YPDB - ECOLI - GREMLIN Contacts

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YPDB - Transcriptional regulatory protein YpdB

UniProt:	P0AE39	Sequences: MKVIIVEDEFLAQQELSWLIKEHSQMEIVGTFDDGLDVLKFLQHNRVDAIFLDINIPSLDGVLLAQNISQFAHKPFIVFITAWKEHAVEAFELEAFDYILKPYQESRITGMLQKLEAAWQQQQTSSTPAATVTRENDTINLVKDERIIVTPINDIYYAEAHEKMTFVYTRRESYVMPMNITEFCSKLPPSHFFRCHRSFCVNLNKIREIEPWFNNTYILRLKDLDFEVPVSRSKVKEFRQLMHL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14149
Length:	244 (187)
Sequences:	50227 (39005)
Seq/√Len:	2852.4

ECOLI - YPDB YEHT ARCB RCSC BARA YHJB YJJQ RSSB QSEB PHOP CUSR CREB UVRY BASR NARP YEDW DCUR NARL EVGA OMPR DPIA YGEK FIMZ TORS PHOB CHEB RCSB KDPE ARCA RSTA BAER BGLJ UHPA CPXR RCSA TORR CSGD GLRR EVGS NTRC ZRAR ATOC RCSD
BACSU - LYTT NATR YESN MALR CITT YVFU YFIK PHOP YXJL GLNL CHEB SP0A CMPA LIAR DEGU DCTR YHCZ DESR YCLJ YVRH YYCF RESD YKOG YDFI YRKP YCBL CSSR BCER YXDJ YVCP YBDJ 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
13_Q	31_T	3.867	1.00
13_Q	33_D	3.452	1.00
17_S	31_T	3.348	1.00
6_V	38_V	2.836	1.00
39_L	67_N	2.523	1.00
30_G	47_V	2.428	1.00
59_L	67_N	2.418	1.00
36_L	58_S	2.417	1.00
32_F	41_F	2.397	1.00
35_G	59_L	2.312	1.00
34_D	58_S	2.278	1.00
19_L	105_E	2.096	1.00
30_G	41_F	2.020	1.00
87_A	107_R	1.970	1.00
79_F	95_A	1.962	1.00
30_G	45_N	1.949	1.00
41_F	45_N	1.932	1.00
65_A	77_I	1.931	1.00
17_S	21_K	1.880	1.00
55_N	83_W	1.853	1.00
60_D	63_L	1.845	1.00
52_L	64_L	1.794	1.00
33_D	37_D	1.785	1.00
4_I	32_F	1.754	1.00
97_D	111_M	1.696	1.00
2_K	28_I	1.692	1.00
23_H	109_T	1.684	1.00
43_Q	71_F	1.680	1.00
79_F	90_A	1.679	1.00
165_T	169_T	1.654	1.00
34_D	37_D	1.628	1.00
135_E	138_T	1.605	1.00
65_A	79_F	1.561	1.00
165_T	168_Y	1.558	1.00
50_I	75_P	1.536	1.00
67_N	71_F	1.521	1.00
69_S	96_F	1.516	1.00
54_I	79_F	1.515	1.00
35_G	64_L	1.513	1.00
83_W	86_H	1.455	1.00
7_E	13_Q	1.453	1.00
41_F	44_H	1.448	1.00
39_L	64_L	1.446	1.00
36_L	59_L	1.440	1.00
42_L	68_I	1.439	1.00
59_L	63_L	1.433	1.00
174_Y	177_P	1.391	1.00
54_I	62_V	1.388	1.00
2_K	30_G	1.372	1.00
96_F	118_A	1.359	1.00
2_K	27_E	1.348	1.00
63_L	66_Q	1.346	1.00
52_L	65_A	1.303	1.00
39_L	59_L	1.271	1.00
164_M	167_V	1.266	1.00
109_T	113_Q	1.258	1.00
67_N	70_Q	1.250	1.00
41_F	47_V	1.238	1.00
8_D	53_D	1.236	1.00
168_Y	171_R	1.234	1.00
32_F	38_V	1.228	1.00
166_F	169_T	1.224	1.00
20_I	112_L	1.214	1.00
6_V	56_I	1.210	1.00
78_V	115_L	1.208	1.00
66_Q	89_E	1.204	1.00
167_V	171_R	1.191	1.00
66_Q	93_L	1.185	1.00
164_M	168_Y	1.184	1.00
40_K	44_H	1.181	1.00
36_L	40_K	1.179	1.00
4_I	41_F	1.171	1.00
62_V	89_E	1.165	1.00
163_K	166_F	1.162	1.00
23_H	113_Q	1.144	1.00
179_N	182_E	1.135	1.00
39_L	43_Q	1.133	1.00
4_I	47_V	1.121	1.00
142_V	145_E	1.120	1.00
96_F	115_L	1.115	1.00
10_F	33_D	1.111	1.00
147_I	155_I	1.110	1.00
4_I	38_V	1.098	1.00
37_D	40_K	1.089	1.00
37_D	41_F	1.086	1.00
43_Q	72_A	1.077	1.00
49_A	112_L	1.075	1.00
76_F	118_A	1.072	1.00
38_V	64_L	1.063	1.00
87_A	100_L	1.054	1.00
163_K	168_Y	1.046	1.00
182_E	185_S	1.041	1.00
72_A	75_P	1.039	1.00
89_E	93_L	1.017	1.00
38_V	42_L	1.007	1.00
14_Q	31_T	1.005	1.00
76_F	96_F	1.005	1.00
10_F	14_Q	1.001	1.00
4_I	30_G	1.001	1.00
78_V	111_M	0.995	1.00
16_L	80_I	0.994	1.00
89_E	92_E	0.994	1.00
107_R	110_G	0.980	1.00
84_K	100_L	0.976	1.00
56_I	64_L	0.967	1.00
92_E	113_Q	0.963	1.00
2_K	45_N	0.957	1.00
65_A	93_L	0.953	1.00
15_E	19_L	0.950	1.00
131_T	144_D	0.943	1.00
4_I	42_L	0.939	1.00
50_I	77_I	0.938	1.00
178_M	182_E	0.934	1.00
165_T	171_R	0.933	1.00
97_D	114_K	0.932	1.00
11_L	15_E	0.929	1.00
52_L	79_F	0.923	1.00
139_I	156_Y	0.922	1.00
153_N	156_Y	0.917	1.00
88_V	92_E	0.916	1.00
164_M	169_T	0.915	1.00
110_G	114_K	0.915	1.00
62_V	90_A	0.914	1.00
92_E	110_G	0.914	1.00
62_V	93_L	0.910	1.00
142_V	147_I	0.909	1.00
6_V	50_I	0.899	1.00
55_N	82_A	0.894	1.00
54_I	60_D	0.882	1.00
178_M	181_T	0.880	1.00
137_D	141_L	0.876	1.00
6_V	32_F	0.875	1.00
49_A	116_E	0.873	1.00
103_Y	108_I	0.866	1.00
63_L	67_N	0.862	1.00
16_L	108_I	0.861	1.00
14_Q	17_S	0.857	1.00
50_I	68_I	0.855	1.00
40_K	43_Q	0.848	1.00
163_K	169_T	0.846	1.00
163_K	167_V	0.845	1.00
42_L	72_A	0.835	1.00
164_M	171_R	0.830	1.00
158_A	162_E	0.829	1.00
51_F	108_I	0.829	1.00
105_E	109_T	0.827	1.00
140_N	147_I	0.827	1.00
32_F	37_D	0.826	1.00
54_I	86_H	0.826	1.00
65_A	95_A	0.824	1.00
51_F	80_I	0.819	1.00
5_I	16_L	0.819	1.00
9_E	12_A	0.814	1.00
159_E	162_E	0.812	1.00
42_L	50_I	0.810	1.00
150_T	154_D	0.800	1.00
5_I	17_S	0.798	1.00
10_F	13_Q	0.794	1.00
133_T	142_V	0.794	1.00
161_H	164_M	0.791	1.00
166_F	170_R	0.789	1.00
18_W	22_E	0.789	1.00
151_P	155_I	0.783	1.00
80_I	103_Y	0.780	1.00
86_H	89_E	0.778	1.00
107_R	111_M	0.766	1.00
5_I	13_Q	0.758	1.00
7_E	56_I	0.755	1.00
90_A	95_A	0.755	1.00
52_L	77_I	0.749	1.00
160_A	164_M	0.745	1.00
42_L	47_V	0.743	1.00
151_P	154_D	0.743	1.00
42_L	75_P	0.740	1.00
64_L	68_I	0.735	1.00
91_F	111_M	0.734	1.00
6_V	64_L	0.723	1.00
134_R	162_E	0.721	1.00
24_S	27_E	0.721	1.00
14_Q	18_W	0.714	1.00
76_F	119_W	0.712	1.00
68_I	77_I	0.702	1.00
59_L	64_L	0.701	1.00
167_V	170_R	0.698	1.00
122_Q	126_S	0.698	1.00
158_A	163_K	0.697	1.00
66_Q	70_Q	0.690	1.00
43_Q	67_N	0.681	1.00
115_L	118_A	0.679	1.00
114_K	117_A	0.677	1.00
176_M	185_S	0.672	1.00
164_M	170_R	0.670	1.00
166_F	171_R	0.667	1.00
68_I	75_P	0.665	1.00
143_K	146_R	0.664	1.00
177_P	181_T	0.664	1.00
148_I	151_P	0.664	1.00
134_R	141_L	0.664	1.00
161_H	168_Y	0.663	1.00
78_V	97_D	0.662	1.00
51_F	78_V	0.661	1.00
35_G	39_L	0.660	1.00
181_T	185_S	0.660	1.00
32_F	35_G	0.659	1.00
51_F	112_L	0.657	1.00
42_L	64_L	0.654	1.00
111_M	115_L	0.651	1.00
184_C	188_P	0.650	1.00
104_Q	107_R	0.647	1.00
76_F	122_Q	0.646	1.00
152_I	156_Y	0.645	1.00
65_A	69_S	0.640	1.00
158_A	161_H	0.639	1.00
13_Q	17_S	0.637	1.00
88_V	106_S	0.635	1.00
174_Y	178_M	0.634	1.00
119_W	123_Q	0.625	1.00
21_K	24_S	0.622	1.00
92_E	97_D	0.620	1.00
180_I	183_F	0.619	1.00
160_A	163_K	0.615	1.00
116_E	119_W	0.613	1.00
106_S	110_G	0.612	1.00
180_I	184_C	0.609	1.00
185_S	189_P	0.608	1.00
39_L	42_L	0.607	1.00
54_I	83_W	0.607	1.00
113_Q	116_E	0.606	1.00
4_I	50_I	0.602	1.00
175_V	179_N	0.599	1.00
88_V	91_F	0.599	1.00
87_A	104_Q	0.597	1.00
114_K	119_W	0.595	1.00
5_I	31_T	0.594	1.00
150_T	160_A	0.593	1.00
162_E	166_F	0.593	1.00
165_T	170_R	0.592	1.00
15_E	18_W	0.590	1.00
81_T	87_A	0.586	1.00
12_A	103_Y	0.583	1.00
35_G	56_I	0.582	1.00
161_H	165_T	0.581	1.00
62_V	86_H	0.580	1.00
3_V	49_A	0.577	1.00
122_Q	127_T	0.577	1.00
2_K	48_D	0.575	1.00
6_V	35_G	0.574	1.00
35_G	58_S	0.572	1.00
54_I	90_A	0.562	1.00
150_T	157_Y	0.561	1.00
110_G	113_Q	0.561	1.00
138_T	142_V	0.558	1.00
154_D	157_Y	0.555	1.00
2_K	47_V	0.553	1.00
76_F	115_L	0.545	1.00
86_H	90_A	0.544	1.00
6_V	52_L	0.540	1.00
136_N	139_I	0.540	1.00
134_R	155_I	0.539	1.00
124_T	127_T	0.539	1.00
17_S	29_V	0.535	1.00
114_K	118_A	0.534	1.00
141_L	148_I	0.534	1.00
128_P	133_T	0.529	1.00
123_Q	126_S	0.529	1.00
120_Q	123_Q	0.528	1.00
141_L	155_I	0.528	1.00
116_E	120_Q	0.527	1.00
106_S	109_T	0.526	1.00
113_Q	117_A	0.525	1.00
69_S	75_P	0.524	1.00
159_E	163_K	0.519	1.00
3_V	20_I	0.519	1.00
27_E	113_Q	0.517	1.00
134_R	137_D	0.517	1.00
74_K	122_Q	0.514	1.00
118_A	122_Q	0.512	1.00
49_A	115_L	0.505	1.00
92_E	107_R	0.502	1.00
139_I	142_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
4cbvA	2	0.959	100	0.287	Contact Map
4gvpA	1	0.791	100	0.386	Contact Map
4g97A	1	0.5205	100	0.39	Contact Map
3n0rA	1	0.4877	100	0.393	Contact Map
1yioA	1	0.7664	100	0.395	Contact Map
1a04A	1	0.7828	100	0.401	Contact Map
4ldzA	2	0.7623	100	0.406	Contact Map
3c3wA	2	0.791	100	0.407	Contact Map
3rqiA	2	0.668	99.9	0.423	Contact Map
4hyeA	2	0.7869	99.9	0.425	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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