ViewGene
Locus Name:
GeneID:
Location:

GeneID:401
TrivialName: PA14_05560
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_05560
PAO1 Ortholog Locus:PA0428
Sequence Length:1920
Protein Length:639
Start: 494556
Stop: 492637
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG03817.1|AE004480_1 (AE004480) probable ATP-dependent RNA helicase [Pseudomonas aeruginosa PAO1]
Identities = 638/639 (99%), Positives = 638/639 (99%)
Sequence:
ATGTCCTTTTCTTCCCTCGGACTCTCCGAGGCGCTTGCCCGCGCTGTGGAGGCTGCGGGCTACAGCCAGCCC
ACTCCCGTGCAACAGCGGGCGATTCCCGCCGTGTTGCAAGGTCGCGACCTGATGGTTGCGGCACAGACCGGC
ACCGGCAAGACCGGTGGTTTCGCCCTGCCGGTACTGGAGCGCCTGTTCCCCGCCGGTCATCCCGACCGCGAA
CACCGCCACGGCCCGCGCCAGGCGCGCGTGCTGGTACTGACCCCGACCCGTGAGCTGGCCGCCCAGGTGCAT
GACAGCTTCAAGGTCTACGCCCGCGACCTGCCGCTGAACAGCACCTGCATCTTCGGCGGGGTTGGCATGAAC
CCGCAGATCCAGGCCCTGGCCAAGGGCGTCGACGTACTCGTCGCCTGCCCCGGCCGCCTGCTCGACCTGGCC
GGGCAGAACAAGGTCGACCTGTCCCACGTGGAAATCCTCGTCCTCGACGAAGCCGACCGCATGCTCGACATG
GGCTTCATCCACGATGTGAAGAAGGTTCTCGCCAAGCTGCCGCCCAAGCGCCAGAACCTGCTGTTCTCGGCT
ACCTTCTCGAAAGACATCGTCGACCTCGCCAACAAGCTCCTGCACAACCCGGAACGCATCGAGGTAACGCCG
CCGAACACCACGGTCGAGCGCATCGAGCAACGCGTGTTCCGCCTGCCGGCGCCGCAGAAGCGCGCCCTGCTG
GCGCACCTGGTGACCGTCGGCGCCTGGGAACAGGTGCTGGTCTTCACCCGTACCAAGCACGGCGCCAACCGT
CTCGCCGAGTACCTGACCAAGCACGGCCTGCCGGCCGCCGCGATCCATGGCAACAAGAGCCAGAACGCGCGG
ACCAAGGCGCTGGCCGACTTCAAGGCCAACGACGTGCGCATCCTGGTGGCGACCGACATCGCCGCCCGCGGC
CTGGATATCGACCAGTTGCCCCATGTGGTCAACTACGAGTTGCCCAACGTCGAGGAAGACTACGTCCACCGC
ATCGGCCGTACCGGCCGCGCCGGACGCAGCGGCGAGGCGATCTCGCTGGTGGCGCCGGACGAAGAGAAGCTG
CTCAAGGCCATCGAGAAGATGACCAGACAGCGTATTCCCGATGGCGATGCCCAGGGTTTCGACCCCGAGGCC
GTGCTGCCCGAGGTGGCCCAGCCGGAGCCCCGCGAAGCGCCGCAGAAGCAGCCGCGCCGCGACAAGGAACGG
CGCAGCAGCCGCGAGCGCAAGCCGAAAGACGCCCAGGCGAGCAACCCCGACAGCAATGTCGCTGCGGCCCAG
GACGGTACCGAGAAGCCGGCCGGCAAGCGCCGCCGTCGCGGTGGCAAGAACAAGGAAAACCGCGAGGCCGGC
CAAGCGCAGCAGCCGCGGCAGAGCCGCGAAGCGCGTCCGGCCAAGCCCAATCGGCCTCCGGAAGTCGACGGT
AATCGCGATCCGGAAGAGTTCCTCGACGACGACTTCGACAATTTCGGCAACCGCGCCGACTACGTCAGCCCC
TACCAGGGCCAGGAAAACAAGGGACGCGGACGCCGCGGTGGCCAGCAGAAACCCCAGGGCGGTACCGGCCAG
CAGGGTCGTGGCCAAGGCCAGGGCCAAGCTCGCGGCAAGAGCCAGGGCGCCGCTCAAGGCGGCGCTCGCGGT
CAGGGTGCCGGCCAGGGCAAGGCGAAGAAACCGCGCGCCAGCAAGCCGCGCGGCCAGGGTCGCGAGAATGCC
TCGCGGATGAGCGACGCGCCGCTGCGCGAGCCGTCCGAGTACGGCACCGGCAAGCAGCCGAGCCGCCAGCCG
GTGGTGATCAACAAGCGCGACCTGGTGCGCATGGATCGCTTCCCCACCGCCGAGCAGCTCGACGAGCTGGAG
CCGCGGCGCAAGGGCGAGCGCCCCGCACTGCTGACCCGCAACCGCTAA
Translation:
MSFSSLGLSEALARAVEAAGYSQPTPVQQRAIPAVLQGRDLMVAAQTGTGKTGGFALPVLERLFPAGHPDRE
HRHGPRQARVLVLTPTRELAAQVHDSFKVYARDLPLNSTCIFGGVGMNPQIQALAKGVDVLVACPGRLLDLA
GQNKVDLSHVEILVLDEADRMLDMGFIHDVKKVLAKLPPKRQNLLFSATFSKDIVDLANKLLHNPERIEVTP
PNTTVERIEQRVFRLPAPQKRALLAHLVTVGAWEQVLVFTRTKHGANRLAEYLTKHGLPAAAIHGNKSQNAR
TKALADFKANDVRILVATDIAARGLDIDQLPHVVNYELPNVEEDYVHRIGRTGRAGRSGEAISLVAPDEEKL
LKAIEKMTRQRIPDGDAQGFDPEAVLPEVAQPEPREAPQKQPRRDKERRSSRERKPKDAQASNPDSNVAAAQ
DGTEKPAGKRRRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEVDGNRDPEEFLDDDFDNFGNRADYVSP
YQGQENKGRGRRGGQQKPQGGTGQQGRGQGQGQARGKSQGAAQGGARGQGAGQGKAKKPRASKPRGQGRENA
SRMSDAPLREPSEYGTGKQPSRQPVVINKRDLVRMDRFPTAEQLDELEPRRKGERPALLTRNR*
AnnotationID:410GeneID:401
AnnotatorUID: diggins
Modification Date/Time: 2005-03-25 09:09:10
Gene Name:
Confidence Code:3
GeneProduct:putative ATP-dependent RNA helicase, DEAD box family
Cell Localization:()
Synonyms:rhlE
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0513,cd00268,pfam00270
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70546.1|AE016697_1 (AE016792) ATP-dependent RNA helicase, DEAD box family [Pseudomonas
           putida KT2440]
          Length = 626

 Score =  844 bits (2181), Expect = 0.0
 Identities = 457/650 (70%), Positives = 512/650 (78%), Gaps = 39/650 (6%)

>gb|AAO58497.1| (AE016874) ATP-dependent RNA helicase rhlE, putative [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 629

 Score =  784 bits (2024), Expect = 0.0
 Identities = 429/653 (65%), Positives = 488/653 (74%), Gaps = 40/653 (6%)

>gb|AAN79353.1|AE016757_257 (AE016757) Putative ATP-dependent RNA helicase rhlE [Escherichia
           coli CFT073]
          Length = 453

 Score =  487 bits (1253), Expect = e-136
 Identities = 263/469 (56%), Positives = 331/469 (70%), Gaps = 17/469 (3%)






 
Structural Features:
COG0513, SrmB, Superfamily II DNA and RNA helicases 
[DNA replication, recombination, and repair / 
Transcription / 
Translation, ribosomal structure and biogenesis]
CD-Length = 513 residues,  94.5% aligned
Score =  415 bits (1068), Expect = 6e-117
Identities = 194/494 (39%), Positives = 264/494 (53%), Gaps = 24/494 (4%)

cd00268, DEADc, DEAD-box helicases.
CD-Length = 203 residues, 100.0% aligned
Score =  257 bits (659), Expect = 3e-69
Identities = 101/211 (47%), Positives = 135/211 (63%), Gaps = 8/211 (3%)

pfam00270, DEAD, DEAD/DEAH box helicase. 
CD-Length = 206 residues, 100.0% aligned
Score =  192 bits (489), Expect = 9e-50
Identities = 92/216 (42%), Positives = 131/216 (60%), Gaps = 12/216 (5%)






   
Genomic Context:






   
Comment:


















    ReferenceID:805




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17947




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:33754




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:401_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:401
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
683
                           PA0428_tr
                           translation of PA0428
                           639
                           99.84
                           99.84
                           0
                           3291.0
     

     
     
31083
                           gb|AAG03817.1|AE004480_1
                           (AE004480) probable ATP-dependent RNA helicase [Pseudomonas aeruginosa PAO1]
                           639
                           99.84
                           99.84
                           0
                           3291.0
     

     
     
31084
                           gb|AAN70546.1|AE016697_1
                           (AE016792) ATP-dependent RNA helicase, DEAD box family [Pseudomonas putida KT2440]
                           653
                           70.29
                           78.86
                           41
                           2222.0
     

     
     
31085
                           gb|AAO58497.1|
                           (AE016874) ATP-dependent RNA helicase rhlE, putative [Pseudomonas syringae pv. tomato str. DC3000]
                           671
                           65.57
                           74.36
                           74
                           2073.0
     

     
     
31086
                           emb|CAD14067.1|
                           (AL646059) PROBABLE ATP-DEPENDENT RNA HELICASE PROTEIN [Ralstonia solanacearum]
                           662
                           46.22
                           58.76
                           145
                           1371.0
     

     






      

          
GC ORFID: 43403How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA0428Glimmer Score: 

          
Start: 6295898Stop: 6293979

          
Length: 1920


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA0428 translation of PA0428Homolog Bit Score 1272.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3735 (ORF: BLASTX 792.0), t_PA0428 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCCTTTTCTTCCCTCGGACTCTCCGAGGCGCTTGCCCGCGCTGTGGAGGCTGCGGGCTACAGCCAGCCC 
ACTCCCGTGCAACAGCGGGCGATTCCCGCCGTGTTGCAAGGTCGCGACCTGATGGTTGCGGCACAGACCGGC 
ACCGGCAAGACCGGTGGTTTCGCCCTGCCGGTACTGGAGCGCCTGTTCCCCGCCGGTCATCCCGACCGCGAA 
CACCGCCACGGCCCGCGCCAGGCGCGCGTGCTGGTACTGACCCCGACCCGTGAGCTGGCCGCCCAGGTGCAT 
GACAGCTTCAAGGTCTACGCCCGCGACCTGCCGCTGAACAGCACCTGCATCTTCGGCGGGGTTGGCATGAAC 
CCGCAGATCCAGGCCCTGGCCAAGGGCGTCGACGTACTCGTCGCCTGCCCCGGCCGCCTGCTCGACCTGGCC 
GGGCAGAACAAGGTCGACCTGTCCCACGTGGAAATCCTCGTCCTCGACGAAGCCGACCGCATGCTCGACATG 
GGCTTCATCCACGATGTGAAGAAGGTTCTCGCCAAGCTGCCGCCCAAGCGCCAGAACCTGCTGTTCTCGGCT 
ACCTTCTCGAAAGACATCGTCGACCTCGCCAACAAGCTCCTGCACAACCCGGAACGCATCGAGGTAACGCCG 
CCGAACACCACGGTCGAGCGCATCGAGCAACGCGTGTTCCGCCTGCCGGCGCCGCAGAAGCGCGCCCTGCTG 
GCGCACCTGGTGACCGTCGGCGCCTGGGAACAGGTGCTGGTCTTCACCCGTACCAAGCACGGCGCCAACCGT 
CTCGCCGAGTACCTGACCAAGCACGGCCTGCCGGCCGCCGCGATCCATGGCAACAAGAGCCAGAACGCGCGG 
ACCAAGGCGCTGGCCGACTTCAAGGCCAACGACGTGCGCATCCTGGTGGCGACCGACATCGCCGCCCGCGGC 
CTGGATATCGACCAGTTGCCCCATGTGGTCAACTACGAGTTGCCCAACGTCGAGGAAGACTACGTCCACCGC 
ATCGGCCGTACCGGCCGCGCCGGACGCAGCGGCGAGGCGATCTCGCTGGTGGCGCCGGACGAAGAGAAGCTG 
CTCAAGGCCATCGAGAAGATGACCAGACAGCGTATTCCCGATGGCGATGCCCAGGGTTTCGACCCCGAGGCC 
GTGCTGCCCGAGGTGGCCCAGCCGGAGCCCCGCGAAGCGCCGCAGAAGCAGCCGCGCCGCGACAAGGAACGG 
CGCAGCAGCCGCGAGCGCAAGCCGAAAGACGCCCAGGCGAGCAACCCCGACAGCAATGTCGCTGCGGCCCAG 
GACGGTACCGAGAAGCCGGCCGGCAAGCGCCGCCGTCGCGGTGGCAAGAACAAGGAAAACCGCGAGGCCGGC 
CAAGCGCAGCAGCCGCGGCAGAGCCGCGAAGCGCGTCCGGCCAAGCCCAATCGGCCTCCGGAAGTCGACGGT 
AATCGCGATCCGGAAGAGTTCCTCGACGACGACTTCGACAATTTCGGCAACCGCGCCGACTACGTCAGCCCC 
TACCAGGGCCAGGAAAACAAGGGACGCGGACGCCGCGGTGGCCAGCAGAAACCCCAGGGCGGTACCGGCCAG 
CAGGGTCGTGGCCAAGGCCAGGGCCAAGCTCGCGGCAAGAGCCAGGGCGCCGCTCAAGGCGGCGCTCGCGGT 
CAGGGTGCCGGCCAGGGCAAGGCGAAGAAACCGCGCGCCAGCAAGCCGCGCGGCCAGGGTCGCGAGAATGCC 
TCGCGGATGAGCGACGCGCCGCTGCGCGAGCCGTCCGAGTACGGCACCGGCAAGCAGCCGAGCCGCCAGCCG 
GTGGTGATCAACAAGCGCGACCTGGTGCGCATGGATCGCTTCCCCACCGCCGAGCAGCTCGACGAGCTGGAG 
CCGCGGCGCAAGGGCGAGCGCCCCGCACTGCTGACCCGCAACCGCTAA