ViewGene
Locus Name:
GeneID:
Location:

GeneID:4560
TrivialName: PA14_49870
AnnotatorUID: danlee
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_49870
PAO1 Ortholog Locus:
Sequence Length:540
Protein Length:179
Start: 4434649
Stop: 4434110
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAO55118.1| (AE016861) polypeptide deformylase [Pseudomonas syringae pv. tomato str. DC3000]
Identities = 142/179 (79%), Positives = 155/179 (86%) Counterpart to PA1122 of PAO1.
Sequence:
ATGATCCGGGAAATCCTCAAGATGGGTGACGAGCGCCTGTTGCGCATTGCGCAGCCGGTGCCGTCCGAACTG
CTCGGCAGCGAGGAGCTGCAACGGCTGATCGACGACATGTTCGAAACCATGCATCACGTCGGCGGGGTAGGG
CTGGCCGCGCCGCAGATCGGCGTCGACCTGCAACTGGTGATCTTCGGTTTCGAGCGCAGCGAGCGCTATCCG
GACGCCCCGGCCGTGCCGCCGACCATCCTGCTGAACCCGCGGATCACCCCGCTGGACGACGAGATGGAAGAG
GGCTGGGAGGGCTGCCTGTCGGTGCCGGGGTTGCGCGGCGCGGTATCGCGCCATCGGCGCATCCGCTACCAG
GGCCTGGACCCGCAGGGACAGCCGATCGACCGCAGCGTCGAAGGGTTCCATGCGCGGGTGGTGCAGCACGAG
TGCGACCACCTGATCGGCCGCCTGTATCCCTCGCGAATCACCGACTTCAGCAAGTTCGGCTTCACCGAGGTG
CTGTTCCCCGACCTGGACCCCGCCGCGGACGATTGA
Translation:
MIREILKMGDERLLRIAQPVPSELLGSEELQRLIDDMFETMHHVGGVGLAAPQIGVDLQLVIFGFERSERYP
DAPAVPPTILLNPRITPLDDEMEEGWEGCLSVPGLRGAVSRHRRIRYQGLDPQGQPIDRSVEGFHARVVQHE
CDHLIGRLYPSRITDFSKFGFTEVLFPDLDPAADD*
AnnotationID:4566GeneID:4560
AnnotatorUID: danlee
Modification Date/Time: 2006-02-06 18:06:24
Gene Name:
Confidence Code:3
GeneProduct: probable peptide deformylase
Cell Localization:()
Synonyms:PA1122?
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:cd00487, pfam01327
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
gi|84322117|ref|ZP_00970462.1|  COG0242: N-formylmethionyl-tRNA deformylase [Pseudomonas aeruginosa 
C3719]
Length=179

 Score =  365 bits (938),  Expect = 3e-100
 Identities = 178/179 (99%), Positives = 178/179 (99%), Gaps = 0/179 (0%)

gi|84328596|ref|ZP_00976600.1|  COG0242: N-formylmethionyl-tRNA deformylase [Pseudomonas aeruginosa 
2192]
Length=179

 Score =  362 bits (928),  Expect = 4e-99
 Identities = 177/179 (98%), Positives = 177/179 (98%), Gaps = 0/179 (0%)

gi|77384573|gb|ABA76086.1|  Formylmethionine deformylase [Pseudomonas fluorescens PfO-1]
 gi|77460570|ref|YP_350077.1|  peptide deformylase [Pseudomonas fluorescens PfO-1]
Length=179

 Score =  298 bits (763),  Expect = 6e-80
 Identities = 146/179 (81%), Positives = 160/179 (89%), Gaps = 0/179 (0%)

>PA1122 [gene=PA1122] [prot=probable peptide deformylase] [comment=PA1122]
          Length = 147

 Score =  253 bits (645), Expect = 2e-068
 Identities = 123/125 (98%), Positives = 124/125 (98%)






 
Structural Features:
cd00487, Pep_deformylase, Polypeptide or peptide deformylase.
             CD-Length = 141 residues, 100.0% aligned
             Score =  174 bits (444), Expect = 4e-45

pfam01327, Pep_deformylase, Polypeptide deformylase..
             CD-Length = 154 residues,  96.1% aligned
             Score =  141 bits (357), Expect = 4e-35






   
Genomic Context:






   
Comment:
Extra length of PA14 ORF due to +1 insertion at position 4434273 of PA14 (gcaGgga).  
Polymorphism confirmed by manual sequence gazing.
Identical in length to corresponding genes from P. aeruginosa strains C3719 and 2192, and from 
other Pseudomonad sp


















    ReferenceID:9121




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:26263




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:4560
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
184613
                           gb|AAO55118.1|
                           (AE016861) polypeptide deformylase [Pseudomonas syringae pv. tomato str. DC3000]
                           179
                           79.32
                           86.59
                           0
                           757.0
     

     
     
184614
                           gb|AAN70132.1|AE016653_3
                           (AE016791) polypeptide deformylase [Pseudomonas putida KT2440]
                           179
                           78.21
                           86.59
                           1
                           749.0
     

     
     
184615
                           emb|CAE40418.1|
                           (BX640411) peptide deformylase [Bordetella pertussis] [Bordetella pertussis Tohama I]
                           179
                           74.86
                           82.12
                           3
                           697.0
     

     
     
184616
                           emb|CAE38944.1|
                           (BX640434) peptide deformylase [Bordetella parapertussis]
                           179
                           74.86
                           82.12
                           3
                           697.0
     

     
     
184617
                           emb|CAE34458.1|
                           (BX640449) peptide deformylase [Bordetella bronchiseptica] [Bordetella bronchiseptica RB50]
                           179
                           74.30
                           81.56
                           3
                           690.0
     

     






      

          
GC ORFID: 47562How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: psyr_15may02_Scaffold5_revised_gene6367Glimmer Score: 

          
Start: 519259Stop: 519798

          
Length: 540


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: psyr_15may02_Scaffold5_revised_gene6367 related to: gi|17546118|ref|NP_519520.1| (NC_003295) PUTATIVE POLYPEPTIDE DEFORMYLASE PROTEIN [Ralstonia solanacearum] emb|CAD15101.1| (AL646064) PUTATIVE POLYPEPTIDE DEFORMYLASE PROTEIN [Ralstonia solanacearum]Homolog Bit Score 295.0

          
Other Homologs:  psyr_15may02_Scaffold5_revised_gene6367 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGATCCGGGAAATCCTCAAGATGGGTGACGAGCGCCTGTTGCGCATTGCGCAGCCGGTGCCGTCCGAACTG 
CTCGGCAGCGAGGAGCTGCAACGGCTGATCGACGACATGTTCGAAACCATGCATCACGTCGGCGGGGTAGGG 
CTGGCCGCGCCGCAGATCGGCGTCGACCTGCAACTGGTGATCTTCGGTTTCGAGCGCAGCGAGCGCTATCCG 
GACGCCCCGGCCGTGCCGCCGACCATCCTGCTGAACCCGCGGATCACCCCGCTGGACGACGAGATGGAAGAG 
GGCTGGGAGGGCTGCCTGTCGGTGCCGGGGTTGCGCGGCGCGGTATCGCGCCATCGGCGCATCCGCTACCAG 
GGCCTGGACCCGCAGGGACAGCCGATCGACCGCAGCGTCGAAGGGTTCCATGCGCGGGTGGTGCAGCACGAG 
TGCGACCACCTGATCGGCCGCCTGTATCCCTCGCGAATCACCGACTTCAGCAAGTTCGGCTTCACCGAGGTG 
CTGTTCCCCGACCTGGACCCCGCCGCGGACGATTGA