ViewGene
Locus Name:
GeneID:
Location:

GeneID:3928
TrivialName: PA14_08860
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_08860
PAO1 Ortholog Locus:PA4262
Sequence Length:603
Protein Length:200
Start: 760208
Stop: 760810
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07650.1|AE004841_28 (AE004841) 50S ribosomal protein L4 [Pseudomonas aeruginosa PAO1]
Identities = 200/200 (100%), Positives = 200/200 (100%)
Sequence:
ATGCAATTGAATGTGAACGGCGCTCAGGCTATCGAAGTCTCCGAGCGTACCTTTGGTGGCGAATTCAACGAG
ACCCTGGTGCACCAGGCAGTCGTGGCCTACATGGCTGGCGGCCGTCAGGGCAGCAAGGCGCAGAAGACTCGC
TCCGAAGTCTCTGGTGGTGGCAAGAAGCCGTGGCGTCAGAAGGGCACCGGTCGTGCTCGCGCTGGCACCATC
CGTAGCCCCATCTGGCGTGGGGGCGGCACCACTTTCGCCGCTAAACCGCGTAGCCACGAACAGAAGCTGAAC
AAGAAGATGTACCGCGCAGCACTGCGCTCCATCCTTGCCGAGCTCGTTCGTCTGGACCGTCTGGTCGTCGTT
GCCGACTTCGCTGTCGATGCACCGAAAACCAAGGGCCTGGTTGCCAAGCTGGACACCCTGGGTCTGAAAGAC
GTGCTGATCGTGACCGATGGTGTCGACGAGAACCTGTACCTCGCTGCGCGCAACCTGGCGCACGTCGATGTA
CGTGATGTCCAAGGTTCCGACCCCGTCAGCCTGATCGCCTACGACAAGGTGCTGGTCACCGTGTCCGCCGTG
AAGAAGTTCGAGGAGCTGCTGGGATGA
Translation:
MQLNVNGAQAIEVSERTFGGEFNETLVHQAVVAYMAGGRQGSKAQKTRSEVSGGGKKPWRQKGTGRARAGTI
RSPIWRGGGTTFAAKPRSHEQKLNKKMYRAALRSILAELVRLDRLVVVADFAVDAPKTKGLVAKLDTLGLKD
VLIVTDGVDENLYLAARNLAHVDVRDVQGSDPVSLIAYDKVLVTVSAVKKFEELLG*
AnnotationID:3935GeneID:3928
AnnotatorUID: diggins
Modification Date/Time: 2005-04-03 16:04:51
Gene Name:rplD
Confidence Code:2
GeneProduct:50S ribosomal protein L4
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:pfam00573
Secondary Functional Category(ies):transcription, RNA processing and degradation
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54169.1| (AE016858) ribosomal protein L4 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 200

 Score =  344 bits (882), Expect = 2e-94
 Identities = 175/200 (87%), Positives = 185/200 (92%)

>gb|AAN66085.1|AE016238_3 (AE016775) ribosomal protein L4 [Pseudomonas putida KT2440]
          Length = 200

 Score =  338 bits (866), Expect = 1e-92
 Identities = 170/200 (85%), Positives = 184/200 (92%)

>gb|AAM87535.1|AE014002_8 (AE014002) 50S ribosomal subunit protein L4 [Yersinia pestis KIM]
          Length = 201

 Score =  270 bits (689), Expect = 5e-72
 Identities = 133/190 (70%), Positives = 159/190 (83%)






 
Structural Features:
pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family.
CD-Length = 200 residues,  99.5% aligned
Score =  145 bits (366), Expect = 5e-36
Identities = 89/200 (44%), Positives = 114/200 (57%), Gaps = 13/200 (6%)






   
Genomic Context:






   
Comment:


















    ReferenceID:7859




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:25001




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36633




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3928_cdd.html


    		




 
URL:

















    ReferenceID:36740




  
Author/Investigator(s):
        Zurawski G, Zurawski SM.





  
Title:
        Structure of the Escherichia coli S10 ribosomal protein operon.




  
PubMed:
        3892488


MedLine:
        




    
Source:
Nucleic Acids Res. 1985 Jun 25;13(12):4521-6.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3892488









           
Homologs By Global Alignment 

           

       



     
Gene ID:3928
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6167
                           PA4262_tr
                           translation of PA4262
                           200
                           99.99
                           99.99
                           0
                           1000.0
     

     
     
171079
                           gb|AAG07650.1|AE004841_28
                           (AE004841) 50S ribosomal protein L4 [Pseudomonas aeruginosa PAO1]
                           200
                           99.99
                           99.99
                           0
                           1000.0
     

     
     
171080
                           gb|AAO54169.1|
                           (AE016858) ribosomal protein L4 [Pseudomonas syringae pv. tomato str. DC3000]
                           200
                           87.50
                           92.50
                           0
                           882.0
     

     
     
171081
                           gb|AAN66085.1|AE016238_3
                           (AE016775) ribosomal protein L4 [Pseudomonas putida KT2440]
                           200
                           85.00
                           92.00
                           0
                           866.0
     

     
     
171082
                           gb|AAF95736.1|
                           (AE004326) ribosomal protein L4 [Vibrio cholerae O1 biovar eltor str. N16961]
                           200
                           74.00
                           84.00
                           0
                           743.0
     

     






      

          
GC ORFID: 46930How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4262Glimmer Score: 

          
Start: 4193731Stop: 4193129

          
Length: 603


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4262 translation of PA4262Homolog Bit Score 389.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5186 (ORF: BLASTX 344.0), t_PA4262 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCAATTGAATGTGAACGGCGCTCAGGCTATCGAAGTCTCCGAGCGTACCTTTGGTGGCGAATTCAACGAG 
ACCCTGGTGCACCAGGCAGTCGTGGCCTACATGGCTGGCGGCCGTCAGGGCAGCAAGGCGCAGAAGACTCGC 
TCCGAAGTCTCTGGTGGTGGCAAGAAGCCGTGGCGTCAGAAGGGCACCGGTCGTGCTCGCGCTGGCACCATC 
CGTAGCCCCATCTGGCGTGGGGGCGGCACCACTTTCGCCGCTAAACCGCGTAGCCACGAACAGAAGCTGAAC 
AAGAAGATGTACCGCGCAGCACTGCGCTCCATCCTTGCCGAGCTCGTTCGTCTGGACCGTCTGGTCGTCGTT 
GCCGACTTCGCTGTCGATGCACCGAAAACCAAGGGCCTGGTTGCCAAGCTGGACACCCTGGGTCTGAAAGAC 
GTGCTGATCGTGACCGATGGTGTCGACGAGAACCTGTACCTCGCTGCGCGCAACCTGGCGCACGTCGATGTA 
CGTGATGTCCAAGGTTCCGACCCCGTCAGCCTGATCGCCTACGACAAGGTGCTGGTCACCGTGTCCGCCGTG 
AAGAAGTTCGAGGAGCTGCTGGGATGA