ViewGene
Locus Name:
GeneID:
Location:

GeneID:3888
TrivialName: PA14_61780
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_61780
PAO1 Ortholog Locus:PA4671
Sequence Length:615
Protein Length:204
Start: 5511409
Stop: 5512023
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08058.1|AE004881_1 (AE004881) probable ribosomal protein L25 [Pseudomonas aeruginosa PAO1]
Identities = 203/204 (99%), Positives = 204/204 (100%)
Sequence:
ATGGTCGACTTTATTCTGAATGCCCAAGTGCGTTCCGATCTGGGGAAAGGTGCGAGCCGCCGCCTGCGTCGT
AACGCCGGTCTGGTTCCTGCTGTCGTTTACGGCGGCGACAAAGAGCCCCAGTCCGTAACCCTGGAACTGCGC
GAAATCGCCAAGCTCCTGGAAAACGAGGCTGCCTTCAGCCACGTGATCGCCCTGAACGTTGGCGGCGCCAAG
GAAACCGTACTGATCAAGGCCCTGCAGCGCCATCCGGCGAAAGGCTTCGTGATGCACGCCGACTTCCTGCGC
GTGGTCGCCGACCACAAGCTGACCGCCCACGTACCGCTGCACTTCATCAACGAAGAAGTAGCCGTTGGCGTC
AAGCAATCCGGTGGCGAGATCTCCCACACCATCTCCGAAGTCGAAGTTTCCTGCCTGCCGAAAGACCTGCCG
GAATTCATCGAAGTCGACATGGCCAAGGTCGAGCTGGGCCAGATCGTTCACCTGTCGGACCTCAAGGCTCCG
AAAGGCGTCGAGCTGGTACAACTGGCCCACGGCAACGACCTGGCCGTTGCCAACATCCACGCTTCCCGCGTG
GTGAAGGAAGAAGGTAGCGAAGAAGGCGCCGCCGAGTAA
Translation:
MVDFILNAQVRSDLGKGASRRLRRNAGLVPAVVYGGDKEPQSVTLELREIAKLLENEAAFSHVIALNVGGAK
ETVLIKALQRHPAKGFVMHADFLRVVADHKLTAHVPLHFINEEVAVGVKQSGGEISHTISEVEVSCLPKDLP
EFIEVDMAKVELGQIVHLSDLKAPKGVELVQLAHGNDLAVANIHASRVVKEEGSEEGAAE*
AnnotationID:3895GeneID:3888
AnnotatorUID: diggins
Modification Date/Time: 2005-03-08 07:07:01
Gene Name:
Confidence Code:3
GeneProduct:putative ribosomal protein L25
Cell Localization:()
Synonyms:rplY
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1825,pfam01386
Secondary Functional Category(ies):adaptation, protection
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54632.1| (AE016859) ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5
           [Pseudomonas syringae pv. tomato str. DC3000]
          Length = 203

 Score =  291 bits (745), Expect = 2e-78
 Identities = 146/206 (70%), Positives = 174/206 (84%), Gaps = 5/206 (2%)

>gb|AAN66346.1|AE016263_3 (AE016776) ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5
           [Pseudomonas putida KT2440]
          Length = 217

 Score =  270 bits (690), Expect = 4e-72
 Identities = 140/204 (68%), Positives = 164/204 (80%), Gaps = 7/204 (3%)

>gb|AAM35838.1| (AE011726) 50S ribosomal protein L25 [Xanthomonas axonopodis pv.
           citri str. 306]
          Length = 211

 Score =  180 bits (456), Expect = 5e-45
 Identities = 93/196 (47%), Positives = 132/196 (67%), Gaps = 1/196 (0%)








 
Structural Features:
COG1825, RplY, Ribosomal protein L25 (general stress protein Ctc) 
[Translation, ribosomal structure and biogenesis]
CD-Length = 93 residues,  98.9% aligned
Score =  101 bits (253), Expect = 7e-23
Identities = 50/94 (53%), Positives = 60/94 (63%), Gaps = 2/94 (2%)

pfam01386, Ribosomal_L25p, Ribosomal L25p family. 
CD-Length = 87 residues, 100.0% aligned
Score = 79.2 bits (195), Expect = 3e-16
Identities = 45/89 (50%), Positives = 60/89 (67%), Gaps = 2/89 (2%)






   
Genomic Context:






   
Comment:


















    ReferenceID:7779




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:24921




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37609




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3888_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:3888
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6123
                           PA4671_tr
                           translation of PA4671
                           204
                           99.50
                           99.99
                           0
                           1013.0
     

     
     
170304
                           gb|AAG08058.1|AE004881_1
                           (AE004881) probable ribosomal protein L25 [Pseudomonas aeruginosa PAO1]
                           204
                           99.50
                           99.99
                           0
                           1013.0
     

     
     
170305
                           gb|AAO54632.1|
                           (AE016859) ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5 [Pseudomonas syringae pv. tomato str. DC3000]
                           206
                           70.87
                           84.46
                           5
                           750.0
     

     
     
170306
                           gb|AAN66346.1|AE016263_3
                           (AE016776) ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5 [Pseudomonas putida KT2440]
                           224
                           62.50
                           73.21
                           27
                           698.0
     

     
     
170308
                           gb|AAF85440.1|AE004071_8
                           (AE004071) 50S ribosomal protein L25 [Xylella fastidiosa 9a5c]
                           211
                           47.86
                           65.87
                           10
                           463.0
     

     






      

          
GC ORFID: 46890How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4671Glimmer Score: 

          
Start: 4775089Stop: 4775703

          
Length: 615


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4671 translation of PA4671Homolog Bit Score 394.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene5096 (ORF: BLASTX 285.0), t_PA4671 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGTCGACTTTATTCTGAATGCCCAAGTGCGTTCCGATCTGGGGAAAGGTGCGAGCCGCCGCCTGCGTCGT 
AACGCCGGTCTGGTTCCTGCTGTCGTTTACGGCGGCGACAAAGAGCCCCAGTCCGTAACCCTGGAACTGCGC 
GAAATCGCCAAGCTCCTGGAAAACGAGGCTGCCTTCAGCCACGTGATCGCCCTGAACGTTGGCGGCGCCAAG 
GAAACCGTACTGATCAAGGCCCTGCAGCGCCATCCGGCGAAAGGCTTCGTGATGCACGCCGACTTCCTGCGC 
GTGGTCGCCGACCACAAGCTGACCGCCCACGTACCGCTGCACTTCATCAACGAAGAAGTAGCCGTTGGCGTC 
AAGCAATCCGGTGGCGAGATCTCCCACACCATCTCCGAAGTCGAAGTTTCCTGCCTGCCGAAAGACCTGCCG 
GAATTCATCGAAGTCGACATGGCCAAGGTCGAGCTGGGCCAGATCGTTCACCTGTCGGACCTCAAGGCTCCG 
AAAGGCGTCGAGCTGGTACAACTGGCCCACGGCAACGACCTGGCCGTTGCCAACATCCACGCTTCCCGCGTG 
GTGAAGGAAGAAGGTAGCGAAGAAGGCGCCGCCGAGTAA