YDGJ - BACSU - GREMLIN Contacts

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YDGJ - Uncharacterized HTH-type transcriptional regulator YdgJ

UniProt:	P96708	Sequences: MTCQSLIYQLIVLTGKKGWVLASFCSEEAEILYQLQGVNKVIGVKFEACTGISQSRLELLTLLYHADEISQSDLQKKVNIDSAAVTRHLKQLESKGMVSRRRKPEDNRITLVRLTDQGRERIESSKKEKERFMKEMLANVSAEERRLLIDVLARMRNNINNIEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	164 (132)
Sequences:	21473 (15996)
Seq/√Len:	1392.3

ECOLI - MPRA SLYA MARR
BACSU - YDGJ YWAE YFIV YCGE YETL YUSO YXAD MHQR YYBA YDGG YSMB YKOM YWHA OHRR YPOP YDCH YHJH YWOH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
101_R	113_R	3.168	1.00
144_E	154_R	2.912	1.00
70_S	109_I	2.658	1.00
103_K	111_L	2.645	1.00
99_S	113_R	2.589	1.00
68_E	113_R	2.492	1.00
141_S	144_E	2.466	1.00
147_L	151_V	2.302	1.00
147_L	150_D	2.234	1.00
64_Y	122_I	2.094	1.00
102_R	110_T	2.065	1.00
56_R	95_K	2.056	1.00
140_V	151_V	1.967	1.00
70_S	73_D	1.936	1.00
64_Y	114_L	1.870	1.00
139_N	158_N	1.855	1.00
103_K	109_I	1.841	1.00
144_E	147_L	1.759	1.00
93_E	100_R	1.723	1.00
117_Q	121_R	1.688	1.00
148_L	151_V	1.678	1.00
59_L	88_H	1.643	1.00
96_G	117_Q	1.616	1.00
56_R	91_Q	1.575	1.00
71_Q	89_L	1.568	1.00
66_A	77_K	1.562	1.00
53_S	56_R	1.559	1.00
89_L	112_V	1.530	1.00
144_E	150_D	1.522	1.00
90_K	94_S	1.479	1.00
121_R	124_S	1.472	1.00
151_V	154_R	1.464	1.00
62_L	77_K	1.451	1.00
36_Q	39_N	1.446	1.00
64_Y	119_R	1.415	1.00
117_Q	120_E	1.382	1.00
50_T	128_E	1.371	1.00
45_K	48_A	1.295	1.00
81_D	84_A	1.288	1.00
144_E	151_V	1.279	1.00
100_R	110_T	1.250	1.00
90_K	107_N	1.235	1.00
71_Q	110_T	1.207	1.00
72_S	82_S	1.206	1.00
73_D	76_K	1.191	1.00
80_I	84_A	1.186	1.00
68_E	111_L	1.177	1.00
150_D	154_R	1.171	1.00
49_C	128_E	1.159	1.00
120_E	124_S	1.158	1.00
72_S	76_K	1.148	1.00
59_L	85_V	1.141	1.00
71_Q	82_S	1.116	1.00
149_I	153_A	1.094	1.00
83_A	86_T	1.093	1.00
71_Q	112_V	1.086	1.00
97_M	121_R	1.068	1.00
143_E	147_L	1.065	1.00
66_A	69_I	1.052	1.00
71_Q	85_V	1.052	1.00
145_R	149_I	1.041	1.00
84_A	87_R	1.017	1.00
86_T	90_K	1.010	1.00
69_I	73_D	1.006	1.00
55_S	88_H	1.005	1.00
50_T	124_S	0.993	1.00
81_D	87_R	0.988	1.00
99_S	115_T	0.977	1.00
50_T	125_S	0.959	1.00
90_K	93_E	0.956	1.00
69_I	77_K	0.949	1.00
114_L	118_G	0.936	1.00
34_Q	156_R	0.926	1.00
73_D	77_K	0.924	1.00
95_K	117_Q	0.923	1.00
95_K	121_R	0.920	1.00
128_E	131_R	0.914	1.00
119_R	123_E	0.910	1.00
102_R	107_N	0.909	1.00
63_L	98_V	0.908	1.00
67_D	119_R	0.901	1.00
40_K	43_G	0.898	1.00
58_E	78_V	0.898	1.00
106_D	109_I	0.897	1.00
39_N	43_G	0.891	1.00
133_M	136_M	0.887	1.00
80_I	85_V	0.877	1.00
142_A	146_R	0.868	1.00
116_D	120_E	0.865	1.00
30_E	34_Q	0.862	1.00
103_K	106_D	0.862	1.00
44_V	47_E	0.852	1.00
116_D	119_R	0.846	1.00
97_M	117_Q	0.845	1.00
87_R	90_K	0.840	1.00
71_Q	86_T	0.838	1.00
64_Y	126_K	0.836	1.00
51_G	95_K	0.833	1.00
64_Y	123_E	0.831	1.00
127_K	131_R	0.831	1.00
34_Q	153_A	0.823	1.00
89_L	98_V	0.817	1.00
67_D	113_R	0.814	1.00
101_R	111_L	0.811	1.00
57_L	125_S	0.809	1.00
140_V	155_M	0.807	1.00
55_S	84_A	0.803	1.00
124_S	128_E	0.800	1.00
89_L	93_E	0.797	1.00
129_K	133_M	0.795	1.00
147_L	154_R	0.794	1.00
68_E	101_R	0.792	1.00
93_E	98_V	0.786	1.00
87_R	91_Q	0.784	1.00
131_R	134_K	0.781	1.00
146_R	149_I	0.779	1.00
60_L	122_I	0.768	1.00
93_E	99_S	0.765	1.00
57_L	129_K	0.765	1.00
90_K	100_R	0.764	1.00
91_Q	94_S	0.763	1.00
104_P	111_L	0.754	1.00
66_A	73_D	0.752	1.00
59_L	74_L	0.751	1.00
32_L	35_L	0.749	1.00
59_L	78_V	0.748	1.00
38_V	156_R	0.747	1.00
75_Q	85_V	0.746	1.00
62_L	66_A	0.746	1.00
131_R	135_E	0.735	1.00
35_L	39_N	0.734	1.00
114_L	119_R	0.722	1.00
75_Q	82_S	0.721	1.00
141_S	145_R	0.719	1.00
34_Q	149_I	0.708	1.00
137_L	145_R	0.705	1.00
36_Q	40_K	0.705	1.00
153_A	157_N	0.701	1.00
37_G	41_V	0.699	1.00
62_L	78_V	0.697	1.00
130_E	134_K	0.689	1.00
43_G	47_E	0.686	1.00
146_R	150_D	0.680	1.00
85_V	89_L	0.679	1.00
44_V	48_A	0.672	1.00
127_K	130_E	0.665	1.00
91_Q	95_K	0.662	1.00
143_E	146_R	0.661	1.00
62_L	69_I	0.657	1.00
34_Q	39_N	0.657	1.00
135_E	138_A	0.656	1.00
154_R	158_N	0.652	1.00
56_R	88_H	0.640	1.00
124_S	127_K	0.637	1.00
34_Q	37_G	0.636	1.00
140_V	145_R	0.634	1.00
132_F	135_E	0.624	1.00
63_L	114_L	0.623	1.00
35_L	38_V	0.620	1.00
39_N	42_I	0.618	1.00
33_Y	37_G	0.616	1.00
96_G	99_S	0.615	1.00
61_T	65_H	0.614	1.00
63_L	69_I	0.611	1.00
62_L	74_L	0.609	1.00
32_L	42_I	0.608	1.00
43_G	46_F	0.606	1.00
61_T	126_K	0.603	1.00
151_V	155_M	0.600	1.00
28_E	31_I	0.598	1.00
57_L	122_I	0.598	1.00
38_V	41_V	0.598	1.00
72_S	75_Q	0.597	1.00
41_V	45_K	0.596	1.00
120_E	123_E	0.594	1.00
28_E	32_L	0.585	1.00
58_E	62_L	0.582	1.00
38_V	43_G	0.569	1.00
126_K	130_E	0.558	1.00
82_S	86_T	0.555	1.00
55_S	80_I	0.543	1.00
113_R	119_R	0.540	1.00
72_S	109_I	0.538	1.00
70_S	103_K	0.530	1.00
151_V	158_N	0.529	1.00
92_L	97_M	0.527	1.00
32_L	36_Q	0.526	1.00
102_R	106_D	0.521	1.00
123_E	126_K	0.521	1.00
30_E	33_Y	0.521	1.00
36_Q	43_G	0.520	1.00
141_S	154_R	0.517	1.00
60_L	64_Y	0.513	1.00
129_K	132_F	0.511	1.00
29_A	33_Y	0.509	1.00
33_Y	36_Q	0.508	1.00
42_I	46_F	0.504	1.00
138_A	158_N	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
4rguA	4	0.8537	99.9	0.34	Contact Map
3cjnA	2	0.872	99.9	0.344	Contact Map
3bj6A	2	0.9146	99.9	0.347	Contact Map
3e6mA	2	0.9024	99.9	0.348	Contact Map
3boqA	2	0.811	99.9	0.353	Contact Map
3deuA	2	0.7805	99.9	0.355	Contact Map
3u2rA	4	0.7927	99.9	0.357	Contact Map
3bddA	2	0.8476	99.9	0.359	Contact Map
2nyxA	2	0.878	99.9	0.361	Contact Map
3zplA	2	0.9207	99.9	0.361	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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