YYCF - BACSU - GREMLIN Contacts

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YYCF - Transcriptional regulatory protein YycF

UniProt:	P37478	Sequences: MDKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRRQLTTAPAEEEPSSNEIHIGSLVIFPDAYVVSKRDETIELTHREFELLHYLAKHIGQVMTREHLLQTVWGYDYFGDVRTVDVTVRRLREKIEDNPSHPNWIVTRRGVGYYLRNPEQD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	235 (201)
Sequences:	73933 (51998)
Seq/√Len:	3667.6

ECOLI - TORR RSTA BAER KDPE ARCA CPXR OMPR YEDW PHOB CREB BASR PHOP QSEB CUSR DPIA DCUR BARA UVRY FIMZ YHJB NARL EVGA YJJQ NARP RCSB YGEK TORS BGLJ RSSB UHPA CHEB RCSC ARCB CSGD RCSA YEHT EVGS YPDB NTRC GLRR ZRAR ATOC RCSD
BACSU - YYCF YVRH PHOP YRKP YVCP YCBL CSSR RESD YXDJ YCLJ BCER CITT YKOG DCTR MALR YFIK CMPA YXJL DEGU LIAR YDFI YBDJ YVFU DESR YHCZ GLNL CHEB YESN LYTT SP0A NATR CHEV CHEY
HALSA - CHEB Q9HR09 Q9HNM3 BAT Q9HRE5 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
15_A	31_C	3.776	1.00
15_A	33_H	3.294	1.00
19_E	31_C	3.289	1.00
8_V	38_A	2.781	1.00
39_V	67_E	2.744	1.00
36_N	58_N	2.563	1.00
30_H	47_P	2.415	1.00
59_K	67_E	2.399	1.00
35_G	59_K	2.321	1.00
43_E	71_K	2.315	1.00
34_D	58_N	2.311	1.00
4_K	30_H	2.206	1.00
25_E	110_L	2.119	1.00
19_E	23_R	2.092	1.00
21_N	106_T	2.067	1.00
32_A	41_M	2.042	1.00
4_K	28_E	1.990	1.00
55_M	82_K	1.928	1.00
52_L	64_V	1.879	1.00
33_H	37_E	1.827	1.00
30_H	41_M	1.826	1.00
88_K	108_E	1.816	1.00
196_R	199_D	1.791	1.00
65_C	76_I	1.781	1.00
34_D	37_E	1.762	1.00
41_M	45_L	1.744	1.00
161_R	164_E	1.744	1.00
78_M	91_G	1.706	1.00
69_R	97_D	1.703	1.00
67_E	71_K	1.690	1.00
6_L	32_A	1.665	1.00
30_H	45_L	1.653	1.00
78_M	96_A	1.602	1.00
66_R	94_I	1.601	1.00
168_Y	185_T	1.599	1.00
179_R	199_D	1.589	1.00
59_K	63_E	1.588	1.00
85_E	105_S	1.578	1.00
35_G	64_V	1.570	1.00
98_D	112_R	1.554	1.00
167_H	171_K	1.519	1.00
82_K	87_D	1.515	1.00
42_V	68_V	1.502	1.00
22_L	113_V	1.489	1.00
60_D	63_E	1.487	1.00
177_M	185_T	1.477	1.00
41_M	44_E	1.462	1.00
36_N	59_K	1.452	1.00
50_I	74_M	1.443	1.00
67_E	70_K	1.439	1.00
136_H	141_V	1.436	1.00
201_T	204_R	1.420	1.00
49_L	113_V	1.378	1.00
178_T	181_H	1.359	1.00
12_K	33_H	1.357	1.00
77_I	116_N	1.349	1.00
65_C	78_M	1.343	1.00
63_E	66_R	1.336	1.00
54_I	62_V	1.328	1.00
39_V	64_V	1.295	1.00
134_E	141_V	1.264	1.00
41_M	47_P	1.261	1.00
4_K	45_L	1.253	1.00
27_Y	114_K	1.252	1.00
162_E	208_K	1.231	1.00
8_V	56_L	1.230	1.00
39_V	59_K	1.230	1.00
97_D	119_R	1.229	1.00
139_S	152_R	1.225	1.00
62_V	91_G	1.214	1.00
168_Y	172_H	1.202	1.00
84_S	87_D	1.198	1.00
110_L	114_K	1.191	1.00
40_E	44_E	1.188	1.00
97_D	116_N	1.186	1.00
10_D	53_D	1.181	1.00
6_L	47_P	1.180	1.00
9_D	15_A	1.173	1.00
32_A	38_A	1.156	1.00
90_I	94_I	1.154	1.00
37_E	40_E	1.154	1.00
141_V	150_S	1.151	1.00
37_E	41_M	1.149	1.00
148_V	155_T	1.146	1.00
52_L	65_C	1.142	1.00
54_I	78_M	1.138	1.00
181_H	185_T	1.132	1.00
62_V	90_I	1.117	1.00
36_N	40_E	1.116	1.00
26_G	114_K	1.111	1.00
25_E	114_K	1.110	1.00
212_N	216_P	1.106	1.00
168_Y	177_M	1.088	1.00
6_L	38_A	1.082	1.00
85_E	89_V	1.081	1.00
200_V	203_R	1.068	1.00
180_E	195_V	1.067	1.00
108_E	111_A	1.066	1.00
5_I	27_Y	1.058	1.00
93_E	114_K	1.049	1.00
86_I	90_I	1.047	1.00
39_V	43_E	1.046	1.00
49_L	117_L	1.046	1.00
32_A	37_E	1.044	1.00
6_L	41_M	1.040	1.00
111_A	115_A	1.039	1.00
143_F	146_A	1.038	1.00
163_F	167_H	1.026	1.00
7_V	18_L	1.025	1.00
133_N	145_D	1.021	1.00
89_V	93_E	1.013	1.00
38_A	64_V	1.006	1.00
19_E	29_V	1.002	1.00
144_P	167_H	0.996	1.00
4_K	48_D	0.977	1.00
177_M	181_H	0.973	1.00
38_A	42_V	0.965	1.00
88_K	101_T	0.962	1.00
16_D	31_C	0.954	1.00
66_R	90_I	0.954	1.00
54_I	60_D	0.951	1.00
212_N	215_H	0.945	1.00
50_I	68_V	0.943	1.00
13_P	17_I	0.942	1.00
18_L	79_L	0.933	1.00
8_V	32_A	0.932	1.00
197_T	201_T	0.932	1.00
12_K	16_D	0.923	1.00
196_R	200_V	0.923	1.00
6_L	42_V	0.923	1.00
65_C	96_A	0.921	1.00
62_V	94_I	0.912	1.00
116_N	119_R	0.911	1.00
52_L	76_I	0.908	1.00
65_C	94_I	0.906	1.00
164_E	167_H	0.904	1.00
160_H	164_E	0.900	1.00
150_S	155_T	0.893	1.00
142_I	170_A	0.879	1.00
20_F	24_K	0.876	1.00
63_E	67_E	0.875	1.00
75_P	97_D	0.872	1.00
83_D	101_T	0.858	1.00
196_R	203_R	0.857	1.00
40_E	43_E	0.857	1.00
52_L	78_M	0.855	1.00
202_V	206_R	0.854	1.00
8_V	50_I	0.848	1.00
85_E	88_K	0.848	1.00
27_Y	110_L	0.837	1.00
16_D	19_E	0.836	1.00
12_K	15_A	0.835	1.00
50_I	76_I	0.834	1.00
195_V	199_D	0.830	1.00
134_E	143_F	0.826	1.00
142_I	163_F	0.821	1.00
54_I	82_K	0.813	1.00
7_V	29_V	0.812	1.00
147_Y	164_E	0.811	1.00
211_D	217_N	0.807	1.00
203_R	207_E	0.806	1.00
108_E	112_R	0.804	1.00
51_L	109_L	0.798	1.00
115_A	120_Q	0.796	1.00
77_I	112_R	0.794	1.00
42_V	74_M	0.793	1.00
90_I	93_E	0.784	1.00
105_S	108_E	0.779	1.00
89_V	107_R	0.777	1.00
56_L	64_V	0.776	1.00
64_V	68_V	0.774	1.00
54_I	87_D	0.772	1.00
106_T	110_L	0.768	1.00
79_L	104_F	0.765	1.00
179_R	195_V	0.765	1.00
59_K	64_V	0.763	1.00
168_Y	171_K	0.763	1.00
159_T	208_K	0.758	1.00
14_I	104_F	0.753	1.00
68_V	72_Y	0.751	1.00
51_L	79_L	0.747	1.00
136_H	139_S	0.746	1.00
87_D	90_I	0.743	1.00
4_K	47_P	0.737	1.00
16_D	20_F	0.736	1.00
168_Y	182_L	0.735	1.00
42_V	47_P	0.735	1.00
204_R	207_E	0.733	1.00
200_V	204_R	0.733	1.00
181_H	184_Q	0.720	1.00
66_R	70_K	0.717	1.00
86_I	107_R	0.717	1.00
8_V	64_V	0.712	1.00
55_M	81_A	0.700	1.00
35_G	39_V	0.698	1.00
5_I	49_L	0.696	1.00
165_L	169_L	0.692	1.00
18_L	109_L	0.688	1.00
140_L	151_K	0.687	1.00
115_A	118_R	0.687	1.00
39_V	71_K	0.684	1.00
21_N	110_L	0.680	1.00
51_L	113_V	0.678	1.00
42_V	50_I	0.674	1.00
180_E	184_Q	0.673	1.00
35_G	58_N	0.669	1.00
39_V	42_V	0.669	1.00
210_E	216_P	0.666	1.00
117_L	120_Q	0.666	1.00
17_I	21_N	0.665	1.00
92_L	112_R	0.665	1.00
112_R	116_N	0.659	1.00
98_D	115_A	0.656	1.00
73_D	122_T	0.655	1.00
91_G	96_A	0.654	1.00
9_D	56_L	0.653	1.00
137_I	140_L	0.652	1.00
23_R	29_V	0.650	1.00
211_D	220_V	0.648	1.00
69_R	75_P	0.648	1.00
210_E	217_N	0.646	1.00
150_S	153_D	0.644	1.00
35_G	56_L	0.640	1.00
206_R	211_D	0.638	1.00
120_Q	124_A	0.638	1.00
15_A	19_E	0.638	1.00
104_F	108_E	0.636	1.00
88_K	105_S	0.634	1.00
75_P	117_L	0.633	1.00
104_F	109_L	0.632	1.00
171_K	177_M	0.632	1.00
199_D	202_V	0.632	1.00
135_I	139_S	0.627	1.00
171_K	185_T	0.626	1.00
43_E	67_E	0.626	1.00
7_V	31_C	0.625	1.00
93_E	111_A	0.623	1.00
147_Y	163_F	0.622	1.00
68_V	76_I	0.616	1.00
144_P	171_K	0.604	1.00
135_I	144_P	0.603	1.00
54_I	91_G	0.602	1.00
169_L	202_V	0.600	1.00
62_V	87_D	0.599	1.00
164_E	168_Y	0.597	1.00
11_E	81_A	0.596	1.00
22_L	27_Y	0.594	1.00
11_E	14_I	0.593	1.00
75_P	119_R	0.593	1.00
107_R	111_A	0.592	1.00
21_N	25_E	0.590	1.00
7_V	19_E	0.589	1.00
53_D	102_K	0.589	1.00
216_P	219_I	0.588	1.00
85_E	107_R	0.588	1.00
5_I	22_L	0.586	1.00
133_N	144_P	0.581	1.00
65_C	69_R	0.580	1.00
77_I	98_D	0.578	1.00
51_L	77_I	0.575	1.00
73_D	123_T	0.574	1.00
151_K	210_E	0.574	1.00
111_A	114_K	0.573	1.00
194_D	197_T	0.570	1.00
161_R	201_T	0.568	1.00
134_E	138_G	0.566	1.00
69_R	74_M	0.562	1.00
142_I	149_V	0.561	1.00
10_D	80_T	0.560	1.00
52_L	56_L	0.555	1.00
151_K	154_E	0.554	1.00
49_L	116_N	0.552	1.00
139_S	151_K	0.551	1.00
119_R	123_T	0.549	1.00
86_I	89_V	0.547	1.00
37_E	58_N	0.545	1.00
14_I	17_I	0.542	1.00
46_Q	72_Y	0.537	1.00
27_Y	117_L	0.537	1.00
193_G	198_V	0.536	1.00
114_K	118_R	0.531	1.00
151_K	212_N	0.530	1.00
42_V	71_K	0.529	1.00
89_V	92_L	0.525	1.00
162_E	165_L	0.525	1.00
143_F	148_V	0.524	1.00
135_I	138_G	0.522	1.00
215_H	218_W	0.521	1.00
133_N	136_H	0.521	1.00
17_I	20_F	0.519	1.00
83_D	103_P	0.518	1.00
80_T	88_K	0.515	1.00
142_I	167_H	0.513	1.00
23_R	28_E	0.512	1.00
42_V	64_V	0.512	1.00
68_V	74_M	0.510	1.00
20_F	23_R	0.507	1.00
75_P	120_Q	0.505	1.00
179_R	202_V	0.505	1.00
5_I	113_V	0.505	1.00
52_L	68_V	0.503	1.00
8_V	52_L	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	0.9489	100	0.195	Contact Map
2oqrA	2	0.9617	100	0.211	Contact Map
4b09A	2	0.9106	100	0.217	Contact Map
1ys7A	2	0.9574	100	0.22	Contact Map
3r0jA	2	0.9362	100	0.222	Contact Map
4kfcA	2	0.9532	100	0.224	Contact Map
1kgsA	1	0.9277	100	0.234	Contact Map
1p2fA	1	0.9191	100	0.25	Contact Map
3q9sA	1	0.8894	100	0.264	Contact Map
2hqrA	2	0.9277	100	0.274	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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