YXDJ - BACSU - GREMLIN Contacts

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YXDJ - Transcriptional regulatory protein YxdJ

UniProt:	P42421	Sequences: MNKIMIVEDSEDIRGLLQNYLEKYGYQTVVAADFTAVLDVFLREKPDVVLLDINLPAYDGYYWCRQIRQHSTSPIIFISARSGEMDQVMAIENGGDDYIEKPFSYDIVLAKIKSQIRRAYGEYAAKQGEKVVEYAGVQLFVERFELRFQDEKSELSKKESKLLEVLLERGEKVTSRDRLMEKTWDTDIFIDDNTLNVYITRLRKKLRELNAPVSIEAVRGEGYQLRAQS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	229 (208)
Sequences:	77350 (54939)
Seq/√Len:	3809.3

ECOLI - RSTA KDPE YEDW CPXR ARCA CUSR PHOP BAER PHOB QSEB TORR CREB OMPR BASR UVRY DCUR DPIA YHJB EVGA NARP FIMZ YJJQ UHPA NARL RCSB YGEK BGLJ YEHT CSGD RCSA RSSB BARA CHEB TORS ARCB RCSC YPDB NTRC GLRR EVGS ATOC ZRAR RCSD
BACSU - YXDJ YVCP BCER YCLJ YVRH YYCF YCBL PHOP YRKP CSSR CITT YKOG YFIK RESD MALR CMPA YDFI LIAR YVFU DCTR DESR YXJL DEGU YBDJ YHCZ YESN LYTT CHEB GLNL NATR SP0A CHEV CCDB
HALSA - CHEB Q9HR09 Q9HNM3 Q9HRE5 BAT O51970 Q9HP91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	30_V	3.741	1.00
14_R	32_A	3.299	1.00
18_Q	30_V	3.178	1.00
7_V	37_V	2.777	1.00
38_L	66_Q	2.699	1.00
35_T	57_A	2.610	1.00
34_F	58_Y	2.520	1.00
29_V	46_P	2.517	1.00
42_L	70_H	2.430	1.00
33_D	57_A	2.421	1.00
58_Y	66_Q	2.363	1.00
3_K	29_V	2.200	1.00
3_K	27_Q	2.100	1.00
20_Y	105_Y	2.059	1.00
31_A	40_V	2.025	1.00
18_Q	22_E	2.022	1.00
24_Y	109_L	1.951	1.00
87_Q	107_I	1.904	1.00
193_N	196_N	1.904	1.00
32_A	36_A	1.903	1.00
54_N	81_R	1.901	1.00
51_L	63_W	1.878	1.00
64_C	75_I	1.843	1.00
158_K	161_K	1.820	1.00
77_F	90_A	1.773	1.00
33_D	36_A	1.729	1.00
40_V	44_E	1.728	1.00
29_V	40_V	1.722	1.00
5_M	31_A	1.719	1.00
66_Q	70_H	1.711	1.00
84_E	104_S	1.705	1.00
77_F	95_G	1.704	1.00
68_R	96_D	1.681	1.00
29_V	44_E	1.646	1.00
58_Y	62_Y	1.622	1.00
164_E	168_E	1.608	1.00
59_D	62_Y	1.572	1.00
34_F	63_W	1.559	1.00
97_D	111_K	1.545	1.00
136_G	149_Q	1.511	1.00
66_Q	69_Q	1.488	1.00
176_R	196_N	1.487	1.00
40_V	43_R	1.479	1.00
198_Y	201_R	1.469	1.00
21_L	112_I	1.467	1.00
65_R	93_N	1.457	1.00
64_C	77_F	1.455	1.00
165_V	182_K	1.446	1.00
41_F	67_I	1.445	1.00
81_R	86_D	1.426	1.00
62_Y	65_R	1.413	1.00
49_V	73_S	1.406	1.00
38_L	63_W	1.384	1.00
96_D	118_R	1.379	1.00
35_T	58_Y	1.377	1.00
48_V	112_I	1.374	1.00
96_D	115_Q	1.331	1.00
40_V	46_P	1.321	1.00
8_E	14_R	1.311	1.00
76_I	115_Q	1.310	1.00
51_L	64_C	1.293	1.00
165_V	169_R	1.287	1.00
11_E	32_A	1.283	1.00
53_I	61_Y	1.265	1.00
53_I	77_F	1.263	1.00
9_D	52_D	1.260	1.00
39_D	43_R	1.255	1.00
199_I	203_R	1.249	1.00
38_L	58_Y	1.243	1.00
3_K	44_E	1.235	1.00
7_V	55_L	1.229	1.00
31_A	37_V	1.212	1.00
140_F	143_R	1.205	1.00
36_A	39_D	1.202	1.00
159_E	205_K	1.194	1.00
41_F	71_S	1.175	1.00
26_Y	113_K	1.174	1.00
36_A	40_V	1.170	1.00
61_Y	90_A	1.167	1.00
5_M	46_P	1.166	1.00
35_T	39_D	1.162	1.00
61_Y	89_M	1.153	1.00
178_R	182_K	1.152	1.00
5_M	37_V	1.142	1.00
83_G	86_D	1.141	1.00
92_E	113_K	1.133	1.00
133_E	138_Q	1.126	1.00
138_Q	147_R	1.119	1.00
131_V	138_Q	1.109	1.00
109_L	113_K	1.109	1.00
89_M	93_N	1.107	1.00
175_S	178_R	1.106	1.00
194_T	198_Y	1.102	1.00
84_E	88_V	1.083	1.00
65_R	89_M	1.081	1.00
24_Y	113_K	1.075	1.00
4_I	26_Y	1.073	1.00
37_V	63_W	1.067	1.00
48_V	116_I	1.063	1.00
160_S	164_E	1.052	1.00
170_G	182_K	1.049	1.00
5_M	40_V	1.042	1.00
197_V	200_T	1.037	1.00
25_G	113_K	1.036	1.00
38_L	42_L	1.027	1.00
107_I	110_A	1.024	1.00
110_A	114_S	1.022	1.00
208_E	217_A	1.015	1.00
170_G	174_T	1.010	1.00
145_E	152_K	1.003	1.00
15_G	30_V	0.998	1.00
88_V	92_E	0.997	1.00
85_M	89_M	0.993	1.00
177_D	192_D	0.988	1.00
61_Y	93_N	0.987	1.00
5_M	41_F	0.984	1.00
144_F	221_E	0.977	1.00
141_V	164_E	0.977	1.00
31_A	36_A	0.976	1.00
37_V	41_F	0.974	1.00
139_L	167_L	0.974	1.00
193_N	197_V	0.970	1.00
161_K	164_E	0.969	1.00
12_D	16_L	0.966	1.00
11_E	15_G	0.964	1.00
49_V	67_I	0.961	1.00
7_V	49_V	0.957	1.00
51_L	75_I	0.957	1.00
6_I	17_L	0.954	1.00
45_K	71_S	0.943	1.00
17_L	78_I	0.942	1.00
18_Q	28_T	0.937	1.00
39_D	42_L	0.929	1.00
53_I	59_D	0.925	1.00
64_C	93_N	0.921	1.00
62_Y	66_Q	0.919	1.00
7_V	31_A	0.919	1.00
49_V	75_I	0.917	1.00
87_Q	100_E	0.915	1.00
51_L	77_F	0.913	1.00
84_E	87_Q	0.909	1.00
89_M	92_E	0.904	1.00
6_I	28_T	0.892	1.00
50_L	108_V	0.889	1.00
76_I	111_K	0.886	1.00
165_V	179_L	0.883	1.00
157_K	161_K	0.881	1.00
115_Q	118_R	0.879	1.00
64_C	95_G	0.877	1.00
11_E	14_R	0.868	1.00
147_R	152_K	0.859	1.00
174_T	178_R	0.858	1.00
82_S	100_E	0.858	1.00
165_V	174_T	0.854	1.00
55_L	63_W	0.853	1.00
15_G	18_Q	0.852	1.00
208_E	213_V	0.849	1.00
26_Y	109_L	0.836	1.00
63_W	67_I	0.832	1.00
131_V	140_F	0.831	1.00
74_P	96_D	0.828	1.00
88_V	106_D	0.823	1.00
3_K	46_P	0.822	1.00
53_I	86_D	0.822	1.00
193_N	200_T	0.820	1.00
201_R	204_K	0.820	1.00
65_R	69_Q	0.813	1.00
58_Y	63_W	0.813	1.00
105_Y	109_L	0.807	1.00
17_L	108_V	0.798	1.00
19_N	23_K	0.790	1.00
107_I	111_K	0.779	1.00
207_R	213_V	0.778	1.00
177_D	181_E	0.777	1.00
114_S	117_R	0.771	1.00
41_F	73_S	0.769	1.00
103_F	108_V	0.768	1.00
50_L	78_I	0.767	1.00
13_I	103_F	0.765	1.00
139_L	160_S	0.759	1.00
133_E	136_G	0.759	1.00
144_F	161_K	0.756	1.00
53_I	81_R	0.754	1.00
34_F	38_L	0.745	1.00
86_D	89_M	0.744	1.00
162_L	166_L	0.742	1.00
42_L	71_S	0.740	1.00
41_F	46_P	0.740	1.00
97_D	114_S	0.739	1.00
178_R	181_E	0.734	1.00
54_N	80_A	0.732	1.00
166_L	170_G	0.728	1.00
78_I	103_F	0.726	1.00
74_P	122_E	0.725	1.00
200_T	204_K	0.723	1.00
7_V	63_W	0.721	1.00
85_M	106_D	0.720	1.00
3_K	47_D	0.720	1.00
91_I	111_K	0.719	1.00
209_L	212_P	0.717	1.00
15_G	19_N	0.715	1.00
167_L	170_G	0.715	1.00
217_A	221_E	0.715	1.00
76_I	97_D	0.713	1.00
74_P	118_R	0.712	1.00
195_L	199_I	0.707	1.00
34_F	57_A	0.707	1.00
104_S	107_I	0.704	1.00
192_D	196_N	0.702	1.00
50_L	112_I	0.701	1.00
116_I	119_A	0.697	1.00
42_L	66_Q	0.695	1.00
67_I	75_I	0.694	1.00
38_L	41_F	0.691	1.00
156_S	205_K	0.690	1.00
90_A	95_G	0.688	1.00
6_I	18_Q	0.685	1.00
119_A	123_Y	0.681	1.00
147_R	150_D	0.681	1.00
197_V	201_R	0.675	1.00
6_I	30_V	0.674	1.00
168_E	182_K	0.672	1.00
72_T	122_E	0.669	1.00
106_D	110_A	0.666	1.00
111_K	115_Q	0.658	1.00
8_E	55_L	0.658	1.00
84_E	106_D	0.657	1.00
176_R	192_D	0.657	1.00
165_V	168_E	0.657	1.00
92_E	110_A	0.656	1.00
41_F	49_V	0.653	1.00
191_D	194_T	0.653	1.00
14_R	18_Q	0.652	1.00
194_T	199_I	0.650	1.00
68_R	74_P	0.649	1.00
20_Y	109_L	0.640	1.00
50_L	76_I	0.634	1.00
210_N	213_V	0.634	1.00
10_S	13_I	0.632	1.00
61_Y	86_D	0.631	1.00
114_S	119_A	0.628	1.00
137_V	148_F	0.627	1.00
144_F	160_S	0.627	1.00
87_Q	104_S	0.625	1.00
16_L	20_Y	0.623	1.00
198_Y	202_L	0.620	1.00
204_K	207_R	0.617	1.00
212_P	215_I	0.614	1.00
136_G	140_F	0.609	1.00
74_P	116_I	0.604	1.00
68_R	73_S	0.603	1.00
38_L	70_H	0.603	1.00
136_G	148_F	0.602	1.00
51_L	55_L	0.602	1.00
22_E	28_T	0.597	1.00
34_F	55_L	0.596	1.00
85_M	88_V	0.594	1.00
113_K	117_R	0.591	1.00
134_Y	138_Q	0.589	1.00
79_S	87_Q	0.587	1.00
190_I	195_L	0.585	1.00
203_R	208_E	0.583	1.00
41_F	63_W	0.583	1.00
207_R	212_P	0.582	1.00
64_C	68_R	0.581	1.00
67_I	73_S	0.581	1.00
72_T	121_G	0.576	1.00
10_S	80_A	0.575	1.00
4_I	21_L	0.574	1.00
134_Y	167_L	0.574	1.00
132_V	141_V	0.572	1.00
52_D	101_K	0.572	1.00
13_I	16_L	0.571	1.00
110_A	113_K	0.568	1.00
53_I	90_A	0.564	1.00
133_E	137_V	0.564	1.00
161_K	165_V	0.560	1.00
67_I	71_S	0.560	1.00
68_R	71_S	0.559	1.00
103_F	107_I	0.559	1.00
80_A	102_P	0.558	1.00
21_L	26_Y	0.557	1.00
152_K	217_A	0.556	1.00
9_D	79_S	0.552	1.00
22_E	27_Q	0.550	1.00
88_V	91_I	0.547	1.00
166_L	199_I	0.546	1.00
199_I	202_L	0.546	1.00
4_I	48_V	0.543	1.00
135_A	138_Q	0.543	1.00
74_P	119_A	0.541	1.00
169_R	182_K	0.539	1.00
207_R	210_N	0.536	1.00
51_L	67_I	0.536	1.00
139_L	146_L	0.535	1.00
20_Y	24_Y	0.531	1.00
139_L	164_E	0.530	1.00
26_Y	116_I	0.529	1.00
213_V	216_E	0.527	1.00
33_D	55_L	0.526	1.00
199_I	211_A	0.525	1.00
196_N	199_I	0.523	1.00
7_V	34_F	0.520	1.00
176_R	180_M	0.518	1.00
190_I	194_T	0.517	1.00
36_A	57_A	0.515	1.00
209_L	213_V	0.512	1.00
6_I	14_R	0.511	1.00
82_S	102_P	0.510	1.00
112_I	116_I	0.505	1.00
148_F	151_E	0.500	1.00
134_Y	137_V	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
1ys7A	2	0.9825	100	0.188	Contact Map
2gwrA	1	0.9651	100	0.192	Contact Map
3r0jA	2	0.9563	100	0.195	Contact Map
2oqrA	2	0.9825	100	0.197	Contact Map
4kfcA	2	0.9738	100	0.199	Contact Map
4b09A	2	0.917	100	0.209	Contact Map
1kgsA	1	0.952	100	0.21	Contact Map
2hqrA	2	0.9432	100	0.239	Contact Map
1p2fA	1	0.9345	100	0.242	Contact Map
3q9sA	1	0.917	100	0.247	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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