RCSA - ECOLI - GREMLIN Contacts

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RCSA - Transcriptional regulatory protein RcsA

UniProt:	P0DMC9	Sequences: MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSQRPSVVFINEDCFIHDASNSQRIKLIINQHPNTLFIVFMAIANVHFDEYLLVRKNLLISSKSIKPESLDDILGDILKKETTITSFLNMPTLSLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10820
Length:	207 (177)
Sequences:	64098 (43459)
Seq/√Len:	3266.6

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

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_R	32_D	3.640	1.00
13_R	34_E	3.112	1.00
17_T	32_D	3.056	1.00
6_M	39_L	2.637	1.00
40_A	70_L	2.426	1.00
37_D	61_D	2.412	1.00
62_A	70_L	2.256	1.00
167_K	170_S	2.231	1.00
35_T	61_D	2.209	1.00
31_N	48_P	2.187	1.00
141_T	144_S	2.136	1.00
36_V	62_A	2.124	1.00
19_Y	110_P	2.104	1.00
17_T	21_L	2.061	1.00
92_D	112_S	2.041	1.00
44_D	74_Q	2.040	1.00
154_G	158_I	1.954	1.00
23_R	114_D	1.931	1.00
2_S	29_E	1.917	1.00
31_N	42_A	1.836	1.00
33_I	42_A	1.819	1.00
34_E	38_D	1.762	1.00
58_F	86_I	1.731	1.00
89_V	109_K	1.730	1.00
82_V	95_L	1.720	1.00
35_T	38_D	1.705	1.00
72_I	101_L	1.702	1.00
31_N	46_Q	1.643	1.00
159_S	162_M	1.601	1.00
20_L	117_L	1.575	1.00
68_I	80_F	1.557	1.00
172_H	175_N	1.555	1.00
4_I	33_I	1.532	1.00
70_L	74_Q	1.529	1.00
82_V	100_N	1.505	1.00
154_G	157_Q	1.503	1.00
42_A	46_Q	1.497	1.00
53_I	67_R	1.487	1.00
147_R	151_A	1.474	1.00
158_I	162_M	1.469	1.00
142_E	179_K	1.464	1.00
36_V	67_R	1.461	1.00
2_S	31_N	1.451	1.00
86_I	91_F	1.438	1.00
81_I	120_I	1.426	1.00
62_A	66_Q	1.397	1.00
51_V	78_T	1.384	1.00
50_V	117_L	1.361	1.00
42_A	45_S	1.361	1.00
10_S	34_E	1.340	1.00
102_L	116_I	1.329	1.00
63_S	66_Q	1.326	1.00
37_D	62_A	1.315	1.00
70_L	73_N	1.281	1.00
43_C	71_I	1.279	1.00
28_R	118_G	1.256	1.00
69_K	98_R	1.247	1.00
68_I	82_V	1.238	1.00
101_L	123_K	1.225	1.00
66_Q	69_K	1.223	1.00
6_M	59_I	1.182	1.00
40_A	67_R	1.182	1.00
27_K	118_G	1.180	1.00
156_I	159_S	1.172	1.00
23_R	27_K	1.170	1.00
97_V	118_G	1.162	1.00
55_E	65_S	1.153	1.00
4_I	48_P	1.152	1.00
7_D	13_R	1.147	1.00
154_G	159_S	1.142	1.00
23_R	118_G	1.136	1.00
128_T	135_T	1.135	1.00
171_S	174_G	1.135	1.00
41_I	45_S	1.131	1.00
153_Q	161_Q	1.130	1.00
148_M	161_Q	1.125	1.00
4_I	39_L	1.121	1.00
50_V	121_L	1.121	1.00
38_D	41_I	1.121	1.00
114_D	118_G	1.116	1.00
88_N	91_F	1.116	1.00
38_D	42_A	1.103	1.00
155_T	170_S	1.089	1.00
55_E	82_V	1.085	1.00
40_A	62_A	1.075	1.00
33_I	39_L	1.071	1.00
75_H	78_T	1.066	1.00
65_S	94_Y	1.045	1.00
120_I	123_K	1.040	1.00
53_I	68_I	1.035	1.00
173_K	177_K	1.033	1.00
89_V	93_E	1.029	1.00
42_A	48_P	1.028	1.00
167_K	171_S	1.022	1.00
37_D	41_I	1.013	1.00
90_H	94_Y	1.007	1.00
65_S	98_R	1.006	1.00
112_S	115_D	0.997	1.00
119_D	124_E	0.992	1.00
115_D	119_D	0.991	1.00
92_D	105_S	0.983	1.00
155_T	159_S	0.983	1.00
4_I	42_A	0.977	1.00
8_L	54_N	0.974	1.00
144_S	147_R	0.971	1.00
130_F	135_T	0.967	1.00
157_Q	161_Q	0.958	1.00
3_T	28_R	0.958	1.00
143_S	147_R	0.958	1.00
94_Y	98_R	0.943	1.00
167_K	174_G	0.938	1.00
140_R	144_S	0.935	1.00
156_I	166_A	0.933	1.00
33_I	38_D	0.930	1.00
65_S	95_L	0.917	1.00
168_T	172_H	0.916	1.00
2_S	46_Q	0.911	1.00
11_Y	15_G	0.908	1.00
139_S	179_K	0.906	1.00
10_S	14_L	0.904	1.00
4_I	31_N	0.903	1.00
28_R	114_D	0.900	1.00
148_M	152_G	0.898	1.00
69_K	94_Y	0.896	1.00
170_S	173_K	0.889	1.00
101_L	120_I	0.888	1.00
39_L	43_C	0.885	1.00
14_L	32_D	0.874	1.00
16_L	83_F	0.867	1.00
149_W	173_K	0.863	1.00
18_G	22_S	0.863	1.00
6_M	51_V	0.841	1.00
55_E	63_S	0.840	1.00
79_L	101_L	0.839	1.00
166_A	170_S	0.834	1.00
6_M	33_I	0.833	1.00
175_N	178_R	0.833	1.00
5_I	16_L	0.832	1.00
96_L	116_I	0.832	1.00
40_A	44_D	0.832	1.00
127_I	144_S	0.830	1.00
177_K	182_T	0.828	1.00
51_V	71_I	0.827	1.00
52_F	83_F	0.820	1.00
93_E	97_V	0.815	1.00
155_T	158_I	0.802	1.00
93_E	111_E	0.795	1.00
68_I	98_R	0.794	1.00
94_Y	97_V	0.786	1.00
87_A	105_S	0.782	1.00
39_L	67_R	0.782	1.00
174_G	178_R	0.781	1.00
41_I	44_D	0.767	1.00
119_D	122_K	0.759	1.00
89_V	92_D	0.752	1.00
10_S	13_R	0.751	1.00
66_Q	70_L	0.749	1.00
156_I	160_D	0.749	1.00
4_I	43_C	0.746	1.00
130_F	133_M	0.739	1.00
16_L	113_L	0.734	1.00
141_T	172_H	0.732	1.00
110_P	114_D	0.730	1.00
90_H	111_E	0.722	1.00
171_S	175_N	0.717	1.00
14_L	18_G	0.717	1.00
53_I	80_F	0.714	1.00
59_I	67_R	0.713	1.00
58_F	85_A	0.712	1.00
14_L	17_T	0.709	1.00
164_I	169_V	0.704	1.00
69_K	73_N	0.704	1.00
127_I	143_S	0.703	1.00
68_I	100_N	0.699	1.00
52_F	113_L	0.698	1.00
91_F	94_Y	0.698	1.00
53_I	82_V	0.690	1.00
71_I	76_P	0.689	1.00
83_F	108_I	0.687	1.00
81_I	102_L	0.686	1.00
112_S	116_I	0.685	1.00
43_C	75_H	0.685	1.00
20_L	28_R	0.685	1.00
131_L	181_K	0.682	1.00
54_N	106_K	0.680	1.00
148_M	158_I	0.678	1.00
154_G	162_M	0.677	1.00
7_D	106_K	0.675	1.00
17_T	30_I	0.674	1.00
84_M	103_I	0.674	1.00
77_N	126_T	0.670	1.00
51_V	80_F	0.670	1.00
44_D	75_H	0.669	1.00
36_V	40_A	0.657	1.00
40_A	43_C	0.656	1.00
142_E	175_N	0.655	1.00
55_E	86_I	0.651	1.00
15_G	19_Y	0.648	1.00
67_R	71_I	0.647	1.00
92_D	109_K	0.646	1.00
7_D	59_I	0.639	1.00
43_C	48_P	0.634	1.00
5_I	17_T	0.634	1.00
148_M	151_A	0.633	1.00
55_E	91_F	0.633	1.00
157_Q	160_D	0.632	1.00
159_S	170_S	0.631	1.00
43_C	78_T	0.630	1.00
62_A	67_R	0.626	1.00
89_V	111_E	0.624	1.00
2_S	49_S	0.624	1.00
97_V	115_D	0.620	1.00
79_L	121_L	0.619	1.00
28_R	121_L	0.619	1.00
13_R	17_T	0.616	1.00
146_L	176_I	0.607	1.00
6_M	67_R	0.607	1.00
121_L	124_E	0.605	1.00
21_L	29_E	0.605	1.00
9_C	85_A	0.604	1.00
111_E	115_D	0.601	1.00
84_M	106_K	0.598	1.00
150_M	153_Q	0.596	1.00
5_I	32_D	0.596	1.00
3_T	50_V	0.592	1.00
23_R	28_R	0.588	1.00
36_V	61_D	0.586	1.00
47_R	75_H	0.581	1.00
43_C	51_V	0.581	1.00
108_I	112_S	0.579	1.00
131_L	134_P	0.579	1.00
19_Y	114_D	0.575	1.00
108_I	113_L	0.575	1.00
109_K	112_S	0.571	1.00
12_T	108_I	0.568	1.00
115_D	118_G	0.568	1.00
153_Q	157_Q	0.565	1.00
84_M	92_D	0.563	1.00
148_M	153_Q	0.558	1.00
81_I	116_I	0.557	1.00
144_S	148_M	0.554	1.00
158_I	161_Q	0.550	1.00
44_D	70_L	0.549	1.00
47_R	76_P	0.546	1.00
154_G	160_D	0.546	1.00
3_T	20_L	0.545	1.00
52_F	117_L	0.537	1.00
36_V	59_I	0.536	1.00
116_I	126_T	0.536	1.00
8_L	84_M	0.533	1.00
15_G	18_G	0.532	1.00
38_D	61_D	0.530	1.00
147_R	150_M	0.528	1.00
68_I	72_I	0.524	1.00
102_L	120_I	0.523	1.00
53_I	59_I	0.523	1.00
145_M	172_H	0.522	1.00
145_M	149_W	0.521	1.00
93_E	96_L	0.520	1.00
139_S	142_E	0.519	1.00
138_L	176_I	0.519	1.00
159_S	163_N	0.508	1.00
95_L	100_N	0.506	1.00
40_A	74_Q	0.504	1.00
129_S	143_S	0.504	1.00
151_A	161_Q	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	0.942	100	0.219	Contact Map
3c3wA	2	0.942	100	0.221	Contact Map
1yioA	1	0.9179	100	0.226	Contact Map
1a04A	1	0.9324	100	0.238	Contact Map
4ldzA	2	0.9082	100	0.249	Contact Map
3kloA	2	0.9372	100	0.259	Contact Map
4hyeA	2	0.9372	100	0.266	Contact Map
3q9sA	1	0.8986	100	0.294	Contact Map
1ys7A	2	0.9469	100	0.298	Contact Map
4b09A	2	0.9179	100	0.313	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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