ViewGene
Locus Name:
GeneID:
Location:

GeneID:1352
TrivialName: PA14_71460
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_71460
PAO1 Ortholog Locus:PA5415
Sequence Length:1254
Protein Length:417
Start: 6366948
Stop: 6368201
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08800.1|AE004954_2 (AE004954) serine hydroxymethyltransferase [Pseudomonas aeruginosa PAO1]
Identities = 416/417 (99%), Positives = 417/417 (100%)
Sequence:
ATGTTCAGCAAGCATGACCAGATCCGCGGCTACGACGACGAACTGCTCGCCGCGATGGACGCCGAAGAGGCC
CGCCAGGAAGACCATCTCGAACTGATTGCCTCGGAGAACTACACCAGCAAGCGGGTCATGCAGGCGCAGGGC
AGCGGCCTGACCAACAAATATGCCGAGGGCTATCCGGGCAAGCGCTACTACGGCGGCTGCGAACACGTCGAC
AAGGTCGAGCAGTTGGCCATCGACCGCGCCAGGCAGCTGTTCGGCGCCGACTACGCCAACGTCCAGCCGCAT
TCCGGTTCCTCGGCCAACGCCGCGGTGTACCTGGCGCTGCTCAACGCCGGCGACACCATCCTCGGCATGAGC
CTGGCCCATGGCGGCCATCTCACCCATGGCGCCAAGGTGTCCTCCTCCGGCAAGCTGTACAACGCCGTGCAG
TACGGCCTGGACACCGCTACCGGGCTGATCGACTACGACGAAGTCGAGCGCCTGGCCGTGGAGCATAAGCCG
AAGATGATCGTCGCCGGCTTCTCCGCCTACTCCAAGACCCTCGACTTCCCGCGCTTCCGCGCCATCGCCGAC
AAGGTCGGCGCGCTGCTGTTCGTCGACATGGCCCACGTTGCCGGGCTGGTCGCTGCCGGCCTCTACCCGAAC
CCGATCCCCTTCGCCGACGTGGTCACCACCACCACCCACAAGACCCTGCGCGGCCCGCGCGGCGGCCTGATC
CTGGCGCGCGCCAACGAGGAGaTcGAGaagaaGCTcaaCTCcGcggtatTTCCcggcgcccAgggCGGCCCG
CTGATGCACGTGATCGCGGCCAaggCgGTGTGCTTCAAGGAAGCGCTGGAGCCgGGCTTCaaGgACTACCAG
GCGcaggTGATCCGCAACGCCaaggcgAtGGCCGAGGTGTTCATCgggcGcggCTacGAcGTGgtttccgGC
GgcACCGACAACCACCTGATGCTGATCAGcCTGGTgcGCCAGGGCCTGACCGGCAAGGAAGCCGACGCCGCC
CTCGGCCGGGTCGGCATCACGGTGAACAAGAACGCCGTGCCGAACGATCCGCAGAGCCCGTTCGTCACCTCC
GGCATCCGCATCGGCACCCCGGCCATCACCACCCGCGGGCTGCAGGAAGCGCAGAGCCGCGAACTGGCCGGC
TGGATCTGCGACATCCTCGACCACCTCGGCGATGCCGACGTGGAAGCCAAGGTCGCCACCCAGGTCGCCGGT
CTCTGCGCGGACTTCCCGGTCTATCGCTGA
Translation:
MFSKHDQIRGYDDELLAAMDAEEARQEDHLELIASENYTSKRVMQAQGSGLTNKYAEGYPGKRYYGGCEHVD
KVEQLAIDRARQLFGADYANVQPHSGSSANAAVYLALLNAGDTILGMSLAHGGHLTHGAKVSSSGKLYNAVQ
YGLDTATGLIDYDEVERLAVEHKPKMIVAGFSAYSKTLDFPRFRAIADKVGALLFVDMAHVAGLVAAGLYPN
PIPFADVVTTTTHKTLRGPRGGLILARANEEIEKKLNSAVFPGAQGGPLMHVIAAKAVCFKEALEPGFKDYQ
AQVIRNAKAMAEVFIGRGYDVVSGGTDNHLMLISLVRQGLTGKEADAALGRVGITVNKNAVPNDPQSPFVTS
GIRIGTPAITTRGLQEAQSRELAGWICDILDHLGDADVEAKVATQVAGLCADFPVYR*
AnnotationID:1361GeneID:1352
AnnotatorUID: danlee
Modification Date/Time: 2006-01-31 12:12:59
Gene Name:glyA1
Confidence Code:1
GeneProduct:serine hydroxymethyltransferase
Cell Localization:(1) Cytoplasmic
Synonyms:
Cell Localization Confidence Code:2
MolecularFunction:
Functional Category:(2) Amino acid biosynthesis and metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0112,pfam00464
Secondary Functional Category(ies):
EC Number:2.1.2.1
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN65953.1|AE016223_7 (AE016775) serine hydroxymethyltransferase [Pseudomonas putida
           KT2440]
          Length = 417

 Score =  755 bits (1950), Expect = 0.0
 Identities = 376/417 (90%), Positives = 394/417 (94%)

>gb|AAO54005.1| (AE016857) serine hydroxymethyltransferase [Pseudomonas syringae
           pv. tomato str. DC3000]
          Length = 417

 Score =  740 bits (1911), Expect = 0.0
 Identities = 364/417 (87%), Positives = 391/417 (93%)

>gb|AAP17919.1| (AE016987) serine hydroxymethyltransferase [Shigella flexneri 2a
           str. 2457T]
          Length = 417

 Score =  601 bits (1549), Expect = e-171
 Identities = 298/417 (71%), Positives = 344/417 (82%), Gaps = 2/417 (0%)








 
Structural Features:
COG0112, GlyA, Glycine/serine hydroxymethyltransferase 
[Amino acid transport and metabolism]
CD-Length = 413 residues,  99.0% aligned
Score =  673 bits (1738), Expect = 0.0
Identities = 284/412 (68%), Positives = 339/412 (82%), Gaps = 3/412 (0%)

pfam00464, SHMT, Serine hydroxymethyltransferase.
CD-Length = 397 residues,  99.2% aligned
Score =  552 bits (1423), Expect = 3e-158
Identities = 232/395 (58%), Positives = 286/395 (72%), Gaps = 20/395 (5%)






   
Genomic Context:






   
Comment:


















    ReferenceID:2707




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:19852




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34686




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1352_cdd.html


    		




 
URL:

















    ReferenceID:35650




  
Author/Investigator(s):
        Plamann MD, Stauffer LT, Urbanowski ML, Stauffer GV.





  
Title:
        Complete nucleotide sequence of the E. coli glyA gene.




  
PubMed:
        6300791


MedLine:
        




    
Source:
Nucleic Acids Res. 1983 Apr 11;11(7):2065-75.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6300791

















    ReferenceID:35651




  
Author/Investigator(s):
        Steiert JG, Urbanowski ML, Stauffer LT, Plamann MD, Stauffer GV.





  
Title:
        Nucleotide sequence of the Salmonella typhimurium glyA gene.




  
PubMed:
        2134182


MedLine:
        




    
Source:
DNA Seq. 1990;1(2):107-13.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2134182

















    ReferenceID:35652




  
Author/Investigator(s):
        Chan VL, Bingham HL.





  
Title:
        Complete sequence of the Campylobacter jejuni glyA gene encoding serine hydroxymethyltransferase.




  
PubMed:
        2060796


MedLine:
        




    
Source:
Gene. 1991 May 15;101(1):51-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2060796

















    ReferenceID:35653




  
Author/Investigator(s):
        Chistoserdova LV, Lidstrom ME.





  
Title:
        Genetics of the serine cycle in Methylobacterium extorquens AM1: cloning, sequence, mutation, and physiological effect of glyA, the gene for serine hydroxymethyltransferase.




  
PubMed:
        7961431


MedLine:
        




    
Source:
J Bacteriol. 1994 Nov;176(21):6759-62.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7961431









           
Homologs By Global Alignment 

           

       



     
Gene ID:1352
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
2459
                           PA5415_tr
                           translation of PA5415
                           417
                           99.76
                           99.99
                           0
                           2137.0
     

     
     
78102
                           gb|AAG08800.1|AE004954_2
                           (AE004954) serine hydroxymethyltransferase [Pseudomonas aeruginosa PAO1]
                           417
                           99.76
                           99.99
                           0
                           2137.0
     

     
     
2460
                           PA2444_tr
                           translation of PA2444
                           418
                           91.14
                           94.25
                           1
                           1971.0
     

     
     
78103
                           gb|AAG05832.1|AE004671_8
                           (AE004671) serine hydroxymethyltransferase [Pseudomonas aeruginosa PAO1]
                           418
                           91.14
                           94.25
                           1
                           1971.0
     

     
     
78104
                           gb|AAN65953.1|AE016223_7
                           (AE016775) serine hydroxymethyltransferase [Pseudomonas putida KT2440]
                           417
                           90.16
                           94.48
                           0
                           1950.0
     

     






      

          
GC ORFID: 44354How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5415Glimmer Score: 

          
Start: 5630637Stop: 5631890

          
Length: 1254


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5415 translation of PA5415Homolog Bit Score 827.0

          
Other Homologs:  t_PA2444 (ORF: BLASTX 764.0), t_PA4602 (ORF: BLASTX 669.0), psyr_15may02_Scaffold4_revised_gene5644 (ORF: BLASTX 659.0), t_PA5415 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTTCAGCAAGCATGACCAGATCCGCGGCTACGACGACGAACTGCTCGCCGCGATGGACGCCGAAGAGGCC 
CGCCAGGAAGACCATCTCGAACTGATTGCCTCGGAGAACTACACCAGCAAGCGGGTCATGCAGGCGCAGGGC 
AGCGGCCTGACCAACAAATATGCCGAGGGCTATCCGGGCAAGCGCTACTACGGCGGCTGCGAACACGTCGAC 
AAGGTCGAGCAGTTGGCCATCGACCGCGCCAGGCAGCTGTTCGGCGCCGACTACGCCAACGTCCAGCCGCAT 
TCCGGTTCCTCGGCCAACGCCGCGGTGTACCTGGCGCTGCTCAACGCCGGCGACACCATCCTCGGCATGAGC 
CTGGCCCATGGCGGCCATCTCACCCATGGCGCCAAGGTGTCCTCCTCCGGCAAGCTGTACAACGCCGTGCAG 
TACGGCCTGGACACCGCTACCGGGCTGATCGACTACGACGAAGTCGAGCGCCTGGCCGTGGAGCATAAGCCG 
AAGATGATCGTCGCCGGCTTCTCCGCCTACTCCAAGACCCTCGACTTCCCGCGCTTCCGCGCCATCGCCGAC 
AAGGTCGGCGCGCTGCTGTTCGTCGACATGGCCCACGTTGCCGGGCTGGTCGCTGCCGGCCTCTACCCGAAC 
CCGATCCCCTTCGCCGACGTGGTCACCACCACCACCCACAAGACCCTGCGCGGCCCGCGCGGCGGCCTGATC 
CTGGCGCGCGCCAACGAGGAGaTcGAGaagaaGCTcaaCTCcGcggtatTTCCcggcgcccAgggCGGCCCG 
CTGATGCACGTGATCGCGGCCAaggCgGTGTGCTTCAAGGAAGCGCTGGAGCCgGGCTTCaaGgACTACCAG 
GCGcaggTGATCCGCAACGCCaaggcgAtGGCCGAGGTGTTCATCgggcGcggCTacGAcGTGgtttccgGC 
GgcACCGACAACCACCTGATGCTGATCAGcCTGGTgcGCCAGGGCCTGACCGGCAAGGAAGCCGACGCCGCC 
CTCGGCCGGGTCGGCATCACGGTGAACAAGAACGCCGTGCCGAACGATCCGCAGAGCCCGTTCGTCACCTCC 
GGCATCCGCATCGGCACCCCGGCCATCACCACCCGCGGGCTGCAGGAAGCGCAGAGCCGCGAACTGGCCGGC 
TGGATCTGCGACATCCTCGACCACCTCGGCGATGCCGACGTGGAAGCCAAGGTCGCCACCCAGGTCGCCGGT 
CTCTGCGCGGACTTCCCGGTCTATCGCTGA