ViewGene
Locus Name:
GeneID:
Location:

GeneID:1429
TrivialName: PA14_55640
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_55640
PAO1 Ortholog Locus:PA4281
Sequence Length:1230
Protein Length:409
Start: 4957850
Stop: 4959079
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07669.1|AE004844_1 (AE004844) exonuclease SbcD [Pseudomonas aeruginosa PAO1]
Identities = 406/409 (99%), Positives = 406/409 (99%)
Sequence:
ATGCGCCTCATACATACCTCCGACTGGCACCTGGGTCAGACCCTGCACGGCCAGGACCGCGATCATGAGCAC
GCGCGCTTCCTCGACTGGCTGCTACGCCAGCTGGAAGAGCAGCGCGCCGATGTCCTGCTGATCGCGGGCGAT
ATCTTCGACACGATCAATCCACCGCTCAAAGCCCAGGAGCGCCTCTACGACTTCATCGTCAGCGCCCATCGG
CGGCTGCCGCGGCTGGAGATCGTGATGATCGCAGGCAACCACGACTCCGGCGCGCGCATCGAACTGCCCGCT
CCGCTGATGAAACGACTGAACGCCCATGCCATCGGCCGGATCGGCTGGATAGACGAAAGCCTCGATAGCGAT
CGCCTGCTGCTGCCCCTGCACGACGCGGATGGCCAGGTCGCCGCCTGGTGCCTGGCCCTGCCCTTCCTGCGT
CCCGCCGAAGTCACCGGAGGCGGGCTCGGCGACGATTACCTGGCCGGTATCCGCCAGGTGCACGAACGCCTG
GTTGCCGCCGCGCAAGCCCGTCGCACGCCGGGACAGGCACTGGTCGCCGTCAGCCACGCACACATGGCCGGC
GGCTCGGTTTCCGAAGACTCCGAGCGAAACCTGATCATCGGCAACGTCGAAGCGCTGCCCGCCAGCCTGTTT
CCGGAGCAGATCGCCTACGTAGCCCTCGGTCATCTGCACAAGCCACAGAAAGTCGCCGGACAGGAGCGCATT
CGCTATAGCGGCTCGCCGCTGCCGCTGTCCTTCGCCGAAGTGAACTATCGCCACCAGGTCCTCCTCGTCACC
CTGGAAGGTGAGCGCCTGAAGGATGTACAGAGTCTCCCGGTGCCACGCGCGGTGGAACTGTTGCGCATCGGC
CCCGCGCCTCTTGGCGAGGTGCTCGATCGAATCGGCGAACTGGCCGAGGCCGACCTGCTGAACGAACAGCGG
CCCTGGCTGGAGGTCCGCGTCATGCTGGATCAGCCGCAACCAGACCTGCGCCAGCAGGTCGAGAGCGCCTTG
CAGGGCAAGGCTTGCCGCCTGGTGCGCATCGCCAGCGAATACCAGCGCCGCGACGAAGAACAGGCGCCGCTG
CTTGGGCTCGACCAACTCACCCCCCAGGAACTGTTCAGCCGCGCCTGGGAAAGCGCCTATGGCTCCGGCCCG
GATGCGCAGGCGTTGGATGACTTCGCCAGCCTGCTGCAAAGCGTCGAACTGGCCACTGAAGAGCCCCCGGGG
AAATAA
Translation:
MRLIHTSDWHLGQTLHGQDRDHEHARFLDWLLRQLEEQRADVLLIAGDIFDTINPPLKAQERLYDFIVSAHR
RLPRLEIVMIAGNHDSGARIELPAPLMKRLNAHAIGRIGWIDESLDSDRLLLPLHDADGQVAAWCLALPFLR
PAEVTGGGLGDDYLAGIRQVHERLVAAAQARRTPGQALVAVSHAHMAGGSVSEDSERNLIIGNVEALPASLF
PEQIAYVALGHLHKPQKVAGQERIRYSGSPLPLSFAEVNYRHQVLLVTLEGERLKDVQSLPVPRAVELLRIG
PAPLGEVLDRIGELAEADLLNEQRPWLEVRVMLDQPQPDLRQQVESALQGKACRLVRIASEYQRRDEEQAPL
LGLDQLTPQELFSRAWESAYGSGPDAQALDDFASLLQSVELATEEPPGK*
AnnotationID:1438GeneID:1429
AnnotatorUID: diggins
Modification Date/Time: 2005-04-03 18:06:48
Gene Name:sbcD
Confidence Code:2
GeneProduct:exonuclease SbcD
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(11) DNA replication, recombination, modification and repair
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0420
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN67639.1|AE016393_8 (AE016781) exonuclease SbcD [Pseudomonas putida KT2440]
          Length = 412

 Score =  558 bits (1437), Expect = e-158
 Identities = 277/412 (67%), Positives = 336/412 (81%), Gaps = 6/412 (1%)

>gb|AAO57234.1| (AE016869) exonuclease SbcD [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 414

 Score =  549 bits (1415), Expect = e-155
 Identities = 272/414 (65%), Positives = 333/414 (80%), Gaps = 8/414 (1%)








 
Structural Features:
COG0420, SbcD, DNA repair exonuclease [DNA replication, recombination, and repair]
CD-Length = 390 residues,  95.9% aligned
Score =  190 bits (482), Expect = 3e-49
Identities = 101/398 (25%), Positives = 169/398 (42%), Gaps = 30/398 (7%)








   
Genomic Context:






   
Comment:


















    ReferenceID:2861




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:20006




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36644




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1469_cdd.html


    		




 
URL:

















    ReferenceID:36789




  
Author/Investigator(s):
        Leach DR, Lloyd RG, Coulson AF.





  
Title:
        The SbcCD protein of Escherichia coli is related to two putative nucleases in the UvrA superfamily of nucleotide-binding proteins.




  
PubMed:
        1490631


MedLine:
        




    
Source:
Genetica. 1992;87(2):95-100.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1490631

















    ReferenceID:36792




  
Author/Investigator(s):
        Connelly JC, de Leau ES, Okely EA, Leach DR.





  
Title:
        Overexpression, purification, and characterization of the SbcCD protein from Escherichia coli.




  
PubMed:
        9242643


MedLine:
        




    
Source:
J Biol Chem. 1997 Aug 8;272(32):19819-26.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9242643









           
Homologs By Global Alignment 

           

       



     
Gene ID:1429
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
2589
                           PA4281_tr
                           translation of PA4281
                           409
                           99.26
                           99.26
                           0
                           2084.0
     

     
     
81480
                           gb|AAG07669.1|AE004844_1
                           (AE004844) exonuclease SbcD [Pseudomonas aeruginosa PAO1]
                           409
                           99.26
                           99.26
                           0
                           2084.0
     

     
     
81481
                           gb|AAN67639.1|AE016393_8
                           (AE016781) exonuclease SbcD [Pseudomonas putida KT2440]
                           415
                           66.74
                           80.96
                           9
                           1444.0
     

     
     
81482
                           gb|AAO57234.1|
                           (AE016869) exonuclease SbcD [Pseudomonas syringae pv. tomato str. DC3000]
                           417
                           65.22
                           79.85
                           11
                           1423.0
     

     






      

          
GC ORFID: 44431How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4281Glimmer Score: 

          
Start: 4221526Stop: 4222755

          
Length: 1230


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4281 translation of PA4281Homolog Bit Score 807.0

          
Other Homologs:  psyr_15may02_Scaffold1_revised_gene669 (ORF: BLASTX 556.0), t_PA4281 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCGCCTCATACATACCTCCGACTGGCACCTGGGTCAGACCCTGCACGGCCAGGACCGCGATCATGAGCAC 
GCGCGCTTCCTCGACTGGCTGCTACGCCAGCTGGAAGAGCAGCGCGCCGATGTCCTGCTGATCGCGGGCGAT 
ATCTTCGACACGATCAATCCACCGCTCAAAGCCCAGGAGCGCCTCTACGACTTCATCGTCAGCGCCCATCGG 
CGGCTGCCGCGGCTGGAGATCGTGATGATCGCAGGCAACCACGACTCCGGCGCGCGCATCGAACTGCCCGCT 
CCGCTGATGAAACGACTGAACGCCCATGCCATCGGCCGGATCGGCTGGATAGACGAAAGCCTCGATAGCGAT 
CGCCTGCTGCTGCCCCTGCACGACGCGGATGGCCAGGTCGCCGCCTGGTGCCTGGCCCTGCCCTTCCTGCGT 
CCCGCCGAAGTCACCGGAGGCGGGCTCGGCGACGATTACCTGGCCGGTATCCGCCAGGTGCACGAACGCCTG 
GTTGCCGCCGCGCAAGCCCGTCGCACGCCGGGACAGGCACTGGTCGCCGTCAGCCACGCACACATGGCCGGC 
GGCTCGGTTTCCGAAGACTCCGAGCGAAACCTGATCATCGGCAACGTCGAAGCGCTGCCCGCCAGCCTGTTT 
CCGGAGCAGATCGCCTACGTAGCCCTCGGTCATCTGCACAAGCCACAGAAAGTCGCCGGACAGGAGCGCATT 
CGCTATAGCGGCTCGCCGCTGCCGCTGTCCTTCGCCGAAGTGAACTATCGCCACCAGGTCCTCCTCGTCACC 
CTGGAAGGTGAGCGCCTGAAGGATGTACAGAGTCTCCCGGTGCCACGCGCGGTGGAACTGTTGCGCATCGGC 
CCCGCGCCTCTTGGCGAGGTGCTCGATCGAATCGGCGAACTGGCCGAGGCCGACCTGCTGAACGAACAGCGG 
CCCTGGCTGGAGGTCCGCGTCATGCTGGATCAGCCGCAACCAGACCTGCGCCAGCAGGTCGAGAGCGCCTTG 
CAGGGCAAGGCTTGCCGCCTGGTGCGCATCGCCAGCGAATACCAGCGCCGCGACGAAGAACAGGCGCCGCTG 
CTTGGGCTCGACCAACTCACCCCCCAGGAACTGTTCAGCCGCGCCTGGGAAAGCGCCTATGGCTCCGGCCCG 
GATGCGCAGGCGTTGGATGACTTCGCCAGCCTGCTGCAAAGCGTCGAACTGGCCACTGAAGAGCCCCCGGGG 
AAATAA