YPKP - BACSU - GREMLIN Contacts

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YPKP - Uncharacterized protein YpkP

UniProt:	P54174	Sequences: MVRYSLLVVYIVYMLLKNMKQLFNQTMLDPRLSYKKQMALVYEQPKAFLEGCIGISGSVVTIHQPEPIPHGPVLYVHPRLRLAELALIAGYIEEPAGFIANPKVFRLPFIGQWLDRMDVISDGDSEKVYEDVTKQLEKGQSLILSLDGSIDPVELAARYHLPLVMVETKGTDNMQNGSFFKRLKPADIELSFSKAYIPANEKQLRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	206 (165)
Sequences:	9021 (6203)
Seq/√Len:	482.9

ECOLI - PLSC
BACSU - YPKP PLSC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
167_E	193_S	4.394	1.00
67_P	194_K	4.156	1.00
63_H	191_S	4.149	1.00
63_H	189_E	3.832	1.00
61_T	189_E	3.648	1.00
61_T	187_D	3.116	1.00
64_Q	67_P	2.937	1.00
59_V	187_D	2.566	1.00
133_T	137_E	2.529	1.00
73_V	141_S	2.300	1.00
162_P	197_I	2.212	1.00
166_V	192_F	2.149	1.00
169_K	189_E	2.142	1.00
134_K	138_K	2.141	1.00
105_F	121_S	2.139	1.00
96_A	143_I	2.092	1.00
71_G	162_P	2.028	1.00
73_V	164_V	1.990	1.00
76_V	152_P	1.920	1.00
105_F	115_D	1.893	1.00
101_N	149_S	1.889	1.00
75_Y	141_S	1.844	1.00
133_T	159_Y	1.811	1.00
133_T	158_R	1.786	1.00
77_H	166_V	1.780	1.00
169_K	191_S	1.778	1.00
97_G	140_Q	1.760	1.00
102_P	106_R	1.759	1.00
75_Y	164_V	1.721	1.00
127_K	131_D	1.668	1.00
136_L	161_L	1.646	1.00
154_E	158_R	1.634	1.00
112_Q	116_R	1.604	1.00
165_M	193_S	1.594	1.00
88_I	166_V	1.590	1.00
100_A	104_V	1.587	1.00
131_D	135_Q	1.561	1.00
103_K	122_D	1.536	1.00
80_L	172_D	1.477	1.00
132_V	155_L	1.464	1.00
197_I	200_N	1.461	1.00
73_V	162_P	1.445	1.00
111_G	115_D	1.419	1.00
131_D	134_K	1.394	1.00
100_A	105_F	1.349	1.00
97_G	135_Q	1.333	1.00
77_H	145_S	1.301	1.00
75_Y	92_I	1.260	1.00
77_H	88_I	1.257	1.00
164_V	195_A	1.256	1.00
62_I	192_F	1.252	1.00
176_N	179_F	1.236	1.00
91_Y	192_F	1.229	1.00
122_D	149_S	1.191	1.00
135_Q	140_Q	1.190	1.00
100_A	119_V	1.177	1.00
101_N	104_V	1.165	1.00
154_E	157_A	1.154	1.00
152_P	163_L	1.136	1.00
80_L	151_D	1.125	1.00
168_T	171_T	1.107	1.00
101_N	122_D	1.096	1.00
108_P	111_G	1.088	1.00
47_A	51_G	1.074	1.00
112_Q	115_D	1.068	1.00
71_G	197_I	1.066	1.00
156_A	163_L	1.057	1.00
107_L	110_I	1.057	1.00
99_I	128_V	1.054	1.00
101_N	150_I	1.045	1.00
74_L	152_P	1.034	1.00
162_P	198_P	1.007	1.00
165_M	195_A	1.006	1.00
134_K	137_E	1.006	1.00
72_P	139_G	0.996	1.00
157_A	201_E	0.991	1.00
35_K	39_A	0.987	1.00
127_K	130_E	0.986	1.00
174_M	186_A	0.985	1.00
91_Y	190_L	0.972	1.00
99_I	120_I	0.969	1.00
130_E	133_T	0.953	1.00
88_I	145_S	0.953	1.00
135_Q	142_L	0.949	1.00
57_G	185_P	0.936	1.00
62_I	65_P	0.930	1.00
197_I	201_E	0.924	1.00
60_V	87_L	0.923	1.00
80_L	171_T	0.921	1.00
160_H	198_P	0.913	1.00
132_V	142_L	0.913	1.00
130_E	134_K	0.908	1.00
104_V	114_L	0.908	1.00
60_V	90_G	0.905	1.00
162_P	195_A	0.891	1.00
98_F	143_I	0.889	1.00
71_G	141_S	0.886	1.00
150_I	170_G	0.882	1.00
92_I	192_F	0.878	1.00
78_P	147_D	0.877	1.00
120_I	142_L	0.867	1.00
77_H	143_I	0.865	1.00
85_L	100_A	0.863	1.00
147_D	151_D	0.857	1.00
152_P	156_A	0.846	1.00
122_D	125_S	0.840	1.00
114_L	119_V	0.834	1.00
49_L	53_I	0.833	1.00
72_P	161_L	0.832	1.00
156_A	159_Y	0.830	1.00
82_L	85_L	0.830	1.00
50_E	54_G	0.826	1.00
51_G	55_I	0.819	1.00
198_P	201_E	0.813	1.00
80_L	150_I	0.809	1.00
156_A	198_P	0.806	1.00
106_R	115_D	0.804	1.00
100_A	114_L	0.802	1.00
99_I	144_L	0.795	1.00
130_E	158_R	0.794	1.00
39_A	43_E	0.791	1.00
72_P	141_S	0.786	1.00
62_I	91_Y	0.784	1.00
50_E	53_I	0.777	1.00
50_E	55_I	0.771	1.00
107_L	111_G	0.768	1.00
133_T	155_L	0.768	1.00
88_I	168_T	0.751	1.00
171_T	188_I	0.751	1.00
120_I	128_V	0.744	1.00
85_L	89_A	0.736	1.00
120_I	132_V	0.727	1.00
81_R	175_Q	0.721	1.00
43_E	46_K	0.719	1.00
68_I	192_F	0.717	1.00
175_Q	179_F	0.717	1.00
128_V	132_V	0.714	1.00
47_A	50_E	0.713	1.00
137_E	159_Y	0.700	1.00
179_F	183_L	0.699	1.00
69_P	73_V	0.695	1.00
39_A	42_Y	0.693	1.00
42_Y	45_P	0.691	1.00
74_L	156_A	0.687	1.00
173_N	186_A	0.686	1.00
68_I	164_V	0.682	1.00
38_M	41_V	0.682	1.00
114_L	121_S	0.680	1.00
120_I	135_Q	0.678	1.00
81_R	171_T	0.677	1.00
155_L	159_Y	0.666	1.00
89_A	98_F	0.665	1.00
136_L	155_L	0.664	1.00
110_I	114_L	0.663	1.00
98_F	145_S	0.662	1.00
46_K	93_E	0.659	1.00
115_D	121_S	0.657	1.00
160_H	199_A	0.654	1.00
64_Q	192_F	0.652	1.00
51_G	54_G	0.650	1.00
82_L	150_I	0.648	1.00
75_Y	166_V	0.648	1.00
50_E	90_G	0.647	1.00
101_N	167_E	0.646	1.00
85_L	98_F	0.644	1.00
170_G	186_A	0.640	1.00
129_Y	132_V	0.640	1.00
36_K	41_V	0.638	1.00
94_E	141_S	0.635	1.00
67_P	192_F	0.631	1.00
40_L	43_E	0.630	1.00
170_G	173_N	0.630	1.00
135_Q	138_K	0.629	1.00
88_I	190_L	0.628	1.00
77_H	168_T	0.627	1.00
82_L	104_V	0.625	1.00
78_P	151_D	0.625	1.00
164_V	193_S	0.622	1.00
105_F	114_L	0.621	0.99
175_Q	178_S	0.620	0.99
41_V	45_P	0.617	0.99
104_V	111_G	0.616	0.99
59_V	185_P	0.614	0.99
92_I	96_A	0.613	0.99
104_V	110_I	0.611	0.99
106_R	109_F	0.608	0.99
118_D	140_Q	0.607	0.99
53_I	90_G	0.604	0.99
35_K	38_M	0.603	0.99
85_L	104_V	0.603	0.99
69_P	164_V	0.602	0.99
88_I	98_F	0.601	0.99
73_V	76_V	0.600	0.99
84_E	168_T	0.598	0.99
97_G	119_V	0.598	0.99
42_Y	46_K	0.597	0.99
102_P	105_F	0.597	0.99
157_A	198_P	0.596	0.99
36_K	39_A	0.596	0.99
44_Q	47_A	0.593	0.99
75_Y	192_F	0.592	0.99
89_A	119_V	0.591	0.99
37_Q	40_L	0.591	0.99
113_W	117_M	0.589	0.99
160_H	197_I	0.586	0.99
129_Y	154_E	0.584	0.99
81_R	150_I	0.584	0.99
43_E	47_A	0.580	0.99
170_G	174_M	0.579	0.99
71_G	94_E	0.578	0.99
45_P	89_A	0.574	0.99
58_S	174_M	0.573	0.99
62_I	190_L	0.572	0.99
144_L	155_L	0.572	0.99
41_V	44_Q	0.570	0.99
48_F	52_C	0.565	0.99
129_Y	158_R	0.562	0.99
60_V	91_Y	0.562	0.99
46_K	50_E	0.559	0.99
174_M	188_I	0.559	0.99
78_P	167_E	0.552	0.99
53_I	60_V	0.552	0.99
166_V	190_L	0.551	0.99
87_L	188_I	0.550	0.99
102_P	123_G	0.546	0.99
82_L	175_Q	0.543	0.99
173_N	176_N	0.539	0.99
84_E	114_L	0.537	0.99
84_E	89_A	0.536	0.99
108_P	112_Q	0.535	0.99
44_Q	48_F	0.533	0.98
118_D	138_K	0.532	0.98
109_F	112_Q	0.531	0.98
68_I	75_Y	0.529	0.98
153_V	163_L	0.528	0.98
99_I	132_V	0.525	0.98
36_K	42_Y	0.525	0.98
64_Q	194_K	0.524	0.98
167_E	191_S	0.523	0.98
85_L	145_S	0.511	0.98
79_R	146_L	0.508	0.98
58_S	188_I	0.504	0.98
65_P	194_K	0.504	0.98
141_S	164_V	0.504	0.98
58_S	87_L	0.503	0.98
123_G	126_E	0.502	0.98
96_A	141_S	0.501	0.98
179_F	182_R	0.500	0.98

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
1iuqA	1	0.9466	100	0.361	Contact Map
3sdbA	6	0.534	20.8	0.937	Contact Map
1k7jA	1	0.432	18.7	0.938	Contact Map
2mr6A	1	0.568	13.3	0.942	Contact Map
1jcuA	1	0.4223	13	0.943	Contact Map
1hruA	2	0.3932	12	0.943	Contact Map
2e11A	2	0.4806	9.7	0.946	Contact Map
3ilvA	2	0.4854	9.4	0.946	Contact Map
3ivzA	2	0.4854	9.2	0.946	Contact Map
2eqaA	1	0.432	7.5	0.948	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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