OPENSEQ.org - YCBV - ECOLI GREMLIN

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YCBV - Uncharacterized fimbrial-like protein YcbV

UniProt:	P75860	Sequence MLKRIIWILFLLGLTWGCELFAHDGTVNISGSFRRNTCVLAQDSKQINVQLGDVSLTRFSHGNYGPEKSFIINLQDCGTDVSTVDVTFSGTPDGVQSEMLSIESGTDAASGLAIAILDDAKILIPLNQASKDYSLHSGKVPLTFYAQLRPVNSDVQSGKVNASATFVLHYD	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13714
Length:	171 (154)
Sequences:	1501
Seq/Len:	9.75

YCBV
Paralog alert: 0.95 [within 20: 0.78] - ratio of genomes with paralogs
Cluster includes: ELFA FIMA1 FIMF FIMG FIMI SFMA SFMF YADN YBGD YCBU YCBV YDER YDES YFCP YFCV YGIL YRAH

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
114_I	146_A	3.409	1.00
110_S	156_Q	3.073	1.00
84_V	168_L	2.909	1.00
115_A	149_R	2.793	1.00
115_A	147_Q	2.789	1.00
148_L	160_V	2.453	1.00
117_L	147_Q	2.368	1.00
39_V	76_D	2.351	1.00
41_A	75_Q	2.284	1.00
99_M	113_A	2.234	1.00
111_G	155_V	2.197	1.00
114_I	162_A	2.18	1.00
41_A	73_N	2.14	1.00
102_I	160_V	2.083	1.00
41_A	44_S	1.997	1.00
100_L	126_L	1.981	1.00
118_D	122_I	1.854	1.00
100_L	164_A	1.851	1.00
60_S	63_N	1.803	1.00
90_G	100_L	1.739	1.00
51_L	160_V	1.738	1.00
115_A	123_L	1.588	1.00
86_V	142_L	1.57	1.00
35_R	56_L	1.569	1.00
71_I	143_T	1.534	1.00
54_V	65_G	1.529	1.00
112_L	148_L	1.521	1.00
92_P	98_E	1.49	1.00
69_S	145_Y	1.483	1.00
93_D	151_V	1.465	1.00
44_S	73_N	1.457	1.00
59_F	150_P	1.453	1.00
125_P	128_Q	1.427	1.00
51_L	114_I	1.386	0.99
39_V	75_Q	1.359	0.99
47_I	72_I	1.345	0.99
99_M	149_R	1.34	0.99
52_G	160_V	1.333	0.99
52_G	66_P	1.33	0.99
150_P	155_V	1.31	0.99
109_A	112_L	1.301	0.99
44_S	47_I	1.27	0.99
32_S	53_D	1.252	0.98
108_A	159_K	1.246	0.98
51_L	148_L	1.216	0.98
121_K	145_Y	1.205	0.98
100_L	162_A	1.2	0.98
59_F	155_V	1.195	0.98
93_D	113_A	1.191	0.98
67_E	147_Q	1.19	0.98
64_Y	149_R	1.188	0.98
25_G	29_I	1.184	0.98
64_Y	115_A	1.162	0.97
89_S	127_N	1.161	0.97
59_F	112_L	1.153	0.97
104_S	107_D	1.136	0.97
28_N	163_S	1.123	0.96
87_T	169_H	1.121	0.96
59_F	151_V	1.12	0.96
100_L	114_I	1.119	0.96
47_I	166_F	1.098	0.96
54_V	148_L	1.094	0.96
30_S	50_Q	1.068	0.95
111_G	153_S	1.062	0.95
52_G	68_K	1.059	0.95
64_Y	147_Q	1.058	0.94
91_T	101_S	1.055	0.94
69_S	143_T	1.054	0.94
58_R	65_G	1.047	0.94
33_F	146_A	1.038	0.94
51_L	68_K	1.036	0.94
31_G	88_F	1.035	0.94
19_E	23_H	1.033	0.94
21_F	24_D	1.028	0.93
111_G	154_D	1.011	0.93
107_D	159_K	1.003	0.92

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
2jmrA	1	0.8772	100	0.244	Contact Map	0.64
2xg5B	1	0.9649	100	0.264	Contact Map	0.691
2jtyA	1	0.8947	100	0.28	Contact Map	0.685
2uy6B	2	0.8772	100	0.29	Contact Map	0.836
1pdkB	1	0.848	100	0.309	Contact Map	0.674
3bwuF	1	0.8012	99.9	0.343	Contact Map	0.79
4dwhB	2	0.8012	99.9	0.368	Contact Map	0.745
2w07B	1	0.8129	99.9	0.382	Contact Map	0.685
3bfqG	1	0.7544	99.9	0.392	Contact Map	0.723
3jwnH	2	0.9123	99.9	0.428	Contact Map	0.739

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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