ViewGene
Locus Name:
GeneID:
Location:

GeneID:2230
TrivialName: PA14_60210
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_60210
PAO1 Ortholog Locus:PA4544
Sequence Length:963
Protein Length:320
Start: 5364282
Stop: 5363320
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07932.1|AE004868_3 (AE004868) pseudouridine synthase [Pseudomonas aeruginosa PAO1]
Identities = 320/320 (100%), Positives = 320/320 (100%)
Sequence:
ATGTCCGATATGATTCAACGCGCGGCCGAGGTGCCGTTCGAGCTGGGTGGCCAGCGTCTCGACCAGATCGCC
GCCCAGCTTTTTCCCGAACACTCCCGCTCCCGTCTGGCCGGCTGGATCAAGGACGGTCGCCTGACCGTCGAC
GGCGCCGTGCTGCGCCCGCGCGACATCGTCCACAGCGGCGCGCAACTGGTCCTGGAGGCCGAGCAGGAAGCC
CAGGGCGAGTGGCTCGCACAGGACATCGAGCTGGAAATCGTCTACGAGGACGAGCACATCCTGGTGATTGAC
AAGCCCGCCGGCCTGGTGGTCCATCCGGCTGCCGGCCATCAGGACGGCACCCTGCTGAATGCCTTGCTCTAC
CATGTCCCGGACATCGCCAATGTGCCGCGCGCCGGGATCGTCCACCGCCTGGACAAGGACACGACCGGCCTG
ATGGTAGTGGCCAAGACGCTGGAGGCCCACACCAAGCTGGTGGCGCAACTGCAGGCACGGTCGGTCAGCCGC
ATCTACGAGGCGATCGTGATCGGCGTGATCACCTCCGGCGGCACCATCGATGCGCCGATCGGACGGCATGGC
GTGCAGCGGCAGAAGATGGCGGTGGTCGACGCCGGCAAGGTGGCGGTCAGCCATTACCGCGTGCTGGAACGC
TTCCGTGCGCACACCCATACCCGGGTCAAGCTGGAGACCGGGCGTACCCACCAGATCCGCGTGCACATGAGC
CATATTGGCTATCCCCTGGTCGGCGATCCGGTCTACGGTGGGCGCTTCAGGATTCCCCCGGTGGCCAGCCAG
ACCCTGGTCCAGACTCTTCGCGAATTCCCCCGGCAGGCGCTGCACGCGCGCTTCCTCGAACTGGATCACCCG
GCCACCGGCGTGCGCATGAAGTGGGAGTCGCCGCTGCCGGAAGACTTCCTCTGGCTGCTCAGCCTGTTGCGC
CAGGATCGCGAGGCGTTCGTCGGTTGA
Translation:
MSDMIQRAAEVPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQLVLEAEQEA
QGEWLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVPRAGIVHRLDKDTTGL
MVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHGVQRQKMAVVDAGKVAVSHYRVLER
FRAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGRFRIPPVASQTLVQTLREFPRQALHARFLELDHP
ATGVRMKWESPLPEDFLWLLSLLRQDREAFVG*
AnnotationID:2238GeneID:2230
AnnotatorUID: diggins
Modification Date/Time: 2005-05-05 05:05:46
Gene Name:rluD
Confidence Code:2
GeneProduct:ribosomal large subunit pseudouridine synthase D
Cell Localization:()
Synonyms:sfhB
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:ftsH mutation suppressor
Functional Category Confidence Code:5
COGs:COG0564,pfam00849
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:5.4.99.-
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAP17972.1| (AE016987) ftsH mutation suppressor [Shigella flexneri 2a str.
           2457T]
          Length = 326

 Score =  360 bits (925), Expect = 5e-99
 Identities = 180/317 (56%), Positives = 233/317 (73%), Gaps = 1/317 (0%)

>gb|AAN81565.1|AE016764_247 (AE016764) Ribosomal large subunit pseudouridine synthase D
           [Escherichia coli CFT073]
          Length = 326

 Score =  360 bits (925), Expect = 5e-99
 Identities = 180/317 (56%), Positives = 233/317 (73%), Gaps = 1/317 (0%)






 
Structural Features:
COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific 
[Translation, ribosomal structure and biogenesis]
CD-Length = 289 residues,  98.6% aligned
Score =  296 bits (760), Expect = 4e-81
Identities = 145/298 (48%), Positives = 193/298 (64%), Gaps = 18/298 (6%)

pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase. 
Members of this family are involved in modifying bases in 
RNA molecules.
CD-Length = 151 residues, 100.0% aligned
Score =  162 bits (410), Expect = 2e-40
Identities = 79/154 (51%), Positives = 99/154 (64%), Gaps = 6/154 (3%)







   
Genomic Context:






   
Comment:


















    ReferenceID:4463




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21609




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31664




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2230_cdd.html


    		




 
URL:

















    ReferenceID:32996




  
Author/Investigator(s):
        Ofengand J, Malhotra A, Remme J, Gutgsell NS, Del Campo M, Jean-Charles S, Peil L, Kaya Y.





  
Title:
        Pseudouridines and pseudouridine synthases of the ribosome.




  
PubMed:
        12762017


MedLine:
        




    
Source:
Cold Spring Harb Symp Quant Biol. 2001;66:147-59.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12762017

















    ReferenceID:32997




  
Author/Investigator(s):
        Raychaudhuri S, Conrad J, Hall BG, Ofengand J.





  
Title:
        A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli.




  
PubMed:
        9814761


MedLine:
        




    
Source:
RNA. 1998 Nov;4(11):1407-17.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9814761









           
Homologs By Global Alignment 

           

       



     
Gene ID:2230
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3786
                           PA4544_tr
                           translation of PA4544
                           320
                           99.99
                           99.99
                           0
                           1643.0
     

     
     
116694
                           gb|AAG07932.1|AE004868_3
                           (AE004868) pseudouridine synthase [Pseudomonas aeruginosa PAO1]
                           320
                           99.99
                           99.99
                           0
                           1643.0
     

     
     
116695
                           gb|AAP81266.1|
                           (AY273871) pseudouridine synthase [Pseudomonas aeruginosa]
                           320
                           99.68
                           99.99
                           0
                           1639.0
     

     
     
116696
                           emb|CAA78140.1|
                           (Z12154) putative protein of unknown function [Pseudomonas aeruginosa]
                           320
                           57.50
                           57.81
                           135
                           928.0
     

     
     
116706
                           dbj|BAC58822.1|
                           (AP005074) ribosomal large subunit pseudouridine synthase D [Vibrio parahaemolyticus]
                           326
                           55.21
                           69.63
                           7
                           896.0
     

     






      

          
GC ORFID: 45232How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4544Glimmer Score: 

          
Start: 4627961Stop: 4626999

          
Length: 963


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4544 translation of PA4544Homolog Bit Score 637.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3547 (ORF: BLASTX 535.0), t_PA4544 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCCGATATGATTCAACGCGCGGCCGAGGTGCCGTTCGAGCTGGGTGGCCAGCGTCTCGACCAGATCGCC 
GCCCAGCTTTTTCCCGAACACTCCCGCTCCCGTCTGGCCGGCTGGATCAAGGACGGTCGCCTGACCGTCGAC 
GGCGCCGTGCTGCGCCCGCGCGACATCGTCCACAGCGGCGCGCAACTGGTCCTGGAGGCCGAGCAGGAAGCC 
CAGGGCGAGTGGCTCGCACAGGACATCGAGCTGGAAATCGTCTACGAGGACGAGCACATCCTGGTGATTGAC 
AAGCCCGCCGGCCTGGTGGTCCATCCGGCTGCCGGCCATCAGGACGGCACCCTGCTGAATGCCTTGCTCTAC 
CATGTCCCGGACATCGCCAATGTGCCGCGCGCCGGGATCGTCCACCGCCTGGACAAGGACACGACCGGCCTG 
ATGGTAGTGGCCAAGACGCTGGAGGCCCACACCAAGCTGGTGGCGCAACTGCAGGCACGGTCGGTCAGCCGC 
ATCTACGAGGCGATCGTGATCGGCGTGATCACCTCCGGCGGCACCATCGATGCGCCGATCGGACGGCATGGC 
GTGCAGCGGCAGAAGATGGCGGTGGTCGACGCCGGCAAGGTGGCGGTCAGCCATTACCGCGTGCTGGAACGC 
TTCCGTGCGCACACCCATACCCGGGTCAAGCTGGAGACCGGGCGTACCCACCAGATCCGCGTGCACATGAGC 
CATATTGGCTATCCCCTGGTCGGCGATCCGGTCTACGGTGGGCGCTTCAGGATTCCCCCGGTGGCCAGCCAG 
ACCCTGGTCCAGACTCTTCGCGAATTCCCCCGGCAGGCGCTGCACGCGCGCTTCCTCGAACTGGATCACCCG 
GCCACCGGCGTGCGCATGAAGTGGGAGTCGCCGCTGCCGGAAGACTTCCTCTGGCTGCTCAGCCTGTTGCGC 
CAGGATCGCGAGGCGTTCGTCGGTTGA