YHJB - ECOLI - GREMLIN Contacts

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YHJB - Putative HTH-type transcriptional regulator YhjB

UniProt:	P37640	Sequences: MQIVMFDRQSIFIHGMKISLQQRIPGVSIQGASQADELWQKLESYPEALVMLDGDQDGEFCYWLLQKTVVQFPEVKVLITATDCNKRWLQEVIHFNVLAIVPRDSTVETFALAVNSAAMGMMFLPGDWRTTPEKDIKDLKSLSARQREILTMLAAGESNKEIGRALNISTGTVKAHLESLYRRLEVKNRTQAAMMLNISS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12246
Length:	200 (183)
Sequences:	80258 (57268)
Seq/√Len:	4233.3

ECOLI - YHJB EVGA FIMZ UVRY YJJQ NARP RCSA YGEK UHPA RCSB BGLJ NARL CUSR DPIA CREB YEDW PHOP CSGD DCUR QSEB BASR PHOB OMPR ARCA KDPE RSTA BAER TORR CPXR YPDB BARA ARCB TORS RSSB RCSC YEHT NTRC CHEB GLRR ZRAR ATOC EVGS RCSD CHEY
BACSU - CMPA LIAR YXJL DEGU YFIK YVFU CITT YDFI YHCZ MALR PHOP DESR YKOG DCTR YVRH RESD YVCP YYCF YXDJ YCBL YCLJ YESN GLNL BCER CSSR YRKP CHEB NATR YBDJ LYTT SP0A CHEV SP0F CHEY CCDB
HALSA - Q9HR09 CHEB Q9HRE5 Q9HNM3 BAT O51970 Q9HP91 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
13_I	33_S	3.289	1.00
13_I	31_G	3.243	1.00
6_F	38_L	2.776	1.00
39_W	67_K	2.601	1.00
36_D	58_G	2.591	1.00
30_Q	47_E	2.510	1.00
35_A	59_E	2.502	1.00
34_Q	58_G	2.399	1.00
43_E	71_Q	2.374	1.00
59_E	67_K	2.335	1.00
17_K	31_G	2.290	1.00
19_S	107_V	2.082	1.00
2_Q	28_S	2.046	1.00
32_A	41_K	2.018	1.00
171_G	174_K	1.999	1.00
2_Q	30_Q	1.985	1.00
52_L	64_L	1.947	1.00
17_K	21_Q	1.897	1.00
89_L	109_T	1.893	1.00
33_S	37_E	1.892	1.00
55_D	83_D	1.877	1.00
79_I	97_V	1.751	1.00
65_L	77_V	1.733	1.00
4_V	32_A	1.727	1.00
69_V	98_L	1.713	1.00
79_I	92_V	1.706	1.00
34_Q	37_E	1.705	1.00
30_Q	41_K	1.684	1.00
67_K	71_Q	1.654	1.00
145_R	148_E	1.599	1.00
25_P	111_A	1.586	1.00
35_A	64_L	1.571	1.00
99_A	113_A	1.546	1.00
59_E	63_W	1.545	1.00
41_K	45_Y	1.537	1.00
159_N	174_K	1.532	1.00
86_K	106_T	1.526	1.00
66_Q	95_F	1.516	1.00
30_Q	45_Y	1.509	1.00
60_F	63_W	1.509	1.00
176_H	179_S	1.484	1.00
72_F	75_V	1.482	1.00
20_L	114_V	1.465	1.00
41_K	44_S	1.423	1.00
83_D	88_W	1.419	1.00
67_K	70_V	1.401	1.00
65_L	79_I	1.401	1.00
158_S	161_E	1.393	1.00
42_L	68_T	1.388	1.00
151_T	155_A	1.384	1.00
146_Q	183_R	1.375	1.00
157_E	165_A	1.358	1.00
39_W	64_L	1.348	1.00
36_D	59_E	1.342	1.00
152_M	165_A	1.339	1.00
50_V	75_V	1.338	1.00
63_W	66_Q	1.333	1.00
49_L	114_V	1.308	1.00
10_S	33_S	1.270	1.00
7_D	13_I	1.268	1.00
41_K	47_E	1.261	1.00
54_G	62_Y	1.242	1.00
98_L	120_G	1.229	1.00
78_L	117_A	1.212	1.00
98_L	117_A	1.210	1.00
6_F	56_Q	1.209	1.00
52_L	65_L	1.196	1.00
32_A	38_L	1.185	1.00
27_V	115_N	1.181	1.00
37_E	41_K	1.181	1.00
39_W	59_E	1.167	1.00
54_G	79_I	1.145	1.00
40_Q	44_S	1.145	1.00
8_R	53_D	1.144	1.00
4_V	38_L	1.144	1.00
85_N	88_W	1.143	1.00
62_Y	92_V	1.132	1.00
111_A	115_N	1.128	1.00
2_Q	45_Y	1.127	1.00
36_D	40_Q	1.122	1.00
152_M	156_G	1.119	1.00
37_E	40_Q	1.113	1.00
62_Y	91_E	1.098	1.00
91_E	95_F	1.087	1.00
26_G	115_N	1.086	1.00
4_V	47_E	1.077	1.00
86_K	90_Q	1.069	1.00
49_L	118_A	1.068	1.00
147_R	151_T	1.067	1.00
3_I	27_V	1.050	1.00
161_E	165_A	1.045	1.00
175_A	178_E	1.035	1.00
132_P	139_L	1.010	1.00
171_G	175_A	1.001	1.00
94_H	115_N	1.001	1.00
90_Q	94_H	0.993	1.00
66_Q	91_E	0.993	1.00
38_L	64_L	0.989	1.00
52_L	77_V	0.987	1.00
42_L	72_F	0.983	1.00
160_K	170_T	0.982	1.00
109_T	112_L	0.980	1.00
4_V	41_K	0.973	1.00
87_R	91_E	0.964	1.00
152_M	157_E	0.964	1.00
112_L	116_S	0.958	1.00
148_E	151_T	0.949	1.00
157_E	161_E	0.949	1.00
10_S	14_H	0.948	1.00
5_M	16_M	0.930	1.00
17_K	29_I	0.925	1.00
16_M	80_T	0.921	1.00
54_G	60_F	0.920	1.00
50_V	68_T	0.919	1.00
32_A	37_E	0.919	1.00
6_F	50_V	0.918	1.00
39_W	43_E	0.914	1.00
6_F	32_A	0.899	1.00
62_Y	95_F	0.896	1.00
38_L	42_L	0.892	1.00
89_L	102_P	0.889	1.00
51_M	110_F	0.887	1.00
4_V	42_L	0.882	1.00
27_V	111_A	0.877	1.00
134_K	139_L	0.875	1.00
65_L	97_V	0.874	1.00
11_I	15_G	0.874	1.00
172_T	176_H	0.869	1.00
10_S	13_I	0.867	1.00
91_E	94_H	0.864	1.00
174_K	177_L	0.861	1.00
177_L	181_Y	0.861	1.00
50_V	77_V	0.857	1.00
109_T	113_A	0.857	1.00
40_Q	43_E	0.854	1.00
65_L	95_F	0.847	1.00
54_G	88_W	0.837	1.00
63_W	67_K	0.833	1.00
86_K	89_L	0.828	1.00
52_L	79_I	0.823	1.00
76_K	98_L	0.818	1.00
170_T	174_K	0.813	1.00
5_M	29_I	0.809	1.00
160_K	164_R	0.809	1.00
144_A	148_E	0.807	1.00
78_L	113_A	0.807	1.00
56_Q	64_L	0.801	1.00
148_E	152_M	0.794	1.00
18_I	22_Q	0.792	1.00
14_H	17_K	0.791	1.00
88_W	91_E	0.781	1.00
179_S	182_R	0.778	1.00
84_C	102_P	0.778	1.00
107_V	111_A	0.777	1.00
171_G	178_E	0.774	1.00
16_M	110_F	0.772	1.00
146_Q	149_I	0.769	1.00
181_Y	186_V	0.768	1.00
93_I	113_A	0.766	1.00
152_M	162_I	0.766	1.00
143_S	183_R	0.761	1.00
66_Q	70_V	0.760	1.00
121_M	125_P	0.754	1.00
51_M	80_T	0.752	1.00
64_L	68_T	0.752	1.00
54_G	83_D	0.748	1.00
131_T	148_E	0.746	1.00
117_A	120_G	0.746	1.00
12_F	105_S	0.744	1.00
161_E	164_R	0.739	1.00
134_K	137_K	0.739	1.00
168_I	173_V	0.739	1.00
116_S	119_M	0.736	1.00
51_M	114_V	0.732	1.00
22_Q	25_P	0.729	1.00
178_E	182_R	0.726	1.00
35_A	39_W	0.724	1.00
105_S	110_F	0.723	1.00
42_L	75_V	0.722	1.00
6_F	64_L	0.719	1.00
25_P	115_N	0.713	1.00
167_N	170_T	0.708	1.00
153_L	177_L	0.707	1.00
2_Q	47_E	0.707	1.00
175_A	179_S	0.705	1.00
42_L	47_E	0.702	1.00
135_D	185_E	0.702	1.00
90_Q	108_E	0.700	1.00
14_H	18_I	0.698	1.00
55_D	82_T	0.696	1.00
118_A	121_M	0.690	1.00
5_M	17_K	0.687	1.00
106_T	109_T	0.687	1.00
35_A	58_G	0.687	1.00
59_E	64_L	0.686	1.00
46_P	72_F	0.683	1.00
39_W	42_L	0.681	1.00
149_I	153_L	0.676	1.00
159_N	163_G	0.676	1.00
9_Q	12_F	0.675	1.00
68_T	77_V	0.668	1.00
158_S	162_I	0.662	1.00
87_R	108_E	0.655	1.00
78_L	99_A	0.655	1.00
80_T	105_S	0.651	1.00
113_A	117_A	0.646	1.00
43_E	72_F	0.646	1.00
131_T	147_R	0.642	1.00
7_D	56_Q	0.640	1.00
43_E	67_K	0.638	1.00
4_V	31_G	0.634	1.00
108_E	112_L	0.630	1.00
76_K	118_A	0.630	1.00
132_P	135_D	0.626	1.00
69_V	76_K	0.625	1.00
12_F	15_G	0.624	1.00
68_T	73_P	0.623	1.00
116_S	121_M	0.621	1.00
9_Q	82_T	0.619	1.00
35_A	56_Q	0.616	1.00
152_M	155_A	0.614	1.00
81_A	89_L	0.611	1.00
15_G	19_S	0.610	1.00
19_S	111_A	0.605	1.00
145_R	176_H	0.604	1.00
94_H	112_L	0.602	1.00
62_Y	88_W	0.602	1.00
155_A	165_A	0.602	1.00
2_Q	48_A	0.599	1.00
143_S	146_Q	0.597	1.00
51_M	78_L	0.594	1.00
92_V	97_V	0.588	1.00
5_M	31_G	0.584	1.00
21_Q	29_I	0.583	1.00
142_L	146_Q	0.581	1.00
99_A	116_S	0.578	1.00
54_G	92_V	0.577	1.00
42_L	50_V	0.575	1.00
13_I	17_K	0.573	1.00
76_K	120_G	0.570	1.00
74_E	124_L	0.569	1.00
52_L	56_Q	0.566	1.00
3_I	49_L	0.563	1.00
87_R	90_Q	0.558	1.00
39_W	71_Q	0.557	1.00
135_D	186_V	0.552	1.00
89_L	106_T	0.552	1.00
127_D	130_T	0.548	1.00
69_V	75_V	0.545	1.00
86_K	108_E	0.543	1.00
105_S	109_T	0.542	1.00
150_L	153_L	0.535	1.00
162_I	166_L	0.532	1.00
76_K	121_M	0.530	1.00
76_K	124_L	0.529	1.00
113_A	116_S	0.526	1.00
115_N	119_M	0.524	1.00
8_R	81_A	0.520	1.00
159_N	170_T	0.520	1.00
65_L	69_V	0.519	1.00
81_A	103_R	0.518	1.00
53_D	103_R	0.517	1.00
31_G	45_Y	0.515	1.00
157_E	162_I	0.513	1.00
52_L	68_T	0.512	1.00
20_L	27_V	0.511	1.00
135_D	138_D	0.510	1.00
151_T	154_A	0.510	1.00
15_G	18_I	0.506	1.00
133_E	147_R	0.504	1.00
21_Q	28_S	0.502	1.00
34_Q	56_Q	0.502	1.00
37_E	58_G	0.501	1.00
27_V	118_A	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
1yioA	1	0.98	100	0.162	Contact Map
3c3wA	2	0.995	100	0.166	Contact Map
4gvpA	1	0.995	100	0.17	Contact Map
1a04A	1	0.975	100	0.188	Contact Map
4ldzA	2	0.96	100	0.192	Contact Map
3kloA	2	0.995	100	0.199	Contact Map
4hyeA	2	0.98	100	0.215	Contact Map
3q9sA	1	0.965	100	0.222	Contact Map
4b09A	2	0.915	100	0.224	Contact Map
1ys7A	2	0.985	100	0.228	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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