PKSA - BACSU - GREMLIN Contacts

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PKSA - HTH-type transcriptional regulator PksA

UniProt:	O34381	Sequences: MPKQIDHEKRRKQIAEATWRVILERGMEGASARNIAKEAGLSLGALRHYFSTQDELLAFAMKLVQEKVTDRIKDIAVRDLLPKEKVLQILLEMVPTNEETIREMEVWFAFTAYARHKKDMFDASHDGIFSGMRNLIAYLDESDLLKQNADKDIEAERLYALVDGLALHAMLDPVRVNKDRIKRVIMQHVESICVEDTRETQKRHP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (185)
Sequences:	47673 (38542)
Seq/√Len:	2833.6

ECOLI - BETI ACRR ENVR UIDR COMR SLMA RUTR FABR NEMR YJDC RCDA BDCR YBIH
BACSU - PKSA YFIR FADR BSCR YVDT YHGD YVKB YTTP YDGC LMRA YEZE YXAF YDES YVAF YCNC YOBS YUXN YERO
HALSA - Q9HRF3
SULSO - Q97VV1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_R	43_L	4.118	1.00
25_R	34_N	3.990	1.00
20_R	38_E	3.497	1.00
51_S	55_E	2.706	1.00
22_I	30_A	2.311	1.00
52_T	55_E	2.239	1.00
21_V	38_E	2.166	1.00
21_V	34_N	2.088	1.00
36_A	46_L	2.067	1.00
11_R	59_F	2.020	1.00
21_V	25_R	1.988	1.00
24_E	38_E	1.985	1.00
17_A	38_E	1.974	1.00
10_R	13_Q	1.926	1.00
21_V	30_A	1.920	1.00
187_Q	191_S	1.913	1.00
12_K	63_L	1.910	1.00
87_L	186_M	1.841	1.00
13_Q	17_A	1.822	1.00
33_R	37_K	1.819	1.00
91_L	182_K	1.774	1.00
85_K	138_Y	1.770	1.00
133_R	152_D	1.762	1.00
17_A	20_R	1.747	1.00
133_R	137_A	1.743	1.00
81_L	84_E	1.737	1.00
19_W	63_L	1.723	1.00
18_T	22_I	1.622	1.00
15_A	59_F	1.620	1.00
42_S	45_A	1.601	1.00
32_A	47_R	1.598	1.00
11_R	49_Y	1.590	1.00
19_W	64_V	1.569	1.00
12_K	16_E	1.562	1.00
137_A	140_D	1.542	1.00
137_A	151_K	1.515	1.00
20_R	24_E	1.499	1.00
32_A	43_L	1.493	1.00
34_N	38_E	1.484	1.00
34_N	37_K	1.476	1.00
137_A	141_E	1.469	1.00
31_S	34_N	1.455	1.00
157_R	161_L	1.447	1.00
59_F	62_K	1.422	1.00
50_F	59_F	1.420	1.00
63_L	67_K	1.409	1.00
19_W	60_A	1.394	1.00
30_A	35_I	1.382	1.00
18_T	56_L	1.374	1.00
138_Y	142_S	1.344	1.00
26_G	30_A	1.311	1.00
25_R	29_G	1.297	1.00
16_E	63_L	1.289	1.00
140_D	147_Q	1.288	1.00
9_K	13_Q	1.288	1.00
187_Q	190_E	1.286	1.00
32_A	46_L	1.267	1.00
58_A	62_K	1.260	1.00
139_L	145_L	1.260	1.00
26_G	29_G	1.252	1.00
17_A	21_V	1.243	1.00
139_L	144_L	1.242	1.00
41_L	45_A	1.206	1.00
45_A	48_H	1.205	1.00
43_L	47_R	1.189	1.00
182_K	186_M	1.185	1.00
87_L	91_L	1.185	1.00
153_I	183_R	1.183	1.00
71_R	92_E	1.173	1.00
186_M	190_E	1.169	1.00
42_S	48_H	1.168	1.00
44_G	48_H	1.152	1.00
83_K	87_L	1.139	1.00
136_I	139_L	1.129	1.00
177_N	180_R	1.119	1.00
73_K	131_G	1.114	1.00
17_A	39_A	1.113	1.00
129_F	133_R	1.112	1.00
55_E	59_F	1.108	1.00
22_I	27_M	1.104	1.00
88_Q	91_L	1.104	1.00
150_D	153_I	1.103	1.00
84_E	88_Q	1.091	1.00
10_R	49_Y	1.084	1.00
9_K	12_K	1.082	1.00
135_L	139_L	1.072	1.00
54_D	58_A	1.071	1.00
18_T	60_A	1.067	1.00
140_D	149_A	1.066	1.00
15_A	60_A	1.058	1.00
15_A	50_F	1.052	1.00
19_W	23_L	1.049	1.00
25_R	38_E	1.042	1.00
47_R	52_T	1.038	1.00
35_I	56_L	1.028	1.00
55_E	58_A	1.023	1.00
16_E	20_R	1.020	1.00
183_R	186_M	1.017	1.00
118_K	121_F	1.012	1.00
27_M	57_L	1.004	1.00
181_I	184_V	0.997	1.00
45_A	49_Y	0.995	1.00
80_L	88_Q	0.994	1.00
178_K	182_K	0.991	1.00
20_R	102_R	0.989	1.00
46_L	56_L	0.978	1.00
28_E	113_Y	0.974	1.00
105_E	109_A	0.969	1.00
110_F	113_Y	0.967	1.00
131_G	134_N	0.967	1.00
10_R	41_L	0.951	1.00
91_L	186_M	0.948	1.00
117_K	120_M	0.943	1.00
36_A	43_L	0.939	1.00
92_E	95_P	0.938	1.00
81_L	144_L	0.936	1.00
73_K	77_V	0.936	1.00
75_I	92_E	0.935	1.00
160_A	164_G	0.922	1.00
85_K	135_L	0.916	1.00
127_G	131_G	0.916	1.00
64_V	67_K	0.908	1.00
7_H	48_H	0.908	1.00
79_D	85_K	0.906	1.00
140_D	151_K	0.906	1.00
59_F	63_L	0.901	1.00
84_E	87_L	0.901	1.00
100_T	103_E	0.899	1.00
69_T	73_K	0.898	1.00
88_Q	92_E	0.896	1.00
62_K	66_E	0.894	1.00
134_N	138_Y	0.894	1.00
129_F	156_E	0.892	1.00
138_Y	141_E	0.891	1.00
188_H	191_S	0.890	1.00
179_D	182_K	0.884	1.00
134_N	137_A	0.881	1.00
146_K	149_A	0.881	1.00
71_R	74_D	0.868	1.00
8_E	12_K	0.866	1.00
15_A	63_L	0.862	1.00
75_I	88_Q	0.857	1.00
7_H	10_R	0.849	1.00
63_L	66_E	0.849	1.00
109_A	113_Y	0.843	1.00
43_L	48_H	0.839	1.00
169_A	172_D	0.838	1.00
152_D	156_E	0.836	1.00
130_S	134_N	0.822	1.00
104_M	107_W	0.820	1.00
21_V	24_E	0.819	1.00
95_P	178_K	0.817	1.00
13_Q	16_E	0.816	1.00
105_E	108_F	0.815	1.00
54_D	117_K	0.815	1.00
37_K	43_L	0.810	1.00
176_V	180_R	0.806	1.00
91_L	95_P	0.802	1.00
149_A	154_E	0.792	1.00
69_T	127_G	0.790	1.00
70_D	74_D	0.787	1.00
13_Q	39_A	0.783	1.00
180_R	184_V	0.780	1.00
133_R	151_K	0.777	1.00
140_D	143_D	0.773	1.00
66_E	70_D	0.763	1.00
135_L	138_Y	0.760	1.00
87_L	182_K	0.756	1.00
182_K	187_Q	0.755	1.00
80_L	84_E	0.755	1.00
82_P	142_S	0.754	1.00
6_D	9_K	0.745	1.00
32_A	53_Q	0.743	1.00
105_E	113_Y	0.740	1.00
14_I	46_L	0.738	1.00
153_I	156_E	0.738	1.00
83_K	190_E	0.731	1.00
153_I	180_R	0.726	1.00
96_T	100_T	0.724	1.00
24_E	34_N	0.723	1.00
133_R	155_A	0.721	1.00
181_I	185_I	0.721	1.00
114_A	118_K	0.715	1.00
16_E	19_W	0.708	1.00
27_M	53_Q	0.706	1.00
23_L	102_R	0.705	1.00
168_H	171_L	0.704	1.00
82_P	139_L	0.702	1.00
160_A	163_D	0.701	1.00
157_R	160_A	0.700	1.00
33_R	47_R	0.700	1.00
127_G	130_S	0.698	1.00
69_T	131_G	0.693	1.00
14_I	39_A	0.689	1.00
15_A	19_W	0.686	1.00
79_D	84_E	0.686	1.00
151_K	155_A	0.685	1.00
25_R	30_A	0.682	1.00
184_V	188_H	0.682	1.00
114_A	117_K	0.679	1.00
62_K	123_A	0.677	1.00
130_S	133_R	0.676	1.00
182_K	185_I	0.672	1.00
32_A	36_A	0.669	1.00
129_F	152_D	0.669	1.00
153_I	157_R	0.668	1.00
10_R	45_A	0.665	1.00
39_A	42_S	0.663	1.00
180_R	183_R	0.661	1.00
168_H	172_D	0.658	1.00
140_D	145_L	0.651	1.00
113_Y	116_H	0.651	1.00
178_K	181_I	0.645	1.00
98_E	178_K	0.644	1.00
101_I	105_E	0.641	1.00
54_D	119_D	0.641	1.00
132_M	139_L	0.633	1.00
90_L	158_L	0.633	1.00
117_K	121_F	0.632	1.00
118_K	122_D	0.631	1.00
179_D	183_R	0.629	1.00
87_L	90_L	0.628	1.00
67_K	70_D	0.628	1.00
139_L	143_D	0.625	1.00
76_A	134_N	0.614	1.00
116_H	119_D	0.613	1.00
74_D	92_E	0.612	1.00
78_R	88_Q	0.611	1.00
115_R	118_K	0.609	1.00
153_I	187_Q	0.607	1.00
79_D	88_Q	0.604	1.00
14_I	49_Y	0.601	1.00
7_H	49_Y	0.595	1.00
104_M	109_A	0.590	1.00
107_W	110_F	0.588	1.00
95_P	99_E	0.587	1.00
183_R	187_Q	0.584	1.00
22_I	57_L	0.579	1.00
43_L	46_L	0.578	1.00
126_D	130_S	0.577	1.00
6_D	10_R	0.576	1.00
71_R	96_T	0.571	1.00
75_I	78_R	0.568	1.00
58_A	119_D	0.564	1.00
82_P	144_L	0.563	1.00
27_M	54_D	0.562	1.00
184_V	187_Q	0.556	1.00
87_L	190_E	0.556	1.00
70_D	73_K	0.552	1.00
184_V	191_S	0.551	1.00
161_L	164_G	0.547	1.00
58_A	123_A	0.545	1.00
19_W	67_K	0.545	1.00
154_E	157_R	0.542	1.00
27_M	30_A	0.541	1.00
39_A	43_L	0.541	1.00
93_M	97_N	0.538	1.00
83_K	144_L	0.537	1.00
119_D	122_D	0.537	1.00
185_I	188_H	0.536	1.00
136_I	151_K	0.536	1.00
81_L	85_K	0.536	1.00
74_D	78_R	0.535	1.00
136_I	140_D	0.529	1.00
114_A	121_F	0.519	1.00
163_D	168_H	0.518	1.00
122_D	126_D	0.517	1.00
36_A	41_L	0.515	1.00
10_R	42_S	0.515	1.00
109_A	112_A	0.514	1.00
90_L	93_M	0.513	1.00
95_P	182_K	0.510	1.00
106_V	110_F	0.510	1.00
90_L	162_V	0.508	1.00
185_I	189_V	0.508	1.00
141_E	145_L	0.507	1.00
33_R	42_S	0.503	1.00
36_A	42_S	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
2gfnA	2	0.9171	100	0.213	Contact Map
1ui5A	2	0.9707	100	0.235	Contact Map
3he0A	2	0.9073	100	0.235	Contact Map
2d6yA	2	0.8927	100	0.24	Contact Map
2xdnA	2	0.9561	100	0.241	Contact Map
2np5A	3	0.9122	100	0.243	Contact Map
2iaiA	2	0.922	100	0.244	Contact Map
2nx4A	2	0.9268	100	0.244	Contact Map
3eupA	2	0.9561	100	0.247	Contact Map
4udsA	2	0.8927	100	0.248	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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