RESD - BACSU - GREMLIN Contacts

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RESD - Transcriptional regulatory protein ResD

UniProt:	P35163	Sequences: MDQTNETKILVVDDEARIRRLLRMYLERENYAIDEAENGDEAIAKGLEANYDLILLDLMMPGTDGIEVCRQIREKKATPIIMLTAKGEEANRVQGFEAGTDDYIVKPFSPREVVLRVKALLRRASQTSYFNANTPTKNVLVFSHLSIDHDAHRVTADGTEVSLTPKEYELLYFLAKTPDKVYDREKLLKEVWQYEFFGDLRTVDTHVKRLREKLNKVSPEAAKKIVTVWGVGYKFEVGAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	240 (204)
Sequences:	76052 (53687)
Seq/√Len:	3758.8

ECOLI - ARCA RSTA YEDW CPXR BAER CREB KDPE OMPR BASR PHOP TORR CUSR QSEB PHOB NARL NARP DPIA YJJQ FIMZ EVGA YHJB UVRY DCUR YGEK RCSB BARA BGLJ CSGD RSSB TORS UHPA RCSC CHEB ARCB RCSA EVGS YEHT NTRC GLRR ATOC YPDB ZRAR RCSD
BACSU - RESD YVRH YYCF YCBL YCLJ YKOG YVCP YXDJ YRKP PHOP CSSR BCER CITT DCTR YFIK MALR YXJL DEGU YBDJ CMPA LIAR YVFU DESR YDFI YHCZ GLNL CHEB SP0A YESN LYTT NATR CHEV
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
19_R	35_E	3.724	1.00
19_R	37_E	3.242	1.00
23_R	35_E	3.177	1.00
12_V	42_A	2.740	1.00
43_I	71_Q	2.648	1.00
40_D	62_G	2.519	1.00
34_D	51_Y	2.478	1.00
39_G	63_T	2.453	1.00
38_N	62_G	2.367	1.00
47_L	75_K	2.365	1.00
63_T	71_Q	2.315	1.00
8_K	34_D	2.190	1.00
8_K	32_A	2.097	1.00
23_R	27_E	2.051	1.00
25_Y	110_P	2.047	1.00
36_A	45_K	1.996	1.00
29_E	114_V	1.994	1.00
92_R	112_E	1.890	1.00
59_M	86_K	1.839	1.00
37_E	41_E	1.832	1.00
56_L	68_V	1.827	1.00
166_K	169_E	1.799	1.00
38_N	41_E	1.793	1.00
201_R	204_D	1.781	1.00
34_D	45_K	1.767	1.00
82_M	95_G	1.760	1.00
69_C	80_I	1.719	1.00
71_Q	75_K	1.703	1.00
10_L	36_A	1.703	1.00
184_R	204_D	1.683	1.00
45_K	49_A	1.670	1.00
89_E	109_S	1.653	1.00
70_R	98_A	1.642	1.00
73_R	101_D	1.639	1.00
34_D	49_A	1.608	1.00
7_T	121_L	1.584	1.00
39_G	68_V	1.572	1.00
82_M	100_T	1.570	1.00
63_T	67_E	1.566	1.00
64_D	67_E	1.560	1.00
173_F	190_E	1.547	1.00
26_L	117_V	1.518	1.00
172_Y	176_K	1.512	1.00
71_Q	74_E	1.468	1.00
45_K	48_E	1.462	1.00
46_G	72_I	1.458	1.00
206_H	209_R	1.432	1.00
86_K	91_N	1.422	1.00
177_T	180_K	1.421	1.00
141_V	146_S	1.419	1.00
102_D	116_R	1.403	1.00
182_Y	190_E	1.393	1.00
69_C	82_M	1.387	1.00
40_D	63_T	1.386	1.00
54_I	78_T	1.379	1.00
53_L	117_V	1.366	1.00
81_I	120_L	1.356	1.00
144_H	157_D	1.349	1.00
67_E	70_R	1.346	1.00
16_A	37_E	1.324	1.00
43_I	68_V	1.323	1.00
101_D	123_R	1.300	1.00
45_K	51_Y	1.281	1.00
167_E	213_K	1.280	1.00
8_K	49_A	1.252	1.00
139_V	146_S	1.250	1.00
183_D	186_K	1.237	1.00
13_D	19_R	1.236	1.00
56_L	69_C	1.233	1.00
12_V	60_M	1.229	1.00
58_L	66_I	1.226	1.00
14_D	57_D	1.220	1.00
44_A	48_E	1.217	1.00
31_Y	118_K	1.215	1.00
43_I	63_T	1.215	1.00
101_D	120_L	1.209	1.00
153_R	160_E	1.205	1.00
66_I	95_G	1.202	1.00
148_D	151_A	1.185	1.00
146_S	155_T	1.177	1.00
94_Q	98_A	1.172	1.00
41_E	44_A	1.171	1.00
36_A	42_A	1.169	1.00
41_E	45_K	1.147	1.00
58_L	82_M	1.146	1.00
10_L	51_Y	1.145	1.00
66_I	94_Q	1.140	1.00
114_V	118_K	1.137	1.00
88_E	91_N	1.134	1.00
40_D	44_A	1.133	1.00
10_L	42_A	1.122	1.00
97_E	118_K	1.121	1.00
205_T	208_K	1.112	1.00
173_F	177_T	1.108	1.00
89_E	93_V	1.103	1.00
30_N	118_K	1.075	1.00
29_E	118_K	1.059	1.00
9_I	31_Y	1.057	1.00
173_F	182_Y	1.050	1.00
53_L	121_L	1.049	1.00
115_L	119_A	1.049	1.00
185_E	200_L	1.045	1.00
10_L	45_K	1.012	1.00
36_A	41_E	1.003	1.00
147_I	175_A	1.003	1.00
112_E	115_L	1.001	1.00
90_A	94_Q	0.992	1.00
42_A	46_G	0.992	1.00
43_I	47_L	0.988	1.00
186_K	190_E	0.985	1.00
149_H	172_Y	0.984	1.00
23_R	33_I	0.971	1.00
20_R	35_E	0.966	1.00
70_R	94_Q	0.966	1.00
42_A	68_V	0.957	1.00
201_R	205_T	0.955	1.00
166_K	192_W	0.946	1.00
56_L	80_I	0.946	1.00
16_A	20_R	0.943	1.00
54_I	72_I	0.936	1.00
11_V	22_L	0.935	1.00
10_L	46_G	0.932	1.00
92_R	105_V	0.931	1.00
58_L	64_D	0.927	1.00
202_T	206_H	0.926	1.00
7_T	31_Y	0.922	1.00
66_I	98_A	0.918	1.00
12_V	36_A	0.918	1.00
22_L	83_L	0.917	1.00
139_V	148_D	0.909	1.00
17_R	21_L	0.909	1.00
93_V	97_E	0.905	1.00
169_E	172_Y	0.905	1.00
12_V	54_I	0.904	1.00
138_N	150_D	0.890	1.00
201_R	208_K	0.887	1.00
150_D	180_K	0.886	1.00
155_T	160_E	0.885	1.00
44_A	47_L	0.884	1.00
67_E	71_Q	0.880	1.00
207_V	211_R	0.880	1.00
69_C	98_A	0.877	1.00
120_L	123_R	0.871	1.00
165_P	169_E	0.867	1.00
8_K	52_D	0.862	1.00
168_Y	172_Y	0.861	1.00
200_L	204_D	0.861	1.00
58_L	91_N	0.860	1.00
24_M	28_R	0.858	1.00
11_V	33_I	0.852	1.00
89_E	92_R	0.843	1.00
31_Y	114_V	0.842	1.00
68_V	72_I	0.841	1.00
182_Y	186_K	0.839	1.00
54_I	80_I	0.835	1.00
94_Q	97_E	0.835	1.00
56_L	82_M	0.829	1.00
147_I	168_Y	0.828	1.00
69_C	100_T	0.827	1.00
87_G	105_V	0.824	1.00
180_K	186_K	0.823	1.00
152_H	169_E	0.821	1.00
55_L	113_V	0.817	1.00
16_A	19_R	0.816	1.00
79_P	101_D	0.810	1.00
18_I	108_F	0.809	1.00
8_K	51_Y	0.807	1.00
208_K	212_E	0.806	1.00
185_E	189_K	0.804	1.00
141_V	144_H	0.803	1.00
155_T	158_G	0.803	1.00
91_N	94_Q	0.797	1.00
81_I	116_R	0.796	1.00
46_G	78_T	0.793	1.00
20_R	23_R	0.791	1.00
164_T	213_K	0.789	1.00
55_L	117_V	0.788	1.00
112_E	116_R	0.788	1.00
110_P	114_V	0.780	1.00
215_N	222_A	0.778	1.00
22_L	113_V	0.776	1.00
93_V	111_R	0.770	1.00
70_R	74_E	0.768	1.00
55_L	83_L	0.767	1.00
7_T	125_S	0.756	1.00
60_M	68_V	0.756	1.00
216_K	225_I	0.754	1.00
217_V	221_A	0.750	1.00
63_T	68_V	0.748	1.00
39_G	43_I	0.746	1.00
72_I	76_K	0.744	1.00
96_F	116_R	0.741	1.00
119_A	124_A	0.739	1.00
119_A	122_R	0.738	1.00
20_R	24_M	0.736	1.00
46_G	51_Y	0.735	1.00
184_R	200_L	0.728	1.00
216_K	223_K	0.726	1.00
90_A	111_R	0.724	1.00
124_A	128_S	0.714	1.00
58_L	86_K	0.713	1.00
83_L	108_F	0.713	1.00
173_F	187_L	0.710	1.00
109_S	112_E	0.709	1.00
217_V	222_A	0.708	1.00
209_R	212_E	0.706	1.00
59_M	85_A	0.695	1.00
198_G	203_V	0.694	1.00
176_K	190_E	0.694	1.00
25_Y	114_V	0.691	1.00
12_V	68_V	0.689	1.00
43_I	46_G	0.688	1.00
121_L	124_A	0.686	1.00
173_F	176_K	0.685	1.00
140_L	149_H	0.684	1.00
39_G	62_G	0.680	1.00
47_L	71_Q	0.674	1.00
211_R	216_K	0.670	1.00
81_I	102_D	0.669	1.00
11_V	23_R	0.668	1.00
13_D	60_M	0.667	1.00
140_L	144_H	0.662	1.00
11_V	35_E	0.662	1.00
204_D	207_V	0.658	1.00
73_R	79_P	0.655	1.00
39_G	60_M	0.649	1.00
148_D	153_R	0.648	1.00
21_L	25_Y	0.646	1.00
92_R	109_S	0.646	1.00
108_F	113_V	0.641	1.00
111_R	115_L	0.637	1.00
186_K	189_K	0.635	1.00
19_R	23_R	0.634	1.00
174_L	207_V	0.633	1.00
46_G	54_I	0.632	1.00
215_N	223_K	0.632	1.00
9_I	26_L	0.627	1.00
27_E	33_I	0.625	1.00
95_G	100_T	0.624	1.00
97_E	115_L	0.623	1.00
89_E	111_R	0.622	1.00
26_L	31_Y	0.622	1.00
57_D	106_K	0.609	1.00
102_D	119_A	0.608	1.00
72_I	80_I	0.608	1.00
77_A	127_T	0.608	1.00
43_I	75_K	0.607	1.00
9_I	53_L	0.606	1.00
77_A	126_Q	0.605	1.00
145_L	156_A	0.604	1.00
79_P	121_L	0.604	1.00
171_L	222_A	0.599	1.00
15_E	85_A	0.596	1.00
205_T	209_R	0.594	1.00
176_K	182_Y	0.592	1.00
152_H	168_Y	0.592	1.00
144_H	156_A	0.591	1.00
84_T	92_R	0.591	1.00
140_L	143_S	0.591	1.00
55_L	81_I	0.589	1.00
199_D	202_T	0.576	1.00
116_R	120_L	0.573	1.00
156_A	215_N	0.572	1.00
147_I	172_Y	0.572	1.00
223_K	226_V	0.571	1.00
15_E	18_I	0.564	1.00
56_L	72_I	0.562	1.00
7_T	52_D	0.562	1.00
79_P	123_R	0.561	1.00
66_I	91_N	0.560	1.00
73_R	78_T	0.557	1.00
115_L	118_K	0.556	1.00
56_L	60_M	0.553	1.00
58_L	95_G	0.552	1.00
69_C	73_R	0.551	1.00
79_P	124_A	0.544	1.00
14_D	84_T	0.543	1.00
140_L	175_A	0.542	1.00
27_E	32_A	0.542	1.00
72_I	78_T	0.540	1.00
93_V	96_F	0.539	1.00
158_G	161_V	0.537	1.00
170_L	174_L	0.532	1.00
118_K	122_R	0.532	1.00
123_R	127_T	0.529	1.00
149_H	176_K	0.528	1.00
79_P	127_T	0.527	1.00
25_Y	29_E	0.523	1.00
46_G	76_K	0.523	1.00
108_F	112_E	0.523	1.00
50_N	76_K	0.520	1.00
139_V	143_S	0.520	1.00
198_G	202_T	0.516	1.00
46_G	68_V	0.514	1.00
142_F	145_L	0.513	1.00
18_I	21_L	0.513	1.00
90_A	93_V	0.512	1.00
46_G	75_K	0.512	1.00
156_A	159_T	0.511	1.00
12_V	39_G	0.509	1.00
142_F	175_A	0.507	1.00
87_G	107_P	0.506	1.00
11_V	19_R	0.505	1.00
41_E	62_G	0.505	1.00
169_E	173_F	0.504	1.00
14_D	60_M	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
2gwrA	1	0.9375	100	0.21	Contact Map
1ys7A	2	0.9375	100	0.222	Contact Map
3r0jA	2	0.925	100	0.224	Contact Map
4b09A	2	0.8875	100	0.224	Contact Map
2oqrA	2	0.9417	100	0.24	Contact Map
4kfcA	2	0.9375	100	0.24	Contact Map
1kgsA	1	0.9083	100	0.253	Contact Map
3q9sA	1	0.875	100	0.258	Contact Map
2hqrA	2	0.9042	100	0.272	Contact Map
1p2fA	1	0.9	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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