ViewGene
Locus Name:
GeneID:
Location:

GeneID:3844
TrivialName: PA14_58670
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_58670
PAO1 Ortholog Locus:PA4522
Sequence Length:567
Protein Length:188
Start: 5229046
Stop: 5228480
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07910.1|AE004866_4 (AE004866) beta-lactamase expression regulator AmpD [Pseudomonas aeruginosa PAO1]
Identities = 188/188 (100%), Positives = 188/188 (100%)
Sequence:
ATGCATTTCGATTCCGTTACCGGCTGGGTCCGTGGCGTCCGCCACTGCCCTTCACCGAATTTCAACCTGCGT
CCGCAAGGGGACGCGGTGTCGCTGCTGGTCATCCACAATATCAGCCTGCCGCCGGGACAGTTCGGCACCGGC
AAGGTCCAGGCGTTCTTCCAGAATCGTCTGGACCCGAACGAACATCCCTATTTCGAGGAGATCCGCCACCTG
ACGGTTTCCGCGCATTTCCTCATCGAACGCGACGGCGCCATCACCCAGTTCGTCTCCTGTCACGACCGCGCC
TGGCATGCCGGGGTTTCCTGCTTCGACGGTCGCGAGGCGTGCAACGACTTCTCCCTTGGCATCGAACTGGAG
GGGACCGACACGGAACCGTACACGGACGCGCAGTACACTGCCCTGGCCGGGCTGACGCGGCTGTTGCGCGCG
GCCTTCCCGGGGATCACCCCGGAACGCATCCAGGGCCACTGCGATATCGCCCCGGAGCGCAAGACCGATCCC
GGCGAGGCTTTCGACTGGTCGCGCTACCGCGCCGGATTGACCGATTCCAAGGAGGAAACATGA
Translation:
MHFDSVTGWVRGVRHCPSPNFNLRPQGDAVSLLVIHNISLPPGQFGTGKVQAFFQNRLDPNEHPYFEEIRHL
TVSAHFLIERDGAITQFVSCHDRAWHAGVSCFDGREACNDFSLGIELEGTDTEPYTDAQYTALAGLTRLLRA
AFPGITPERIQGHCDIAPERKTDPGEAFDWSRYRAGLTDSKEET*
AnnotationID:3851GeneID:3844
AnnotatorUID: diggins
Modification Date/Time: 2005-05-04 15:03:41
Gene Name:ampD
Confidence Code:2
GeneProduct:beta-lactamase expression regulator
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(7) Cell wall / LPS / capsule
Alternate Gene Product Name:N-acetyl-anhydromuramyl-L-alanine amidase
Functional Category Confidence Code:5
COGs:COG3023,pfam01510,smart00644
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66414.1|AE016269_1 (AE016777) N-acetyl-anhydromuramyl-L-alanine amidase AmpD
           [Pseudomonas putida KT2440]
          Length = 190

 Score =  285 bits (729), Expect = 1e-76
 Identities = 133/189 (70%), Positives = 150/189 (79%), Gaps = 2/189 (1%)

>gb|AAF73950.1|AF237388_1 (AF237388) N-acetyl-muramyl-L-alanine amidase [Azotobacter
           vinelandii]
          Length = 187

 Score =  274 bits (700), Expect = 2e-73
 Identities = 131/183 (71%), Positives = 146/183 (79%), Gaps = 1/183 (0%)






 
Structural Features:
COG3023, AmpD, Negative regulator of beta-lactamase expression 
[Defense mechanisms]
CD-Length = 257 residues, only  67.7% aligned
Score =  226 bits (577), Expect = 3e-60
Identities = 94/179 (52%), Positives = 110/179 (61%), Gaps = 9/179 (5%)

pfam01510, Amidase_2, N-acetylmuramoyl-L-alanine amidase.
CD-Length = 150 residues,  95.3% aligned
Score =  122 bits (306), Expect = 8e-29
Identities = 54/164 (32%), Positives = 73/164 (44%), Gaps = 25/164 (15%)

smart00644, Ami_2, Ami_2 domain.
CD-Length = 127 residues,  99.2% aligned
Score =  102 bits (256), Expect = 4e-23
Identities = 43/142 (30%), Positives = 62/142 (43%), Gaps = 21/142 (14%)






   
Genomic Context:






   
Comment:


















    ReferenceID:7691




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:24833




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31569




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3844_cdd.html


    		




 
URL:

















    ReferenceID:32962




  
Author/Investigator(s):
        Bagge N, Ciofu O, Hentzer M, Campbell JI, Givskov M, Hoiby N.





  
Title:
        Constitutive high expression of chromosomal beta-lactamase in Pseudomonas aeruginosa caused by a new insertion sequence (IS1669) located in ampD.




  
PubMed:
        12384343


MedLine:
        




    
Source:
Antimicrob Agents Chemother. 2002 Nov;46(11):3406-11.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12384343

















    ReferenceID:32963




  
Author/Investigator(s):
        Inactivation of the ampD gene in Pseudomonas aeruginosa leads to moderate-basal-level and hyperinducible AmpC beta-lactamase expression.





  
Title:
        Langaee TY, Gagnon L, Huletsky A.




  
PubMed:
        10681322


MedLine:
        




    
Source:
Antimicrob Agents Chemother. 2000 Mar;44(3):583-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10681322

















    ReferenceID:32964




  
Author/Investigator(s):
        An ampD gene in Pseudomonas aeruginosa encodes a negative regulator of AmpC beta-lactamase expression.





  
Title:
        Langaee TY, Dargis M, Huletsky A.




  
PubMed:
        9835532


MedLine:
        




    
Source:
Antimicrob Agents Chemother. 1998 Dec;42(12):3296-300.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9835532









           
Homologs By Global Alignment 

           

       



     
Gene ID:3844
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6069
                           PA4522_tr
                           translation of PA4522
                           188
                           99.99
                           99.99
                           0
                           1027.0
     

     
     
169308
                           gb|AAG07910.1|AE004866_4
                           (AE004866) beta-lactamase expression regulator AmpD [Pseudomonas aeruginosa PAO1]
                           188
                           99.99
                           99.99
                           0
                           1027.0
     

     
     
169309
                           gb|AAC98783.1|
                           (AF082575) N-acetyl-anhydromuramyl-L-alanine amidase [Pseudomonas aeruginosa]
                           188
                           99.99
                           99.99
                           0
                           1027.0
     

     
     
169310
                           gb|AAN66414.1|AE016269_1
                           (AE016777) N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Pseudomonas putida KT2440]
                           190
                           70.00
                           78.94
                           2
                           731.0
     

     
     
169311
                           gb|AAF73950.1|AF237388_1
                           (AF237388) N-acetyl-muramyl-L-alanine amidase [Azotobacter vinelandii]
                           188
                           69.68
                           78.19
                           1
                           697.0
     

     






      

          
GC ORFID: 46846How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4522Glimmer Score: 

          
Start: 4492725Stop: 4492159

          
Length: 567


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4522 translation of PA4522Homolog Bit Score 400.0

          
Other Homologs:  psyr_15may02_Scaffold15_revised_gene2492 (ORF: BLASTX 278.0), t_PA4522 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCATTTCGATTCCGTTACCGGCTGGGTCCGTGGCGTCCGCCACTGCCCTTCACCGAATTTCAACCTGCGT 
CCGCAAGGGGACGCGGTGTCGCTGCTGGTCATCCACAATATCAGCCTGCCGCCGGGACAGTTCGGCACCGGC 
AAGGTCCAGGCGTTCTTCCAGAATCGTCTGGACCCGAACGAACATCCCTATTTCGAGGAGATCCGCCACCTG 
ACGGTTTCCGCGCATTTCCTCATCGAACGCGACGGCGCCATCACCCAGTTCGTCTCCTGTCACGACCGCGCC 
TGGCATGCCGGGGTTTCCTGCTTCGACGGTCGCGAGGCGTGCAACGACTTCTCCCTTGGCATCGAACTGGAG 
GGGACCGACACGGAACCGTACACGGACGCGCAGTACACTGCCCTGGCCGGGCTGACGCGGCTGTTGCGCGCG 
GCCTTCCCGGGGATCACCCCGGAACGCATCCAGGGCCACTGCGATATCGCCCCGGAGCGCAAGACCGATCCC 
GGCGAGGCTTTCGACTGGTCGCGCTACCGCGCCGGATTGACCGATTCCAAGGAGGAAACATGA