Subcellular localization predictions (return to top)
Information about bacterial subcellular localization is important for protein function prediction and identification of suitable diagnostic targets. Predictions generated for Las by PSORTdb are shown are provided (Excel)

Proteins with predicted signal peptides (return to top)
Bacterial proteins mediating interactions with the environment and with host organisms are commonly found in the periplasm and bacterial outer membrane. To identify the likely set of Las-encoded proteins targeted to regions of the cell outside the cytoplasm, all predicted Las proteins were evaluated for the presence of predicted signal peptides using SignalP 3.0. SignalP generates predictions based on a combination of artificial neural networks and hidden Markov models.

• Complete set of predictions generated by both the neural networks and hidden Markov models (Excel)
  
  
• Mature peptides resulting from cleavage of predicted signal peptides:
  To view, open and save LAS_mature_peptides.txt and view using the Artemis genome viewer
  
  
• Summary Table of proteins predicted to have signal pepetides by both artificial neural networks and hidden Markov models:

  Las proteins with predicted signal peptides	Locus Tag	Accession Number
  cationic amino acid ABC transporter, periplasmic binding protein	CLIBASIA_00005	YP_003064583
  outer membrane lipoprotein	CLIBASIA_00420	YP_003064612
  hypothetical protein	CLIBASIA_00460	YP_003064620
  hypothetical protein	CLIBASIA_00470	YP_003064622
  cytochrome-c oxidase assembly factor protein	CLIBASIA_00830	YP_003064694
  putative membrane-bound lytic murein transglycosylase signal peptide protein	CLIBASIA_00965	YP_003064721
  outer membrane protein	CLIBASIA_00995	YP_003064727
  substrate-binding region of ABC-type glycine betaine transport system	CLIBASIA_01135	YP_003064755
  flagellar basal body L-ring protein	CLIBASIA_01295	YP_003064787
  hypothetical protein	CLIBASIA_01300	YP_003064788
  peptidase S11, D-alanyl-D-alanine carboxypeptidase 1	CLIBASIA_01600	YP_003064848
  hypothetical protein	CLIBASIA_01640	YP_003064856
  sensory box/GGDEF family protein	CLIBASIA_01765	YP_003064881
  hypothetical protein	CLIBASIA_03230	YP_003065172
  putative pilus assembly protein	CLIBASIA_03070	YP_003065140
  zinc uptake ABC transporter	CLIBASIA_03020	YP_003065130
  hypothetical protein	CLIBASIA_02610	YP_003065048
  hypothetical protein (gamma-proteobacterial lineage)	CLIBASIA_02470	YP_003065020
  outer membrane protein	CLIBASIA_02425	YP_003065011
  extracellular solute-binding protein (gamma-proteobacterial lineage)	CLIBASIA_02250	YP_003064976
  translocation protein TolB	CLIBASIA_02175	YP_003064961
  metalloprotease	CLIBASIA_02160	YP_003064958
  hypothetical protein	CLIBASIA_02145	YP_003064955
  periplasmic solute binding protein (gamma-proteobacterial lineage)	CLIBASIA_02120	YP_003064950
  hypothetical protein	CLIBASIA_03695	YP_003065257
  hypothetical protein	CLIBASIA_04025	YP_003065319
  hypothetical protein	CLIBASIA_04040	YP_003065322
  rare lipoprotein A	CLIBASIA_04170	YP_003065348
  putative hydrolase serine protease transmembrane protein (gamma-proteobacterial lineage)	CLIBASIA_04290	YP_003065372
  hypothetical protein	CLIBASIA_04520	YP_003065416
  hypothetical protein	CLIBASIA_04580	YP_003065427
  hypothetical protein	CLIBASIA_04900	YP_003065491
  hypothetical protein	CLIBASIA_05115	YP_003065534
  hypothetical protein	CLIBASIA_05150	YP_003065541
  hypothetical protein	CLIBASIA_05315	YP_003065569

Predicted lipoproteins (return to top)
Bacterial lipoproteins are secreted across the bacterial inner membrane where upon attached lipid anchors the protein in the inner or outer membrane. To identify the likely set of Las-encoded lipoproteins, all predicted Las proteins were evaluated for the characteristic lipoprotein signal peptidase cleavage site using LipoP 1.0 which generates predictions using hidden Markov models.

Predicted lipoproteins in Las	Locus Tag	Accession Number
putative ABC transporter protein	CLIBASIA_00100	YP_003064554
hypothetical protein	CLIBASIA_00185	YP_003064567
hypothetical protein	CLIBASIA_00520	YP_003064632
hypothetical protein	CLIBASIA_00525	YP_003064633
hypothetical protein	CLIBASIA_00530	YP_003064634
flagellar basal body L-ring protein	CLIBASIA_01295	YP_003064787
hypothetical protein (similar to CLIBASIA_04405)	CLIBASIA_02215	YP_003064969
thiamine transporter substrate binding subunit (gamma-proteobacterial lineage)	CLIBASIA_02240	YP_003064974
hypothetical protein	CLIBASIA_02305	YP_003064987.2
hypothetical protein	CLIBASIA_02380	YP_003065002
TPR repeat-containing protein	CLIBASIA_02395	YP_003065005
putative phosphate-binding periplasmic protein	CLIBASIA_02970	YP_003065120
hypothetical protein	CLIBASIA_03230	YP_003065172
hypothetical protein	CLIBASIA_03470	YP_003065216
hypothetical protein	CLIBASIA_04025	YP_003065319
hypothetical protein	CLIBASIA_04030	YP_003065320
hypothetical protein	CLIBASIA_04040	YP_003065322
nodulation protein; outer membrane efflux protein	CLIBASIA_04145	YP_003065343
rare lipoprotein A	CLIBASIA_04170	YP_003065348
OmpA; MotB	CLIBASIA_04260	YP_003065366
hypothetical protein (similar to CLIBASIA_02215)	CLIBASIA_04405	YP_003065393
hypothetical protein	CLIBASIA_04410	YP_003065394
hypothetical protein	CLIBASIA_04560	YP_003065423

Predicted transcription factors (return to top)

Predicted RirA binding sites (return to transcription factor list)

Predicted RpoH binding sites (return to transcription factor list)

Repetitive Sequences (return to top)

Predicted repeat families generated with RepeatScout and RepeatMasker/Repbase. To view, open and save the prediction file las_psy62-repeats.txt and view using the Artemis genome viewer

Pseudogenes (return to top)

Summary table

Horizontally transferred regions (return to top)

Summary table