ViewGene
Locus Name:
GeneID:
Location:

GeneID:4948
TrivialName: PA14_71490
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_71490
PAO1 Ortholog Locus:PA5417
Sequence Length:321
Protein Length:106
Start: 6369631
Stop: 6369951
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08802.1|AE004954_4 (AE004954) sarcosine oxidase delta subunit [Pseudomonas aeruginosa PAO1]
Identities = 106/106 (100%), Positives = 106/106 (100%)
Sequence:
ATGCTGAATATCTTCTGCCCCCACTGCGGCGAACTGCGTTCCGAAGAGGAATTCCACGCCAAGGGTCAGGCC
CACATCCCGCGCCCGCTCGACCCGAACGCCTGCAGCGACGAGGAATGGGGCGACTACATGTTCTTCCGCGAC
AACCCGCGCGGCCTCCATCACGAGCTGTGGGTGCACGCCGCCGGCTGCCGCAAGTACTTCAACGTCACCCGC
CATACGGTGACCTACGAAATCCTCGAGACCTACCTGATCGGCGAGCAGCCCAGCGTCGTCGCCGACGGTGAG
AAGAAACCCGCCGTACAAGGGGAACCGGCATGA
Translation:
MLNIFCPHCGELRSEEEFHAKGQAHIPRPLDPNACSDEEWGDYMFFRDNPRGLHHELWVHAAGCRKYFNVTR
HTVTYEILETYLIGEQPSVVADGEKKPAVQGEPA*
AnnotationID:4953GeneID:4948
AnnotatorUID: diggins
Modification Date/Time: 2005-03-17 12:12:19
Gene Name:soxD
Confidence Code:2
GeneProduct:sarcosine oxidase delta subunit
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(5) Carbon compound catabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:pfam04267
Secondary Functional Category(ies):
EC Number:1.5.3.1
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54003.1| (AE016857) sarcosine oxidase, delta subunit [Pseudomonas syringae
          pv. tomato str. DC3000]
          Length = 98

 Score =  183 bits (465), Expect = 1e-46
 Identities = 79/97 (81%), Positives = 87/97 (89%)

>gb|AAN65955.1|AE016223_9 (AE016775) sarcosine oxidase, delta subunit [Pseudomonas putida
           KT2440]
          Length = 111

 Score =  183 bits (464), Expect = 2e-46
 Identities = 81/100 (81%), Positives = 87/100 (87%)

>gb|AAN65214.1|AF329398_4 (AF329398) sarcosine oxidase delta subunit [Streptomyces
          roseochromogenes subsp. oscitans]
          Length = 93

 Score =  105 bits (261), Expect = 7e-23
 Identities = 46/83 (55%), Positives = 58/83 (69%), Gaps = 1/83 (1%)








 
Structural Features:
pfam04267, SoxD, Sarcosine oxidase, delta subunit family.
CD-Length = 83 residues, 100.0% aligned
Score =  130 bits (328), Expect = 4e-32
Identities = 50/85 (58%), Positives = 58/85 (68%), Gaps = 2/85 (2%)






   
Genomic Context:






   
Comment:


















    ReferenceID:9896




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27037




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34691




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4948_cdd.html


    		




 
URL:

















    ReferenceID:35648




  
Author/Investigator(s):
        Quentmeier A, Kraft R, Kostka S, Klockenkamper R, Friedrich CG.





  
Title:
        Characterization of a new type of sulfite dehydrogenase from Paracoccus pantotrophus GB17.




  
PubMed:
        10795683


MedLine:
        




    
Source:
Arch Microbiol. 2000 Feb;173(2):117-25.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10795683

















    ReferenceID:35649




  
Author/Investigator(s):
        Wodara C, Bardischewsky F, Friedrich CG.





  
Title:
        Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation.




  
PubMed:
        9260941


MedLine:
        




    
Source:
J Bacteriol. 1997 Aug;179(16):5014-23.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9260941









           
Homologs By Global Alignment 

           

       



     
Gene ID:4948
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7352
                           PA5417_tr
                           translation of PA5417
                           106
                           99.99
                           99.99
                           0
                           597.0
     

     
     
191000
                           gb|AAG08802.1|AE004954_4
                           (AE004954) sarcosine oxidase delta subunit [Pseudomonas aeruginosa PAO1]
                           106
                           99.99
                           99.99
                           0
                           597.0
     

     
     
191002
                           gb|AAN65955.1|AE016223_9
                           (AE016775) sarcosine oxidase, delta subunit [Pseudomonas putida KT2440]
                           111
                           75.67
                           81.08
                           5
                           467.0
     

     
     
191001
                           gb|AAO54003.1|
                           (AE016857) sarcosine oxidase, delta subunit [Pseudomonas syringae pv. tomato str. DC3000]
                           106
                           74.52
                           82.07
                           8
                           464.0
     

     
     
191003
                           gb|AAN65214.1|AF329398_4
                           (AF329398) sarcosine oxidase delta subunit [Streptomyces roseochromogenes subsp. oscitans]
                           106
                           45.28
                           58.49
                           13
                           259.0
     

     






      

          
GC ORFID: 47950How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5417Glimmer Score: 

          
Start: 5633320Stop: 5633640

          
Length: 321


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5417 translation of PA5417Homolog Bit Score 234.0

          
Other Homologs:  t_PA5417 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCTGAATATCTTCTGCCCCCACTGCGGCGAACTGCGTTCCGAAGAGGAATTCCACGCCAAGGGTCAGGCC 
CACATCCCGCGCCCGCTCGACCCGAACGCCTGCAGCGACGAGGAATGGGGCGACTACATGTTCTTCCGCGAC 
AACCCGCGCGGCCTCCATCACGAGCTGTGGGTGCACGCCGCCGGCTGCCGCAAGTACTTCAACGTCACCCGC 
CATACGGTGACCTACGAAATCCTCGAGACCTACCTGATCGGCGAGCAGCCCAGCGTCGTCGCCGACGGTGAG 
AAGAAACCCGCCGTACAAGGGGAACCGGCATGA