DEGU - BACSU - GREMLIN Contacts

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DEGU - Transcriptional regulatory protein DegU

UniProt:	P13800	Sequences: MTKVNIVIIDDHQLFREGVKRILDFEPTFEVVAEGDDGDEAARIVEHYHPDVVIMDINMPNVNGVEATKQLVELYPESKVIILSIHDDENYVTHALKTGARGYLLKEMDADTLIEAVKVVAEGGSYLHPKVTHNLVNEFRRLATSGVSAHPQHEVYPEIRRPLHILTRRECEVLQMLADGKSNRGIGESLFISEKTVKNHVSNILQKMNVNDRTQAVVVAIKNGWVEMR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	229 (196)
Sequences:	79429 (56928)
Seq/√Len:	4066.3

ECOLI - FIMZ YGEK RCSB NARL EVGA NARP CREB ARCA YHJB YJJQ UVRY DPIA PHOP CUSR YEDW OMPR BGLJ DCUR RCSA BAER CSGD QSEB KDPE PHOB BASR RSTA CPXR UHPA TORR CHEB RSSB RCSC BARA YPDB ARCB TORS NTRC GLRR YEHT EVGS ATOC ZRAR RCSD
BACSU - DEGU YXJL YFIK LIAR CMPA YKOG YVRH CITT PHOP YHCZ YVFU YDFI MALR DESR RESD DCTR YCBL YYCF YVCP BCER YCLJ YXDJ YRKP YBDJ CSSR YESN CHEB SP0A GLNL LYTT NATR CHEV SP0F
HALSA - CHEB Q9HNM3 Q9HR09 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
16_R	34_E	3.794	1.00
16_R	36_D	3.326	1.00
20_K	34_E	3.313	1.00
9_I	41_A	2.759	1.00
42_A	70_Q	2.755	1.00
39_D	61_N	2.539	1.00
38_G	62_V	2.418	1.00
62_V	70_Q	2.326	1.00
46_E	74_L	2.291	1.00
37_D	61_N	2.241	1.00
22_I	110_A	2.130	1.00
26_E	114_I	2.103	1.00
20_K	24_D	2.043	1.00
5_N	30_E	2.039	1.00
35_G	44_I	1.985	1.00
195_K	198_K	1.932	1.00
33_A	44_I	1.915	1.00
92_V	112_T	1.896	1.00
58_N	86_H	1.889	1.00
55_M	67_A	1.839	1.00
36_D	40_E	1.818	1.00
37_D	40_E	1.776	1.00
68_T	80_V	1.752	1.00
69_K	98_T	1.708	1.00
44_I	48_Y	1.706	1.00
7_V	35_G	1.702	1.00
33_A	48_Y	1.698	1.00
70_Q	74_L	1.695	1.00
33_A	50_P	1.693	1.00
82_I	100_A	1.660	1.00
82_I	95_A	1.655	1.00
169_R	172_E	1.645	1.00
5_N	33_A	1.643	1.00
137_N	140_R	1.626	1.00
183_N	198_K	1.614	1.00
72_V	101_R	1.606	1.00
89_E	109_D	1.601	1.00
38_G	67_A	1.554	1.00
62_V	66_E	1.529	1.00
63_N	66_E	1.524	1.00
181_K	189_S	1.515	1.00
102_G	116_A	1.490	1.00
4_V	121_A	1.487	1.00
175_Q	179_D	1.485	1.00
45_V	71_L	1.483	1.00
200_H	203_N	1.479	1.00
182_S	185_G	1.465	1.00
23_L	117_V	1.454	1.00
44_I	47_H	1.447	1.00
176_M	189_S	1.441	1.00
53_V	78_S	1.436	1.00
86_H	91_Y	1.405	1.00
70_Q	73_E	1.395	1.00
13_Q	36_D	1.384	1.00
39_D	62_V	1.371	1.00
52_V	117_V	1.362	1.00
68_T	82_I	1.353	1.00
81_I	120_V	1.333	1.00
170_E	207_K	1.327	1.00
5_N	48_Y	1.312	1.00
42_A	67_A	1.304	1.00
101_R	123_G	1.297	1.00
66_E	69_K	1.294	1.00
137_N	141_R	1.261	1.00
101_R	120_V	1.259	1.00
57_I	65_V	1.257	1.00
44_I	50_P	1.253	1.00
29_F	118_K	1.232	1.00
42_A	62_V	1.223	1.00
9_I	59_M	1.219	1.00
185_G	189_S	1.215	1.00
65_V	95_A	1.200	1.00
10_D	16_R	1.199	1.00
75_Y	78_S	1.187	1.00
43_R	47_H	1.171	1.00
94_H	98_T	1.170	1.00
171_C	175_Q	1.162	1.00
26_E	118_K	1.161	1.00
35_G	41_A	1.139	1.00
114_I	118_K	1.133	1.00
55_M	68_T	1.130	1.00
11_D	56_D	1.125	1.00
7_V	50_P	1.117	1.00
65_V	94_H	1.115	1.00
40_E	43_R	1.107	1.00
6_I	29_F	1.097	1.00
40_E	44_I	1.096	1.00
88_D	91_Y	1.092	1.00
57_I	82_I	1.089	1.00
7_V	41_A	1.073	1.00
39_D	43_R	1.059	1.00
176_M	180_G	1.057	1.00
173_V	177_L	1.053	1.00
195_K	199_N	1.050	1.00
156_Y	163_L	1.043	1.00
52_V	121_A	1.033	1.00
134_N	137_N	1.030	1.00
199_N	202_S	1.027	1.00
184_R	194_E	1.021	1.00
97_K	118_K	1.020	1.00
35_G	40_E	1.011	1.00
7_V	44_I	1.009	1.00
115_E	119_V	1.008	1.00
90_N	94_H	0.996	1.00
42_A	46_E	0.994	1.00
89_E	93_T	0.984	1.00
172_E	175_Q	0.983	1.00
209_N	212_D	0.979	1.00
181_K	185_G	0.977	1.00
112_T	115_E	0.968	1.00
69_K	94_H	0.965	1.00
92_V	105_L	0.964	1.00
176_M	181_K	0.962	1.00
28_T	118_K	0.957	1.00
8_I	19_V	0.954	1.00
93_T	97_K	0.954	1.00
53_V	71_L	0.953	1.00
168_R	172_E	0.948	1.00
17_E	34_E	0.943	1.00
41_A	67_A	0.942	1.00
41_A	45_V	0.922	1.00
14_L	18_G	0.918	1.00
13_Q	17_E	0.909	1.00
20_K	31_V	0.905	1.00
57_I	63_N	0.897	1.00
5_N	51_D	0.896	1.00
9_I	35_G	0.893	1.00
65_V	98_T	0.892	1.00
134_N	138_E	0.892	1.00
172_E	176_M	0.887	1.00
7_V	33_A	0.886	1.00
196_T	200_H	0.883	1.00
4_V	29_F	0.883	1.00
158_E	163_L	0.881	1.00
19_V	83_L	0.877	1.00
43_R	46_E	0.867	1.00
55_M	80_V	0.864	1.00
68_T	98_T	0.861	1.00
136_V	139_F	0.858	1.00
89_E	92_V	0.844	1.00
9_I	53_V	0.843	1.00
176_M	186_I	0.842	1.00
201_V	205_L	0.836	1.00
55_M	82_I	0.835	1.00
7_V	45_V	0.833	1.00
53_V	80_V	0.833	1.00
81_I	116_A	0.831	1.00
199_N	203_N	0.830	1.00
13_Q	16_R	0.829	1.00
68_T	100_A	0.827	1.00
155_V	172_E	0.826	1.00
79_K	101_R	0.825	1.00
54_I	113_L	0.818	1.00
194_E	198_K	0.815	1.00
29_F	114_I	0.808	1.00
15_F	108_M	0.806	1.00
87_D	105_L	0.806	1.00
185_G	188_E	0.806	1.00
138_E	141_R	0.804	1.00
134_N	139_F	0.800	1.00
66_E	70_Q	0.797	1.00
94_H	97_K	0.797	1.00
184_R	188_E	0.795	1.00
54_I	117_V	0.793	1.00
21_R	25_F	0.793	1.00
91_Y	94_H	0.792	1.00
120_V	123_G	0.791	1.00
17_E	20_K	0.789	1.00
198_K	201_V	0.788	1.00
67_A	71_L	0.783	1.00
57_I	91_Y	0.782	1.00
5_N	50_P	0.781	1.00
110_A	114_I	0.777	1.00
136_V	140_R	0.766	1.00
203_N	206_Q	0.766	1.00
112_T	116_A	0.762	1.00
135_L	138_E	0.762	1.00
31_V	34_E	0.746	1.00
167_T	207_K	0.745	1.00
69_K	73_E	0.745	1.00
119_V	122_E	0.743	1.00
176_M	179_D	0.742	1.00
57_I	86_H	0.741	1.00
205_L	210_V	0.738	1.00
195_K	202_S	0.734	1.00
45_V	78_S	0.732	1.00
8_I	31_V	0.724	1.00
17_E	21_R	0.724	1.00
45_V	50_P	0.723	1.00
135_L	139_F	0.720	1.00
45_V	75_Y	0.718	1.00
83_L	108_M	0.716	1.00
59_M	67_A	0.711	1.00
38_G	42_A	0.708	1.00
38_G	61_N	0.705	1.00
54_I	83_L	0.704	1.00
124_G	128_H	0.703	1.00
19_V	113_L	0.686	1.00
62_V	67_A	0.684	1.00
109_D	112_T	0.684	1.00
90_N	111_D	0.681	1.00
202_S	206_Q	0.680	1.00
93_T	111_D	0.680	1.00
58_N	85_I	0.677	1.00
30_E	33_A	0.675	1.00
174_L	177_L	0.675	1.00
155_V	171_C	0.674	1.00
158_E	161_R	0.671	1.00
22_I	114_I	0.670	1.00
9_I	67_A	0.666	1.00
121_A	124_G	0.663	1.00
96_L	116_A	0.660	1.00
159_I	209_N	0.659	1.00
10_D	59_M	0.656	1.00
119_V	124_G	0.656	1.00
72_V	79_K	0.655	1.00
45_V	53_V	0.647	1.00
79_K	123_G	0.646	1.00
108_M	113_L	0.644	1.00
134_N	141_R	0.642	1.00
42_A	74_L	0.638	1.00
46_E	70_Q	0.637	1.00
18_G	22_I	0.636	1.00
132_T	136_V	0.630	1.00
135_L	140_R	0.626	1.00
38_G	59_M	0.625	1.00
177_L	201_V	0.625	1.00
71_L	80_V	0.622	1.00
136_V	141_R	0.621	1.00
116_A	120_V	0.620	1.00
8_I	20_K	0.619	1.00
16_R	20_K	0.619	1.00
24_D	31_V	0.616	1.00
71_L	76_P	0.615	1.00
97_K	115_E	0.613	1.00
42_A	45_V	0.611	1.00
81_I	102_G	0.609	1.00
77_E	127_L	0.609	1.00
102_G	119_V	0.605	1.00
169_R	200_H	0.604	1.00
111_D	115_E	0.597	1.00
183_N	187_G	0.592	1.00
23_L	29_F	0.592	1.00
89_E	111_D	0.592	1.00
134_N	140_R	0.591	1.00
4_V	125_S	0.588	1.00
6_I	52_V	0.588	1.00
12_H	85_I	0.588	1.00
54_I	81_I	0.588	1.00
132_T	135_L	0.584	1.00
84_S	92_V	0.584	1.00
8_I	34_E	0.583	1.00
79_K	121_A	0.581	1.00
56_D	106_K	0.579	1.00
92_V	109_D	0.579	1.00
26_E	29_F	0.578	1.00
192_I	197_V	0.578	1.00
183_N	194_E	0.577	1.00
6_I	23_L	0.576	1.00
118_K	122_E	0.576	1.00
159_I	211_N	0.574	1.00
77_E	126_Y	0.565	1.00
182_S	186_I	0.564	1.00
49_H	75_Y	0.562	1.00
180_G	189_S	0.558	1.00
167_T	170_E	0.556	1.00
95_A	100_A	0.551	1.00
133_H	136_V	0.550	1.00
159_I	162_P	0.549	1.00
130_K	133_H	0.548	1.00
65_V	91_Y	0.548	1.00
133_H	137_N	0.546	1.00
46_E	75_Y	0.544	1.00
108_M	112_T	0.540	1.00
68_T	72_V	0.540	1.00
22_I	26_E	0.537	1.00
12_H	15_F	0.536	1.00
115_E	118_K	0.533	1.00
55_M	59_M	0.532	1.00
4_V	51_D	0.526	1.00
191_F	194_E	0.526	1.00
181_K	186_I	0.525	1.00
166_L	170_E	0.524	1.00
79_K	127_L	0.523	1.00
90_N	93_T	0.523	1.00
25_F	28_T	0.520	1.00
55_M	71_L	0.519	1.00
11_D	84_S	0.518	1.00
179_D	189_S	0.517	1.00
177_L	180_G	0.516	1.00
15_F	18_G	0.511	1.00
93_T	96_L	0.508	1.00
37_D	59_M	0.506	1.00
174_L	178_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
4gvpA	1	0.9083	100	0.21	Contact Map
1a04A	1	0.8952	100	0.216	Contact Map
1yioA	1	0.8646	100	0.228	Contact Map
3c3wA	2	0.9214	100	0.233	Contact Map
4ldzA	2	0.8515	100	0.249	Contact Map
4hyeA	2	0.8734	100	0.265	Contact Map
1ys7A	2	0.9432	100	0.265	Contact Map
3kloA	2	0.9345	100	0.268	Contact Map
3q9sA	1	0.8777	100	0.277	Contact Map
4b09A	2	0.8734	100	0.281	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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