ViewGene
Locus Name:
GeneID:
Location:

GeneID:3072
TrivialName: PA14_25780
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_25780
PAO1 Ortholog Locus:PA2959
Sequence Length:777
Protein Length:258
Start: 2249685
Stop: 2250461
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06347.1|AE004722_3 (AE004722) conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
Identities = 258/258 (100%), Positives = 258/258 (100%)
Sequence:
ATGCTGGTCGATTCCCACTGCCACCTCGATCGCCTCGACCTGGCCGCCCATGGCGGCTCGCTCGATGCGGCG
CTGGATGCCGCGCGAGCGCGTGGCGTCGGTCAATTCCTCTGCATCGGCGTCAGCGCCGACAATGCCCAGGCG
GTGAAGGCCCTGGCCGAGCGCTATGCCGACGTGCACTGTTCGGTCGGCGTGCACCCGCTGGACCTGGAGCCC
GGAAGCGCGCCAGCGCTGGACTGGCTGCTAGGCGAACTGGCGCATCCGCGGGTGGTGGCGATCGGCGAGACC
GGCCTCGACTACCACTACGAACCGGAAGCCGCCGAGTTGCAGCAGGAGGCGTTTCGCCTGCACCTGGAAGCC
GCGCGGATCACCGCCAAGCCAGTGATCGTGCACACCCGCGAGGCGCGCGCCGATACGCTGGCGCTGCTGCGC
GAGGCGGCGTTGCCGCAGGCCGGCGTGCTGCATTGCTTCACCGAGGACTGGGAGATGGCGCGATCGGCGCTG
GACCTGGGCTTCTACATTTCCCTGTCCGGCATCGTCACCTTCCGCAATGCCGATGCCCTGCGCGAGGTGGCT
CGCCAGGTACCGGCCGACCGCCTGCTGGTGGAGACCGACTCGCCCTACCTGGCGCCGATTCCCCATCGCGGC
AAGCCGAACCTGCCGGAATACGTGCGCGATGTCGCCGAATTCCTCGCGACGTTGCGTGGCGTCAGCCTGGAA
ACCCTGGCGGAGCAGACTACCGCCAATTTCCATCGGCTGTTTCCGTTGGCCCGCTAG
Translation:
MLVDSHCHLDRLDLAAHGGSLDAALDAARARGVGQFLCIGVSADNAQAVKALAERYADVHCSVGVHPLDLEP
GSAPALDWLLGELAHPRVVAIGETGLDYHYEPEAAELQQEAFRLHLEAARITAKPVIVHTREARADTLALLR
EAALPQAGVLHCFTEDWEMARSALDLGFYISLSGIVTFRNADALREVARQVPADRLLVETDSPYLAPIPHRG
KPNLPEYVRDVAEFLATLRGVSLETLAEQTTANFHRLFPLAR*
AnnotationID:3080GeneID:3072
AnnotatorUID: diggins
Modification Date/Time: 2005-04-10 11:11:05
Gene Name:
Confidence Code:3
GeneProduct:putative deoxyribonuclease, TatD family
Cell Localization:()
Synonyms:ycfH
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:COG0084,cd01310,pfam01026
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN67582.1|AE016388_2 (AE016781) deoxyribonuclease, TatD family [Pseudomonas putida
           KT2440]
          Length = 260

 Score =  446 bits (1146), Expect = e-125
 Identities = 221/258 (85%), Positives = 236/258 (91%)

>gb|AAO57292.1| (AE016869) deoxyribonuclease, TatD family [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 261

 Score =  441 bits (1134), Expect = e-123
 Identities = 216/257 (84%), Positives = 235/257 (91%)

>gb|AAP96656.1| (AE017156) putative deoxyribonuclease [Haemophilus ducreyi 35000HP]
          Length = 262

 Score =  272 bits (695), Expect = 2e-72
 Identities = 139/257 (54%), Positives = 176/257 (68%), Gaps = 2/257 (0%)






 
Structural Features:
COG0084, TatD, Mg-dependent DNase 
[DNA replication, recombination, and repair]
CD-Length = 256 residues,  99.6% aligned
Score =  302 bits (776), Expect = 2e-83
Identities = 133/258 (51%), Positives = 172/258 (66%), Gaps = 5/258 (1%)

cd01310, TatD_DNAse, TatD like proteins
CD-Length = 251 residues,  99.6% aligned
Score =  288 bits (738), Expect = 6e-79

pfam01026, TatD_DNase, TatD related DNase.
CD-Length = 250 residues, 100.0% aligned
Score =  249 bits (637), Expect = 2e-67
Identities = 129/257 (50%), Positives = 167/257 (64%), Gaps = 10/257 (3%)








   
Genomic Context:






   
Comment:


















    ReferenceID:6147




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:23289




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36088




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3072_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:3072
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
4955
                           PA2959_tr
                           translation of PA2959
                           258
                           99.99
                           99.99
                           0
                           1324.0
     

     
     
139890
                           gb|AAG06347.1|AE004722_3
                           (AE004722) conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
                           258
                           99.99
                           99.99
                           0
                           1324.0
     

     
     
139891
                           gb|AAN67582.1|AE016388_2
                           (AE016781) deoxyribonuclease, TatD family [Pseudomonas putida KT2440]
                           260
                           85.00
                           90.76
                           2
                           1146.0
     

     
     
139892
                           gb|AAO57292.1|
                           (AE016869) deoxyribonuclease, TatD family [Pseudomonas syringae pv. tomato str. DC3000]
                           261
                           82.75
                           90.03
                           3
                           1134.0
     

     
     
139895
                           emb|CAC90429.1|
                           (AJ414149) putative deoxyribonuclease [Yersinia pestis CO92]
                           273
                           56.04
                           65.20
                           19
                           688.0
     

     






      

          
GC ORFID: 46074How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA2959Glimmer Score: 

          
Start: 2704240Stop: 2703464

          
Length: 777


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: t_PA2959 translation of PA2959Homolog Bit Score 514.0

          
Other Homologs:  psyr_15may02_Scaffold16_revised_gene2616 (ORF: BLASTX 446.0), t_PA2959 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCTGGTCGATTCCCACTGCCACCTCGATCGCCTCGACCTGGCCGCCCATGGCGGCTCGCTCGATGCGGCG 
CTGGATGCCGCGCGAGCGCGTGGCGTCGGTCAATTCCTCTGCATCGGCGTCAGCGCCGACAATGCCCAGGCG 
GTGAAGGCCCTGGCCGAGCGCTATGCCGACGTGCACTGTTCGGTCGGCGTGCACCCGCTGGACCTGGAGCCC 
GGAAGCGCGCCAGCGCTGGACTGGCTGCTAGGCGAACTGGCGCATCCGCGGGTGGTGGCGATCGGCGAGACC 
GGCCTCGACTACCACTACGAACCGGAAGCCGCCGAGTTGCAGCAGGAGGCGTTTCGCCTGCACCTGGAAGCC 
GCGCGGATCACCGCCAAGCCAGTGATCGTGCACACCCGCGAGGCGCGCGCCGATACGCTGGCGCTGCTGCGC 
GAGGCGGCGTTGCCGCAGGCCGGCGTGCTGCATTGCTTCACCGAGGACTGGGAGATGGCGCGATCGGCGCTG 
GACCTGGGCTTCTACATTTCCCTGTCCGGCATCGTCACCTTCCGCAATGCCGATGCCCTGCGCGAGGTGGCT 
CGCCAGGTACCGGCCGACCGCCTGCTGGTGGAGACCGACTCGCCCTACCTGGCGCCGATTCCCCATCGCGGC 
AAGCCGAACCTGCCGGAATACGTGCGCGATGTCGCCGAATTCCTCGCGACGTTGCGTGGCGTCAGCCTGGAA 
ACCCTGGCGGAGCAGACTACCGCCAATTTCCATCGGCTGTTTCCGTTGGCCCGCTAG