ViewGene
Locus Name:
GeneID:
Location:

GeneID:2310
TrivialName: PA14_60330
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_60330
PAO1 Ortholog Locus:PA4557
Sequence Length:945
Protein Length:314
Start: 5378394
Stop: 5377450
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAP81279.1| (AY273871) drug tolerance protein [Pseudomonas aeruginosa]
Identities = 314/314 (100%), Positives = 314/314 (100%)
Sequence:
ATGCAAATCAAACTCGCCAATCCCCGCGGCTTCTGCGCCGGCGTGGATCGCGCCATCGAGATCGTCAACCGT
GCCCTCGATGTCTTCGGCCCGCCGATCTACGTGCGTCACGAGGTGGTGCACAACAAGTTCGTCGTGGACAAC
CTGCGCCAGCGCGGCGCCATCTTCGTCGAGGAACTCGATCAGGTGCCGGACAACGTCATCGTCATCTTCAGC
GCCCACGGCGTTTCCCAGGCGGTCCGCAAGGAAGCCGAGGGGCGCGGCCTGAAGGTTTTCGACGCGACCTGC
CCGCTGGTGACCAAGGTGCACATGGAAGTGGTGCGCTACAGCCGCGACGGCCACGAATGCGTGCTGATCGGG
CATGAAGGCCACCCCGAGGTGGAAGGCACCATGGGCCAGTACGATGCCAGCAACGGCGGTGCCATCTACCTG
GTGGAGGACGAGGCCGACGTCGCCGCGCTGGAGGTGCGCAAGCCCGAAGCCCTGCACTACGTGACCCAGACC
ACCCTGTCGATGGACGACACCTCGAAGGTCATCGATGCCCTGCGCGCCAAGTTCCCGCAGATCCAGGGGCCG
CGCAAGAACGACATCTGCTATGCCACCCAGAACCGCCAGGATGCCGTGAAGGAACTGGCCGACCAGTGCGAC
ATGGTCCTGGTGGTGGGCAGCCCCAACAGTTCCAACTCCAACCGCCTGCGCGAACTCGCCGAGCGCATGGGC
ACGCCGGCCTACCTGATCGACGGCGCCGAGGACATGCAACGCGGCTGGTTCGACGGTGTGCGTCGCATCGGA
ATCACCGCAGGCGCCTCCGCGCCGGAAGTGCTGGTGCGCGGAGTGATCGCCCAGCTACGTGAGTGGGGGGCG
TCGGAAGAGCAGGAACTGGAGGGACGGGAGGAGAACATTACCTTCTCGATGCCCAAGGAACTGCGGGTCAAG
GCTTTGTAA
Translation:
MQIKLANPRGFCAGVDRAIEIVNRALDVFGPPIYVRHEVVHNKFVVDNLRQRGAIFVEELDQVPDNVIVIFS
AHGVSQAVRKEAEGRGLKVFDATCPLVTKVHMEVVRYSRDGHECVLIGHEGHPEVEGTMGQYDASNGGAIYL
VEDEADVAALEVRKPEALHYVTQTTLSMDDTSKVIDALRAKFPQIQGPRKNDICYATQNRQDAVKELADQCD
MVLVVGSPNSSNSNRLRELAERMGTPAYLIDGAEDMQRGWFDGVRRIGITAGASAPEVLVRGVIAQLREWGA
SEEQELEGREENITFSMPKELRVKAL*
AnnotationID:2318GeneID:2310
AnnotatorUID: danlee
Modification Date/Time: 2005-10-05 17:05:05
Gene Name:lytB
Confidence Code:2
GeneProduct:penicillin tolerance protein, LytB
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(3) Antibiotic resistance and susceptibility
Alternate Gene Product Name:hydroxymethylbutenyl pyrophosphate reductase
Functional Category Confidence Code:5
COGs:COG0761,pfam02401
Secondary Functional Category(ies):
EC Number:1.17.1.2
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66232.1|AE016251_8 (AE016776) hydroxymethylbutenyl pyrophosphate reductase
           [Pseudomonas putida KT2440]
          Length = 315

 Score =  546 bits (1407), Expect = e-155
 Identities = 270/314 (85%), Positives = 294/314 (93%)

>gb|AAM36128.1| (AE011755) penicillin tolerance protein [Xanthomonas axonopodis pv.
           citri str. 306]
          Length = 316

 Score =  434 bits (1116), Expect = e-121
 Identities = 216/313 (69%), Positives = 256/313 (81%), Gaps = 1/313 (0%)

>gb|AAN78533.1|AE016755_33 (AE016755) IspH protein [Escherichia coli CFT073]
          Length = 331

 Score =  419 bits (1076), Expect = e-116
 Identities = 210/311 (67%), Positives = 251/311 (80%), Gaps = 1/311 (0%)






 
Structural Features:
COG0761, LytB, Penicillin tolerance protein 
[Lipid metabolism / Cell envelope biogenesis, outer membrane]
CD-Length = 294 residues,  99.7% aligned
Score =  459 bits (1182), Expect = 5e-130
Identities = 196/296 (66%), Positives = 241/296 (81%), Gaps = 3/296 (1%)

pfam02401, LYTB, LytB protein. 
CD-Length = 280 residues,  99.6% aligned
Score =  390 bits (1003), Expect = 2e-109
Identities = 167/283 (59%), Positives = 213/283 (75%), Gaps = 4/283 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4623




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21769




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31656




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2310_cdd.html


    		




 
URL:

















    ReferenceID:33011




  
Author/Investigator(s):
        McAteer S, Coulson A, McLennan N, Masters M.





  
Title:
        The lytB gene of Escherichia coli is essential and specifies a product needed for isoprenoid biosynthesis.




  
PubMed:
        11717301


MedLine:
        




    
Source:
J Bacteriol. 2001 Dec;183(24):7403-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11717301

















    ReferenceID:33012




  
Author/Investigator(s):
        Potter S, Yang X, Boulanger MJ, Ishiguro EE.





  
Title:
        Occurrence of homologs of the Escherichia coli lytB gene in gram-negative bacterial species.




  
PubMed:
        9537400


MedLine:
        




    
Source:
J Bacteriol. 1998 Apr;180(7):1959-61.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9537400

















    ReferenceID:33013




  
Author/Investigator(s):
        Gustafson CE, Kaul S, Ishiguro EE.





  
Title:
        Identification of the Escherichia coli lytB gene, which is involved in penicillin tolerance and control of the stringent response.




  
PubMed:
        8432714


MedLine:
        




    
Source:
J Bacteriol. 1993 Feb;175(4):1203-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8432714

















    ReferenceID:33014




  
Author/Investigator(s):
        Gustafson CE, Kaul S, Ishiguro EE.





  
Title:
        Identification of the Escherichia coli lytB gene, which is involved in penicillin tolerance and control of the stringent response.




  
PubMed:
        8432714


MedLine:
        




    
Source:
J Bacteriol. 1993 Feb;175(4):1203-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8432714

















    ReferenceID:33015




  
Author/Investigator(s):
        Harkness RE, Kusser W, Qi BJ, Ishiguro EE.





  
Title:
        Genetic mapping of the lytA and lytB loci of Escherichia coli, which are involved in penicillin tolerance and control of the stringent response.




  
PubMed:
        1464070


MedLine:
        




    
Source:
Can J Microbiol. 1992 Sep;38(9):975-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1464070

















    ReferenceID:33016




  
Author/Investigator(s):
        Lazarevic V, Margot P, Soldo B, Karamata D.





  
Title:
        Sequencing and analysis of the Bacillus subtilis lytRABC divergon: a regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier.




  
PubMed:
        1357079


MedLine:
        




    
Source:
J Gen Microbiol. 1992 Sep;138 ( Pt 9):1949-61.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1357079









           
Homologs By Global Alignment 

           

       



     
Gene ID:2310
           
Identity:

                               
                                   0%
                               
                                   10%
                               
                                   20%
                               
                                   30%
                               
                                   40%
                               
                                   50%
                               
                                   60%
                               
                                   70%
                               
                                   80%
                               
                                   90%
                               
                                   100%
                               
                             

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
119997
                           gb|AAP81279.1|
                           (AY273871) drug tolerance protein [Pseudomonas aeruginosa]
                           314
                           99.99
                           99.99
                           0
                           1616.0
     

     
     
3935
                           PA4557_tr
                           translation of PA4557
                           314
                           99.68
                           99.99
                           0
                           1611.0
     

     
     
119998
                           gb|AAG07945.1|AE004869_9
                           (AE004869) LytB protein [Pseudomonas aeruginosa PAO1]
                           314
                           99.68
                           99.99
                           0
                           1611.0
     

     
     
119999
                           gb|AAO54351.1|
                           (AE016858) hydroxymethylbutenyl pyrophosphate reductase [Pseudomonas syringae pv. tomato str. DC3000]
                           315
                           86.98
                           93.33
                           1
                           1425.0
     

     
     
120000
                           gb|AAN66232.1|AE016251_8
                           (AE016776) hydroxymethylbutenyl pyrophosphate reductase [Pseudomonas putida KT2440]
                           315
                           85.71
                           93.33
                           1
                           1407.0
     

     






      

          
GC ORFID: 45312How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4557Glimmer Score: 

          
Start: 4642073Stop: 4641129

          
Length: 945


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4557 translation of PA4557Homolog Bit Score 625.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3537 (ORF: BLASTX 553.0), t_PA4557 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCAAATCAAACTCGCCAATCCCCGCGGCTTCTGCGCCGGCGTGGATCGCGCCATCGAGATCGTCAACCGT 
GCCCTCGATGTCTTCGGCCCGCCGATCTACGTGCGTCACGAGGTGGTGCACAACAAGTTCGTCGTGGACAAC 
CTGCGCCAGCGCGGCGCCATCTTCGTCGAGGAACTCGATCAGGTGCCGGACAACGTCATCGTCATCTTCAGC 
GCCCACGGCGTTTCCCAGGCGGTCCGCAAGGAAGCCGAGGGGCGCGGCCTGAAGGTTTTCGACGCGACCTGC 
CCGCTGGTGACCAAGGTGCACATGGAAGTGGTGCGCTACAGCCGCGACGGCCACGAATGCGTGCTGATCGGG 
CATGAAGGCCACCCCGAGGTGGAAGGCACCATGGGCCAGTACGATGCCAGCAACGGCGGTGCCATCTACCTG 
GTGGAGGACGAGGCCGACGTCGCCGCGCTGGAGGTGCGCAAGCCCGAAGCCCTGCACTACGTGACCCAGACC 
ACCCTGTCGATGGACGACACCTCGAAGGTCATCGATGCCCTGCGCGCCAAGTTCCCGCAGATCCAGGGGCCG 
CGCAAGAACGACATCTGCTATGCCACCCAGAACCGCCAGGATGCCGTGAAGGAACTGGCCGACCAGTGCGAC 
ATGGTCCTGGTGGTGGGCAGCCCCAACAGTTCCAACTCCAACCGCCTGCGCGAACTCGCCGAGCGCATGGGC 
ACGCCGGCCTACCTGATCGACGGCGCCGAGGACATGCAACGCGGCTGGTTCGACGGTGTGCGTCGCATCGGA 
ATCACCGCAGGCGCCTCCGCGCCGGAAGTGCTGGTGCGCGGAGTGATCGCCCAGCTACGTGAGTGGGGGGCG 
TCGGAAGAGCAGGAACTGGAGGGACGGGAGGAGAACATTACCTTCTCGATGCCCAAGGAACTGCGGGTCAAG 
GCTTTGTAA