00
217_L	224_V	1.810	1.00
126_Q	139_I	1.803	1.00
117_H	120_D	1.783	1.00
163_H	197_L	1.782	1.00
48_L	202_V	1.764	1.00
48_L	168_F	1.728	1.00
190_G	194_E	1.720	1.00
124_T	163_H	1.692	1.00
30_P	165_K	1.673	1.00
129_L	139_I	1.660	1.00
131_E	195_L	1.613	1.00
127_K	131_E	1.591	1.00
15_Y	20_G	1.591	1.00
189_R	211_L	1.589	1.00
126_Q	130_E	1.584	1.00
103_G	107_G	1.583	1.00
103_G	140_D	1.547	1.00
141_D	145_T	1.471	1.00
102_A	146_F	1.460	1.00
10_N	25_S	1.447	1.00
124_T	127_K	1.446	1.00
103_G	139_I	1.435	1.00
32_E	214_D	1.435	1.00
14_L	58_Q	1.430	1.00
13_H	55_L	1.429	1.00
13_H	58_Q	1.425	1.00
49_K	55_L	1.417	1.00
26_F	217_L	1.413	1.00
28_L	34_L	1.410	1.00
5_L	65_E	1.383	1.00
63_H	68_S	1.334	1.00
107_G	121_I	1.318	1.00
12_T	22_S	1.317	1.00
122_R	126_Q	1.292	1.00
203_T	209_A	1.285	1.00
131_E	190_G	1.259	1.00
220_K	225_V	1.257	1.00
47_L	219_M	1.250	1.00
105_N	158_R	1.247	1.00
15_Y	46_T	1.243	1.00
29_W	215_R	1.228	1.00
165_K	197_L	1.218	1.00
8_V	26_F	1.217	1.00
68_S	71_A	1.205	1.00
65_E	84_E	1.203	1.00
8_V	51_I	1.201	1.00
192_V	199_V	1.197	1.00
33_V	201_I	1.190	1.00
101_S	104_G	1.187	1.00
33_V	192_V	1.184	1.00
191_L	197_L	1.176	1.00
11_L	57_P	1.174	1.00
34_L	215_R	1.169	1.00
228_G	233_V	1.167	1.00
103_G	122_R	1.160	1.00
192_V	214_D	1.159	1.00
50_S	57_P	1.157	1.00
34_L	227_S	1.153	1.00
21_F	50_S	1.151	1.00
123_A	127_K	1.146	1.00
226_E	237_P	1.145	1.00
33_V	213_A	1.142	1.00
52_S	87_V	1.142	1.00
9_N	27_D	1.133	1.00
210_R	231_D	1.130	1.00
53_A	56_T	1.114	1.00
163_H	195_L	1.099	1.00
226_E	236_D	1.098	1.00
35_G	209_A	1.097	1.00
103_G	125_A	1.096	1.00
182_A	186_D	1.091	1.00
169_M	188_L	1.088	1.00
117_H	121_I	1.081	1.00
176_L	184_L	1.081	1.00
185_L	208_V	1.068	1.00
33_V	199_V	1.052	1.00
110_L	161_V	1.048	1.00
187_L	190_G	1.048	1.00
181_Q	205_D	1.026	1.00
127_K	130_E	1.026	1.00
24_V	47_L	1.020	1.00
181_Q	208_V	1.019	1.00
128_W	161_V	1.018	1.00
167_V	197_L	1.018	1.00
26_F	47_L	1.015	1.00
132_V	157_A	1.003	1.00
30_P	65_E	1.001	1.00
5_L	30_P	0.992	1.00
128_W	157_A	0.992	1.00
120_D	123_A	0.992	1.00
171_E	204_H	0.988	1.00
36_I	47_L	0.972	1.00
14_L	20_G	0.968	1.00
9_N	25_S	0.964	1.00
232_R	236_D	0.961	1.00
106_I	161_V	0.961	1.00
86_G	164_P	0.959	1.00
131_E	194_E	0.959	1.00
104_G	107_G	0.959	1.00
103_G	126_Q	0.958	1.00
189_R	192_V	0.957	1.00
118_Y	122_R	0.950	1.00
107_G	125_A	0.949	1.00
52_S	168_F	0.934	1.00
116_R	121_I	0.933	1.00
8_V	62_I	0.932	1.00
5_L	29_W	0.932	1.00
119_G	123_A	0.929	1.00
125_A	128_W	0.929	1.00
36_I	217_L	0.923	1.00
124_T	128_W	0.918	1.00
5_L	27_D	0.914	1.00
118_Y	121_I	0.912	1.00
8_V	47_L	0.911	1.00
39_E	220_K	0.907	1.00
169_M	199_V	0.905	1.00
216_L	230_T	0.902	1.00
28_L	198_A	0.889	1.00
185_L	211_L	0.885	1.00
142_L	145_T	0.885	1.00
51_I	200_V	0.884	1.00
120_D	124_T	0.884	1.00
167_V	199_V	0.876	1.00
33_V	189_R	0.875	1.00
10_N	59_Q	0.874	1.00
113_T	162_T	0.872	1.00
183_R	186_D	0.870	1.00
11_L	50_S	0.869	1.00
86_G	159_N	0.869	1.00
80_L	83_T	0.863	1.00
117_H	126_Q	0.863	1.00
28_L	200_V	0.859	1.00
186_D	189_R	0.858	1.00
73_S	80_L	0.857	1.00
13_H	46_T	0.849	1.00
88_V	169_M	0.848	1.00
146_F	154_L	0.842	1.00
88_V	156_I	0.840	1.00
23_D	223_Q	0.835	1.00
67_R	84_E	0.835	1.00
102_A	154_L	0.828	1.00
133_E	183_R	0.823	1.00
226_E	233_V	0.819	1.00
186_D	190_G	0.819	1.00
110_L	113_T	0.818	1.00
138_R	146_F	0.816	1.00
231_D	235_D	0.814	1.00
107_G	122_R	0.808	1.00
101_S	142_L	0.807	1.00
21_F	24_V	0.802	1.00
116_R	120_D	0.800	1.00
190_G	195_L	0.797	1.00
90_Q	148_G	0.794	1.00
110_L	121_I	0.793	1.00
34_L	200_V	0.792	1.00
135_P	139_I	0.788	1.00
96_L	151_Q	0.788	1.00
67_R	72_M	0.782	1.00
57_P	70_Y	0.782	1.00
138_R	150_M	0.779	1.00
224_V	227_S	0.766	1.00
97_R	108_E	0.763	1.00
37_V	209_A	0.762	1.00
50_S	62_I	0.760	1.00
50_S	55_L	0.759	1.00
36_I	200_V	0.759	1.00
121_I	126_Q	0.758	1.00
80_L	84_E	0.755	1.00
79_R	83_T	0.750	1.00
101_S	140_D	0.748	1.00
152_Q	175_G	0.746	1.00
37_V	218_V	0.746	1.00
56_T	70_Y	0.744	1.00
134_I	137_N	0.742	1.00
96_L	105_N	0.739	1.00
42_S	219_M	0.739	1.00
99_Q	144_T	0.737	1.00
88_V	159_N	0.727	1.00
128_W	132_V	0.720	1.00
6_L	64_Y	0.705	1.00
143_P	154_L	0.705	1.00
232_R	235_D	0.704	1.00
40_S	180_V	0.700	1.00
111_M	121_I	0.697	1.00
173_T	184_L	0.696	1.00
6_L	166_L	0.695	1.00
182_A	211_L	0.691	1.00
37_V	206_L	0.691	1.00
96_L	143_P	0.690	1.00
32_E	227_S	0.690	1.00
63_H	66_N	0.689	1.00
230_T	234_L	0.686	1.00
106_I	129_L	0.686	1.00
30_P	196_N	0.683	1.00
15_Y	55_L	0.682	1.00
166_L	198_A	0.682	1.00
61_E	70_Y	0.682	1.00
6_L	51_I	0.682	1.00
114_G	117_H	0.674	1.00
23_D	59_Q	0.670	1.00
180_V	183_R	0.669	1.00
101_S	105_N	0.663	1.00
134_I	138_R	0.660	1.00
188_L	199_V	0.658	1.00
148_G	153_R	0.658	1.00
137_N	141_D	0.658	1.00
107_G	111_M	0.655	1.00
121_I	125_A	0.653	1.00
14_L	59_Q	0.652	1.00
30_P	198_A	0.650	1.00
29_W	198_A	0.648	1.00
127_K	163_H	0.647	1.00
27_D	227_S	0.647	1.00
126_Q	135_P	0.647	1.00
67_R	80_L	0.643	1.00
14_L	18_G	0.640	1.00
40_S	204_H	0.639	1.00
122_R	125_A	0.638	1.00
168_F	200_V	0.637	1.00
186_D	211_L	0.634	1.00
147_S	150_M	0.632	1.00
203_T	208_V	0.632	1.00
68_S	72_M	0.631	1.00
210_R	234_L	0.631	1.00
100_V	108_E	0.630	1.00
21_F	47_L	0.629	1.00
213_A	230_T	0.628	1.00
128_W	131_E	0.627	1.00
226_E	232_R	0.625	1.00
177_D	180_V	0.622	1.00
24_V	224_V	0.620	1.00
201_I	213_A	0.620	1.00
44_K	171_E	0.619	1.00
146_F	150_M	0.617	1.00
19_K	23_D	0.612	1.00
105_N	143_P	0.612	1.00
14_L	22_S	0.609	1.00
10_N	13_H	0.608	1.00
100_V	105_N	0.605	1.00
72_M	80_L	0.605	1.00
14_L	17_P	0.603	1.00
210_R	230_T	0.597	1.00
91_H	151_Q	0.590	1.00
45_T	170_D	0.588	1.00
209_A	213_A	0.585	1.00
5_L	64_Y	0.583	1.00
5_L	198_A	0.583	1.00
218_V	233_V	0.582	1.00
128_W	160_L	0.577	1.00
44_K	170_D	0.576	1.00
205_D	208_V	0.575	1.00
85_W	166_L	0.575	1.00
86_G	162_T	0.574	1.00
19_K	59_Q	0.573	1.00
50_S	58_Q	0.572	1.00
110_L	162_T	0.572	1.00
55_L	58_Q	0.571	1.00
106_I	120_D	0.571	1.00
45_T	49_K	0.571	1.00
132_V	187_L	0.569	1.00
7_S	66_N	0.569	1.00
49_K	54_R	0.565	1.00
120_D	126_Q	0.560	1.00
81_L	85_W	0.560	1.00
97_R	100_V	0.559	1.00
5_L	166_L	0.558	1.00
51_I	62_I	0.557	1.00
26_F	34_L	0.555	1.00
153_R	183_R	0.551	1.00
44_K	204_H	0.551	1.00
110_L	114_G	0.548	1.00
123_A	126_Q	0.547	1.00
40_S	171_E	0.547	1.00
215_R	229_L	0.546	1.00
51_I	168_F	0.540	1.00
64_Y	166_L	0.540	1.00
103_G	106_I	0.540	1.00
97_R	105_N	0.536	1.00
36_I	202_V	0.536	1.00
230_T	233_V	0.536	1.00
40_S	153_R	0.535	1.00
192_V	197_L	0.534	1.00
120_D	129_L	0.534	1.00
105_N	108_E	0.533	1.00
13_H	16_A	0.533	1.00
220_K	223_Q	0.532	1.00
209_A	230_T	0.532	1.00
33_V	214_D	0.527	1.00
65_E	166_L	0.526	1.00
181_Q	185_L	0.525	1.00
173_T	208_V	0.524	1.00
191_L	195_L	0.522	1.00
106_I	157_A	0.521	1.00
159_N	167_V	0.519	1.00
192_V	195_L	0.511	1.00
156_I	184_L	0.510	1.00
13_H	20_G	0.510	1.00
153_R	180_V	0.508	1.00
98_R	151_Q	0.507	1.00
13_H	21_F	0.506	1.00
129_L	135_P	0.506	1.00
116_R	124_T	0.506	1.00
22_S	221_Q	0.504	1.00
62_I	69_L	0.501	1.00
179_S	183_R	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
3tuiC	2	0.9683	100	0.059	Contact Map
1g291	4	0.9762	100	0.066	Contact Map
2it1A	1	0.9524	100	0.071	Contact Map
2yyzA	1	0.9484	100	0.071	Contact Map
1v43A	2	0.9206	100	0.072	Contact Map
3rlfA	2	0.9484	100	0.079	Contact Map
1oxxK	1	0.9722	100	0.081	Contact Map
4mkiB	2	0.9802	100	0.083	Contact Map
4huqB	1	0.9603	100	0.084	Contact Map
3fvqA	2	0.9683	100	0.084	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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