ViewGene
Locus Name:
GeneID:
Location:

GeneID:42
TrivialName: PA14_25230
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_25230
PAO1 Ortholog Locus:PA3002
Sequence Length:3447
Protein Length:1148
Start: 2208469
Stop: 2205023
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06390.1|AE004725_3 (AE004725) transcription-repair coupling protein Mfd [Pseudomonas aeruginosa PAO1]
Identities = 1147/1148 (99%), Positives = 1147/1148 (99%)
Sequence:
GTGTCCGTACTGCGTCTTCCCAGCCTGCCGGCCAGCGCCGGCAAGCAACACTGGGGCAACCTCCCCGGTGCC
GCGCTGAGCCTGGCTGTCGCCGAGGCCGCCAGTTCCGCCAAGCGCTTCACCTTGCTGCTGACCGCCGACAGC
CAGAATGCCGAACGCCTGGAACAGGAACTGCGGTTCTTCGCCCCCGACCTGCCGGTATTGCATTTCCCCGAT
TGGGAAACCCTGCCCTACGACGTCTTTTCGCCGCATCAGGACATCATTTCCCAGCGCATCGCCGCCCTCTAC
CAGTTGCCGCAGCTCAAGCACGGCGTGCTGGTGGTGCCGATCTCCACCGCCTTGCACCGCCTGGCGCCGACC
CGCTTCCTGCTCGGCAGCAGCCTGGTCCTCGACGTCGGCCAGAAACTCGACGTCGAGCGGATGCGCCTGCGC
CTGGAAGGCGCCGGCTACCGCTGCGTCGACACGGTCTACGAGCACGGCGAGTTCGCCGTCCGCGGCGCACTG
ATCGACCTGTTCCCGATGGGCAGCGAGTTGCCCTTCCGTATCGACCTGTTCGACGACGAGATCGAGACCCTG
CGCACCTTCGACCCGGAGACCCAGCGCTCCATCGACAAGGTCGAGTCAATCCGCCTGCTGCCGGCACGCGAA
TTCCCCCTGAACAAGGAAGCGGTCACCGGTTTCCGCGGCCGCTTCCGCGAGCGCTTCGACGTCGACTACCGG
CGCTGCCCGATCTACCAGGACCTCGCCAGCGGTTTGACACCCTCGGGAATCGAGTACTACCTGCCGCTGTTC
TTCGAGGAAACCGCGACCCTCTTCGACTACCTGCCGCAAGACACCCAGGTGTTCTCCCTGCCCGGCATCGAA
CAGGCCGCCGAGCAGTTCTGGAATGACGTACGCAGCCGCTACGAGGACCGCCGGGTCGATCCGGAACGGCCA
TTGCTGCCGCCGGCGGAAGTGTTCCTTCCGGTGGAAGACTGCTTCGCCCGGCTGAAGAACTGGCCACGGGTG
GTCGCCAGCCAGGAGGACGTCGAGCCGGGCGTCGGGCGCGAGCGCTTCCCGGCCCTGCCGCTGCCGAACCTG
GCGATCGAAGCCAAGGCCGCCGAGCCGCTGGCCGCGCTGCGCCGGTTCATCGAGGAGTTCCCCGGCCGCGTA
CTGTTCTGCGCCGAATCGCCCGGACGCCGGGAAGTCCTGCTGGAGCTGCTGGCCCGACTGAAGCTGCGCCCC
GAGGAAGTCGACGGCTGGCCGGCCTTCCTCGCCAGCCAGGCACGCCTGGCGATCAGCATCGCGCCGCTGGAC
GAGGGCCTGCTGCTGGACCATCCGGCACTCGCCCTGGTCGCCGAAAGCCCGCTGTTCGGCCAGCGCGTCATG
CAGCGCCGGCGCCGGGAAAAGACCCGCGACGGCGGCGACGCGGTGATCAAGAACCTCACCGAGCTGCGCGAA
GGCGCGCCGGTGGTGCACATCGACCATGGCGTCGGCCGCTACCTGGGCCTGATCACCCTCGAGGTGGACAAC
CAGCAGGCGGAATTCCTCATGCTGCAATACGCCGAGGACGCCAAACTCTACGTGCCGGTCGCCAACCTGCAC
CTGATCGCCCGCTACACCGGCGCCGACGACGCCCTGGCGCCGCTGCACCGACTCGGCTCGGAAACCTGGCAG
AAGGCCAAGCGCAAGGCCGCCGAACAGGTTCGCGACGTCGCCGCCGAACTGCTCGACATCTACGCCCGCCGC
GCCGCCCGCGAAGGCTTCGCGTTCAAGGATCCGCAGGCCGACTACGCGACCTTCTCGGCCGGCTTCCCGTTC
GAGGAGACGCCGGACCAGCAAAGCGCCATCGAGGCGGTGGTCGCCGACATGCTCGCGCCCAGGCCCATGGAC
CGCCTGGTCTGCGGCGACGTCGGCTTCGGCAAGACCGAAGTGGCGATGCGCGCGGCGTTCGTCGCCGTGCAT
AGCGGCAAGCAGGTGGCGGTGCTGGTGCCCACCACCCTGCTCGCCCAGCAGCACTACAACAGCTTCCGCGAC
CGCTTCGCCGACTGGCCGGTGAGCGTCGAGGTGATGAGCCGCTTCAAGAGCGCCAAGGAAGTCGAGAACGCC
GCGCGGCTACTGGCCGAAGGCAAGATCGACATCCTCATCGGGACCCACAAGCTGCTCCAGGAAGACGTGAAG
TTCGCCAACCTGGGGTTGGTCGTGATCGACGAGGAACACCGCTTCGGGGTGCGCCAGAAGGAGCAGCTCAAG
GCCCTGCGCAGCGAAGTGGATATCCTCACCCTCACCGCCACGCCGATCCCGCGGACCCTGAACATGGCCGTC
TCCGGCATGCGCGACCTGTCCATCATCGCCACGCCGCCGGCGCGCCGCCTGTCGGTGCGCACCTTCGTCATG
GAGCAGCAGAACGCGGTGATCAAGGAAGCGCTGCTCCGCGAACTGCTGCGCGGCGGCCAGGTGTACTACCTG
CACAACGAAGTGAAGACCATCGAGAAGTGCGCCCGCGACCTCGCCGAACTGGTCCCGGAGGCGCGCATCGGC
ATCGGCCACGGACAGATGCACGAGCGCGAGCTGGAACAGGTGATGAGCGACTTCTACCACAAGCGCTTCAAC
GTGCTGGTGGCCTCGACCATCATCGAGACCGGCATCGACGTGCCCAGCGCCAACACCATCCTCATCGAGCGC
GCCGACAAGTTCGGCCTGGCCCAGTTGCACCAGTTGCGCGGCCGCGTCGGTCGCAGCCACCACCAGGCCTAC
GCCTACCTGCTGACACCGCCGCGCCGTCAGATGACCCCGGACGCCGAGAAGCGCCTGGAAGCCATCGCCAAC
GCCCAGGACCTGGGCGCCGGCTTCGTCCTCGCCACCCACGACCTGGAGATCCGCGGCGCCGGCGAGTTGCTC
GGCGACGGCCAGAGCGGGCAGATCCAGGCGGTCGGCTTCACCCTCTACATGGAAATGCTCGAACGGGCGGTG
AAGGCCATCCGCAAGGGCGAGCAGCCGAACCTCGAGCAGCCGCTGGGCGGTGGGCCGGAGGTCAACCTGCGG
GTGCCTGCGCTGATCCCCGAGGATTACCTGCCCGACGTGCATGCCCGGCTGATCCTCTACAAGCGCATCGCC
AACGCCCCTGACGAGGAAGGTTTGCGCGAGTTGCAGGTGGAGATGATCGACCGCTTCGGGCTCCTGCCCGAT
CCGGCGAAGAACCTGATGCGCCTGACCCTTCTGAAGCTGCAGGCGGAAAAACTTGGAATCCTCAAGGTCGAT
GCCGGACCGCAGGGCGGTCGTATAGAATTCGCCGCCGATACCCAGGTCGACCCGCTGGTACTGATCAAGCTG
ATCCAGGGCCAGCCGAACCGCTACAAGTTCGAAGGCGCAACCCTGTTCCGCTTCCAGGTGCCCATGGAACGA
CCGGAAGAACGCTTCAATACCCTGGAGGCGCTGTTCGAGCGCCTGACACCGCAAACCACCTAA
Translation:
MSVLRLPSLPASAGKQHWGNLPGAALSLAVAEAASSAKRFTLLLTADSQNAERLEQELRFFAPDLPVLHFPD
WETLPYDVFSPHQDIISQRIAALYQLPQLKHGVLVVPISTALHRLAPTRFLLGSSLVLDVGQKLDVERMRLR
LEGAGYRCVDTVYEHGEFAVRGALIDLFPMGSELPFRIDLFDDEIETLRTFDPETQRSIDKVESIRLLPARE
FPLNKEAVTGFRGRFRERFDVDYRRCPIYQDLASGLTPSGIEYYLPLFFEETATLFDYLPQDTQVFSLPGIE
QAAEQFWNDVRSRYEDRRVDPERPLLPPAEVFLPVEDCFARLKNWPRVVASQEDVEPGVGRERFPALPLPNL
AIEAKAAEPLAALRRFIEEFPGRVLFCAESPGRREVLLELLARLKLRPEEVDGWPAFLASQARLAISIAPLD
EGLLLDHPALALVAESPLFGQRVMQRRRREKTRDGGDAVIKNLTELREGAPVVHIDHGVGRYLGLITLEVDN
QQAEFLMLQYAEDAKLYVPVANLHLIARYTGADDALAPLHRLGSETWQKAKRKAAEQVRDVAAELLDIYARR
AAREGFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVH
SGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVK
FANLGLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARRLSVRTFVM
EQQNAVIKEALLRELLRGGQVYYLHNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFN
VLVASTIIETGIDVPSANTILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRRQMTPDAEKRLEAIAN
AQDLGAGFVLATHDLEIRGAGELLGDGQSGQIQAVGFTLYMEMLERAVKAIRKGEQPNLEQPLGGGPEVNLR
VPALIPEDYLPDVHARLILYKRIANAPDEEGLRELQVEMIDRFGLLPDPAKNLMRLTLLKLQAEKLGILKVD
AGPQGGRIEFAADTQVDPLVLIKLIQGQPNRYKFEGATLFRFQVPMERPEERFNTLEALFERLTPQTT*
AnnotationID:52GeneID:42
AnnotatorUID: diggins
Modification Date/Time: 2005-04-11 17:05:24
Gene Name:mfd
Confidence Code:2
GeneProduct:transcription-repair coupling factor
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(11) DNA replication, recombination, modification and repair
Alternate Gene Product Name:mutation frequency decline factor
Functional Category Confidence Code:5
COGs:COG1197
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO55619.1| (AE016863) transcription-repair coupling factor [Pseudomonas syringae
            pv. tomato str. DC3000]
          Length = 1150

 Score = 2001 bits (5185), Expect = 0.0
 Identities = 1003/1149 (87%), Positives = 1077/1149 (93%), Gaps = 2/1149 (0%)

>gb|AAN67761.1|AE016407_5 (AE016782) transcription-repair coupling factor [Pseudomonas putida
            KT2440]
          Length = 1149

 Score = 1963 bits (5085), Expect = 0.0
 Identities = 987/1147 (86%), Positives = 1063/1147 (92%), Gaps = 1/1147 (0%)

>dbj|BAB34915.1| (AP002555) transcription-repair coupling factor [Escherichia coli
            O157:H7]
          Length = 1148

 Score = 1275 bits (3299), Expect = 0.0
 Identities = 653/1138 (57%), Positives = 836/1138 (73%), Gaps = 5/1138 (0%)








 
Structural Features:
COG1197, Mfd, Transcription-repair coupling factor 
(superfamily II helicase) 
[DNA replication, recombination, and repair / Transcription]
CD-Length = 1139 residues,  99.9% aligned
Score = 1491 bits (3862), Expect = 0.0
Identities = 633/1146 (55%), Positives = 811/1146 (70%), Gaps = 12/1146 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:14037




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17229




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36045




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:42_cdd.html


    		




 
URL:

















    ReferenceID:36474




  
Author/Investigator(s):
        Selby CP, Sancar A.





  
Title:
        Molecular mechanism of transcription-repair coupling.




  
PubMed:
        8465200


MedLine:
        




    
Source:
Science. 1993 Apr 2;260(5104):53-8.

Comment in:
    * Science. 1993 Apr 2;260(5104):37-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=93219833&dopt=Abstract









           
Homologs By Global Alignment 

           

       



     
Gene ID:42
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
83
                           PA3002_tr
                           translation of PA3002
                           1148
                           99.91
                           99.91
                           0
                           5839.0
     

     
     
11532
                           gb|AAG06390.1|AE004725_3
                           (AE004725) transcription-repair coupling protein Mfd [Pseudomonas aeruginosa PAO1]
                           1148
                           99.82
                           99.91
                           0
                           5836.0
     

     
     
11533
                           gb|AAO55619.1|
                           (AE016863) transcription-repair coupling factor [Pseudomonas syringae pv. tomato str. DC3000]
                           1150
                           87.13
                           93.65
                           2
                           5183.0
     

     
     
11534
                           gb|AAN67761.1|AE016407_5
                           (AE016782) transcription-repair coupling factor [Pseudomonas putida KT2440]
                           1149
                           85.81
                           92.51
                           1
                           5082.0
     

     
     
11540
                           dbj|BAB34915.1|
                           (AP002555) transcription-repair coupling factor [Escherichia coli O157:H7]
                           1161
                           56.58
                           72.52
                           26
                           3305.0
     

     






      

          
GC ORFID: 43044How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3002Glimmer Score: 

          
Start: 2745457Stop: 2748903

          
Length: 3447


          
Start Codon: GTGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA3002 translation of PA3002Homolog Bit Score 2253.0

          
Other Homologs:  psyr_15may02_Scaffold1_revised_gene523 (ORF: BLASTX 1991.0), t_PA3002 (ORF: GLIMMER)

          
GC ORF Sequence

           
GTGTCCGTACTGCGTCTTCCCAGCCTGCCGGCCAGCGCCGGCAAGCAACACTGGGGCAACCTCCCCGGTGCC 
GCGCTGAGCCTGGCTGTCGCCGAGGCCGCCAGTTCCGCCAAGCGCTTCACCTTGCTGCTGACCGCCGACAGC 
CAGAATGCCGAACGCCTGGAACAGGAACTGCGGTTCTTCGCCCCCGACCTGCCGGTATTGCATTTCCCCGAT 
TGGGAAACCCTGCCCTACGACGTCTTTTCGCCGCATCAGGACATCATTTCCCAGCGCATCGCCGCCCTCTAC 
CAGTTGCCGCAGCTCAAGCACGGCGTGCTGGTGGTGCCGATCTCCACCGCCTTGCACCGCCTGGCGCCGACC 
CGCTTCCTGCTCGGCAGCAGCCTGGTCCTCGACGTCGGCCAGAAACTCGACGTCGAGCGGATGCGCCTGCGC 
CTGGAAGGCGCCGGCTACCGCTGCGTCGACACGGTCTACGAGCACGGCGAGTTCGCCGTCCGCGGCGCACTG 
ATCGACCTGTTCCCGATGGGCAGCGAGTTGCCCTTCCGTATCGACCTGTTCGACGACGAGATCGAGACCCTG 
CGCACCTTCGACCCGGAGACCCAGCGCTCCATCGACAAGGTCGAGTCAATCCGCCTGCTGCCGGCACGCGAA 
TTCCCCCTGAACAAGGAAGCGGTCACCGGTTTCCGCGGCCGCTTCCGCGAGCGCTTCGACGTCGACTACCGG 
CGCTGCCCGATCTACCAGGACCTCGCCAGCGGTTTGACACCCTCGGGAATCGAGTACTACCTGCCGCTGTTC 
TTCGAGGAAACCGCGACCCTCTTCGACTACCTGCCGCAAGACACCCAGGTGTTCTCCCTGCCCGGCATCGAA 
CAGGCCGCCGAGCAGTTCTGGAATGACGTACGCAGCCGCTACGAGGACCGCCGGGTCGATCCGGAACGGCCA 
TTGCTGCCGCCGGCGGAAGTGTTCCTTCCGGTGGAAGACTGCTTCGCCCGGCTGAAGAACTGGCCACGGGTG 
GTCGCCAGCCAGGAGGACGTCGAGCCGGGCGTCGGGCGCGAGCGCTTCCCGGCCCTGCCGCTGCCGAACCTG 
GCGATCGAAGCCAAGGCCGCCGAGCCGCTGGCCGCGCTGCGCCGGTTCATCGAGGAGTTCCCCGGCCGCGTA 
CTGTTCTGCGCCGAATCGCCCGGACGCCGGGAAGTCCTGCTGGAGCTGCTGGCCCGACTGAAGCTGCGCCCC 
GAGGAAGTCGACGGCTGGCCGGCCTTCCTCGCCAGCCAGGCACGCCTGGCGATCAGCATCGCGCCGCTGGAC 
GAGGGCCTGCTGCTGGACCATCCGGCACTCGCCCTGGTCGCCGAAAGCCCGCTGTTCGGCCAGCGCGTCATG 
CAGCGCCGGCGCCGGGAAAAGACCCGCGACGGCGGCGACGCGGTGATCAAGAACCTCACCGAGCTGCGCGAA 
GGCGCGCCGGTGGTGCACATCGACCATGGCGTCGGCCGCTACCTGGGCCTGATCACCCTCGAGGTGGACAAC 
CAGCAGGCGGAATTCCTCATGCTGCAATACGCCGAGGACGCCAAACTCTACGTGCCGGTCGCCAACCTGCAC 
CTGATCGCCCGCTACACCGGCGCCGACGACGCCCTGGCGCCGCTGCACCGACTCGGCTCGGAAACCTGGCAG 
AAGGCCAAGCGCAAGGCCGCCGAACAGGTTCGCGACGTCGCCGCCGAACTGCTCGACATCTACGCCCGCCGC 
GCCGCCCGCGAAGGCTTCGCGTTCAAGGATCCGCAGGCCGACTACGCGACCTTCTCGGCCGGCTTCCCGTTC 
GAGGAGACGCCGGACCAGCAAAGCGCCATCGAGGCGGTGGTCGCCGACATGCTCGCGCCCAGGCCCATGGAC 
CGCCTGGTCTGCGGCGACGTCGGCTTCGGCAAGACCGAAGTGGCGATGCGCGCGGCGTTCGTCGCCGTGCAT 
AGCGGCAAGCAGGTGGCGGTGCTGGTGCCCACCACCCTGCTCGCCCAGCAGCACTACAACAGCTTCCGCGAC 
CGCTTCGCCGACTGGCCGGTGAGCGTCGAGGTGATGAGCCGCTTCAAGAGCGCCAAGGAAGTCGAGAACGCC 
GCGCGGCTACTGGCCGAAGGCAAGATCGACATCCTCATCGGGACCCACAAGCTGCTCCAGGAAGACGTGAAG 
TTCGCCAACCTGGGGTTGGTCGTGATCGACGAGGAACACCGCTTCGGGGTGCGCCAGAAGGAGCAGCTCAAG 
GCCCTGCGCAGCGAAGTGGATATCCTCACCCTCACCGCCACGCCGATCCCGCGGACCCTGAACATGGCCGTC 
TCCGGCATGCGCGACCTGTCCATCATCGCCACGCCGCCGGCGCGCCGCCTGTCGGTGCGCACCTTCGTCATG 
GAGCAGCAGAACGCGGTGATCAAGGAAGCGCTGCTCCGCGAACTGCTGCGCGGCGGCCAGGTGTACTACCTG 
CACAACGAAGTGAAGACCATCGAGAAGTGCGCCCGCGACCTCGCCGAACTGGTCCCGGAGGCGCGCATCGGC 
ATCGGCCACGGACAGATGCACGAGCGCGAGCTGGAACAGGTGATGAGCGACTTCTACCACAAGCGCTTCAAC 
GTGCTGGTGGCCTCGACCATCATCGAGACCGGCATCGACGTGCCCAGCGCCAACACCATCCTCATCGAGCGC 
GCCGACAAGTTCGGCCTGGCCCAGTTGCACCAGTTGCGCGGCCGCGTCGGTCGCAGCCACCACCAGGCCTAC 
GCCTACCTGCTGACACCGCCGCGCCGTCAGATGACCCCGGACGCCGAGAAGCGCCTGGAAGCCATCGCCAAC 
GCCCAGGACCTGGGCGCCGGCTTCGTCCTCGCCACCCACGACCTGGAGATCCGCGGCGCCGGCGAGTTGCTC 
GGCGACGGCCAGAGCGGGCAGATCCAGGCGGTCGGCTTCACCCTCTACATGGAAATGCTCGAACGGGCGGTG 
AAGGCCATCCGCAAGGGCGAGCAGCCGAACCTCGAGCAGCCGCTGGGCGGTGGGCCGGAGGTCAACCTGCGG 
GTGCCTGCGCTGATCCCCGAGGATTACCTGCCCGACGTGCATGCCCGGCTGATCCTCTACAAGCGCATCGCC 
AACGCCCCTGACGAGGAAGGTTTGCGCGAGTTGCAGGTGGAGATGATCGACCGCTTCGGGCTCCTGCCCGAT 
CCGGCGAAGAACCTGATGCGCCTGACCCTTCTGAAGCTGCAGGCGGAAAAACTTGGAATCCTCAAGGTCGAT 
GCCGGACCGCAGGGCGGTCGTATAGAATTCGCCGCCGATACCCAGGTCGACCCGCTGGTACTGATCAAGCTG 
ATCCAGGGCCAGCCGAACCGCTACAAGTTCGAAGGCGCAACCCTGTTCCGCTTCCAGGTGCCCATGGAACGA 
CCGGAAGAACGCTTCAATACCCTGGAGGCGCTGTTCGAGCGCCTGACACCGCAAACCACCTAA