ViewGene
Locus Name:
GeneID:
Location:

GeneID:326
TrivialName: PA14_42500
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_42500
PAO1 Ortholog Locus:PA1703
Sequence Length:2121
Protein Length:706
Start: 3785400
Stop: 3783280
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05092.1|AE004597_6 (AE004597) type III secretory apparatus protein PcrD [Pseudomonas aeruginosa PAO1]
Identities = 705/706 (99%), Positives = 705/706 (99%)
Sequence:
ATGAACGACCTGAGCGGGCTTCTCGGCCGGGTCGGCGAGCGCAAGGACATCCTGCTGGTGGTGTTGCTGCTG
GCGGTGGTGTTCATGATGGTGCTGCCGTTGCCACCGCTGCTGCTGGACATCCTCATCGCCGTCAACATCACC
ATCTCCGTGGTCCTGCTGATGATGTCGGTGTACATCGGCTCGCCGTTGCAGTTCTCGGTGTTCCCGGCAGTG
CTGCTGATCACCACGCTGTTCCGCCTGGCGCTGTCGGTGAGCACCACGCGGATGATCCTGCTGCAGGCCGAC
GCGGGGCAGATCGTCAACACCTTCGGCAGCTTCGTGGTCGGCGGCAACCTGGTGGTGGGCATCATCATCTTC
CTGATCATCACCATCGTGCAGTTCCTGGTGATCACCAAGGGTGCCGAGCGGGTCGCCGAGGTCAGCGCGCGC
TTTTCCCTGGATGCCATGCCGGGCAAGCAGATGAGCATCGACGGCGACATGCGTGCCGGCGTGATCGATGTC
AACGAGGCGCGGGCGCGGCGCGCGGTGATCGAAAAGGAAAGCCAGATGTTCGGCTCTATGGACGGCGCGATG
AAATTCGTCAAGGGCGACGCCATCGCCGGGCTGATCATTATCGTCGTCAACATCCTCGGCGGCATCGCCATC
GGCGTCACGCAGAAGGGCCTGAGCACCGCCGACGCGCTGCAACTGTACGCGGTGCTGACCGTCGGCGATGGC
ATGGTCTCGCAGGTGCCGGCGTTGCTGATCGCCATCACCGCCGGGATCATCGTCACGCGGGTGTCTTCCGAC
GAATCGGCGGACCTCGGCAGCGACATCGGCGAACAGGTGGTGGCGCAGCCCAAGGCGCTGCTGATCGGCGGC
CTGTTGCTGGTGCTGTTCGGCCTGATTCCCGGTTTCCCGACCCTGACCTTCCTGGCTCTCGCGCTGCTGGTC
GGCGGCGGCGGCTACTTCATGCTCTGGCGCCAGCGGCTCCAGGCCAGCGCCGGTTCCCGCGACCTGCCGGCG
CTGCTCGCGCAGGGCGCCGGAGCGCCATCGGCCAAGGCGCGCGGCAAGGCTGGCGGCGGCAAGCCGAAGGCC
GGGCGTCTCGCCGAGCAGGAAGAATTCGCCCTCACCGTGCCGTTGCTGATCGACGTCGATGCCAGCCTCCAG
GAACGTCTGGAGGCGATGTCGCTGAACGAGGAACTGGTGCGGGTACGACGCGCGCTGTACCTGGATTTCGGC
GTGCCGTTCCCGGGTATCCACTTGCGCTTCAACGAAGCGATGGGCGATGGCGAATACCTGGTGCAGCTACAG
GAGGTCCCGGTCGCGCGCGGATGCCTGCGGCCGGGCTGGTTGCTGGTGCGCGAACGCGCCGCGCAGCTGGAA
TTGCTCGCGGTCCCCCACGAGCCGGCGGAGCTGCAGGTGCCGGGAGAGGAAGCGAGCTGGGTGGAGCAGGCG
CATCAGGATCGCCTGGAGCGTTCCGGCTGTGCCTGCCTGGGCCTGGAGCAGGTGCTCACCTGGCACCTGTCC
CATGTGCTGCGGGAGTACGCCGAGGATTTCATCGGCATCCAGGAGACGCGCTACCTGCTGGAGCAGATGGAG
CAGGGTTACGGCGAGCTGGTGAAGGAGGCACAGCGGATCGTTCCCCTGCAGCGGATGACCGAGATTCTCCAG
CGCCTGGTCGGCGAGGACATCTCGATCCGCAACATGCGGGCGATCCTCGAGGCGATGGTGGAGTGGGGGCAG
AAGGAGAAGGACGTGGTGCAGCTCACCGAGTACATCCGCAGCAGCCTCAAGCGCTACATCTGCTACAAGTAC
TCCAGCGGCAACAACATCCTTCCCGCCTATCTGCTGGACCAGGCGGTGGAGGAGCAGATCCGCGGTGGCATC
CGCCAGACCAGCGCCGGCAGCTACCTGGCCCTCGACCCGGCGATAACCCAGGCCTTCCTCGAGCGCGTGCGG
CAGACCGTCGGCGATCTCGCGCAGATGCAGAACCGGCCGGTGCTGATCGTTTCCATGGATATCCGCCGCTAC
GTGCGCAAGCTGGTGGAGAGCGACTATGCCGGGCTGCCGGTGCTGTCCTACCAGGAGCTGACCCAGCAGATC
AACATCCAGCCGCTTGGCAGGATCGTGTTGTGA
Translation:
MNDLSGLLGRVGERKDILLVVLLLAVVFMMVLPLPPLLLDILIAVNITISVVLLMMSVYIGSPLQFSVFPAV
LLITTLFRLALSVSTTRMILLQADAGQIVNTFGSFVVGGNLVVGIIIFLIITIVQFLVITKGAERVAEVSAR
FSLDAMPGKQMSIDGDMRAGVIDVNEARARRAVIEKESQMFGSMDGAMKFVKGDAIAGLIIIVVNILGGIAI
GVTQKGLSTADALQLYAVLTVGDGMVSQVPALLIAITAGIIVTRVSSDESADLGSDIGEQVVAQPKALLIGG
LLLVLFGLIPGFPTLTFLALALLVGGGGYFMLWRQRLQASAGSRDLPALLAQGAGAPSAKARGKAGGGKPKA
GRLAEQEEFALTVPLLIDVDASLQERLEAMSLNEELVRVRRALYLDFGVPFPGIHLRFNEAMGDGEYLVQLQ
EVPVARGCLRPGWLLVRERAAQLELLAVPHEPAELQVPGEEASWVEQAHQDRLERSGCACLGLEQVLTWHLS
HVLREYAEDFIGIQETRYLLEQMEQGYGELVKEAQRIVPLQRMTEILQRLVGEDISIRNMRAILEAMVEWGQ
KEKDVVQLTEYIRSSLKRYICYKYSSGNNILPAYLLDQAVEEQIRGGIRQTSAGSYLALDPAITQAFLERVR
QTVGDLAQMQNRPVLIVSMDIRRYVRKLVESDYAGLPVLSYQELTQQINIQPLGRIVL*
AnnotationID:336GeneID:326
AnnotatorUID: diggins
Modification Date/Time: 2005-02-28 06:06:43
Gene Name:pcrD
Confidence Code:1
GeneProduct:type III secretory apparatus protein PcrD
Cell Localization:()
Synonyms:lcrD
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(19) Protein secretion/export apparatus
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG4789,pfam00771,COG1298
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO18050.1| (AY144116) LssD [Photorhabdus luminescens]
          Length = 705

 Score = 1105 bits (2859), Expect = 0.0
 Identities = 567/700 (81%), Positives = 637/700 (91%), Gaps = 1/700 (0%)

>gb|AAN37522.1| (AY150843) LcrD [Yersinia enterocolitica]
          Length = 704

 Score = 1082 bits (2798), Expect = 0.0
 Identities = 558/699 (79%), Positives = 630/699 (90%), Gaps = 3/699 (0%)

>emb|CAE32109.1| (BX640441) putative type III secretion pore protein [Bordetella
           bronchiseptica]
          Length = 699

 Score =  798 bits (2062), Expect = 0.0
 Identities = 410/695 (58%), Positives = 531/695 (76%), Gaps = 17/695 (2%)








 
Structural Features:
pfam00771, FHIPEP, FHIPEP family.
CD-Length = 655 residues, 100.0% aligned
Score =  837 bits (2164), Expect = 0.0
Identities = 357/675 (52%), Positives = 465/675 (68%), Gaps = 21/675 (3%)

COG4789, EscV, Type III secretory pathway, component EscV 
[Intracellular trafficking and secretion]
CD-Length = 689 residues,  99.9% aligned
Score =  960 bits (2484), Expect = 0.0
Identities = 423/707 (59%), Positives = 538/707 (76%), Gaps = 22/707 (3%)

COG1298, FlhA, Flagellar biosynthesis pathway, component FlhA 
[Cell motility and secretion / Intracellular trafficking and secretion]
CD-Length = 696 residues,  97.8% aligned
Score =  573 bits (1479), Expect = 2e-164
Identities = 268/699 (38%), Positives = 416/699 (59%), Gaps = 21/699 (3%)







   
Genomic Context:






   
Comment:


















    ReferenceID:655




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17797




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37210




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:326_cdd.html


    		




 
URL:

















    ReferenceID:37854




  
Author/Investigator(s):
        Plano GV, Barve SS, Straley SC.





  
Title:
        LcrD, a membrane-bound regulator of the Yersinia pestis low-calcium response.




  
PubMed:
        1657887


MedLine:
        




    
Source:
J Bacteriol. 1991 Nov;173(22):7293-303.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1657887









           
Homologs By Global Alignment 

           

       



     
Gene ID:326
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
537
                           PA1703_tr
                           translation of PA1703
                           706
                           99.85
                           99.85
                           0
                           3474.0
     

     
     
26655
                           gb|AAG05092.1|AE004597_6
                           (AE004597) type III secretory apparatus protein PcrD [Pseudomonas aeruginosa PAO1]
                           706
                           99.85
                           99.85
                           0
                           3474.0
     

     
     
26656
                           gb|AAC45944.1|
                           (AF010150) PcrD [Pseudomonas aeruginosa]
                           706
                           99.71
                           99.71
                           0
                           3469.0
     

     
     
26659
                           emb|CAE16133.1|
                           (BX571871) Type III secretion protein SctV [Photorhabdus luminescens subsp. laumondii TTO1]
                           707
                           80.62
                           90.80
                           3
                           2859.0
     

     
     
26658
                           gb|AAO18050.1|
                           (AY144116) LssD [Photorhabdus luminescens]
                           706
                           80.45
                           90.50
                           1
                           2859.0
     

     






      

          
GC ORFID: 43328How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1703Glimmer Score: 

          
Start: 1168509Stop: 1170629

          
Length: 2121


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA1703 translation of PA1703Homolog Bit Score 1342.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4878 (ORF: BLASTX 486.0), t_PA1703 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAACGACCTGAGCGGGCTTCTCGGCCGGGTCGGCGAGCGCAAGGACATCCTGCTGGTGGTGTTGCTGCTG 
GCGGTGGTGTTCATGATGGTGCTGCCGTTGCCACCGCTGCTGCTGGACATCCTCATCGCCGTCAACATCACC 
ATCTCCGTGGTCCTGCTGATGATGTCGGTGTACATCGGCTCGCCGTTGCAGTTCTCGGTGTTCCCGGCAGTG 
CTGCTGATCACCACGCTGTTCCGCCTGGCGCTGTCGGTGAGCACCACGCGGATGATCCTGCTGCAGGCCGAC 
GCGGGGCAGATCGTCAACACCTTCGGCAGCTTCGTGGTCGGCGGCAACCTGGTGGTGGGCATCATCATCTTC 
CTGATCATCACCATCGTGCAGTTCCTGGTGATCACCAAGGGTGCCGAGCGGGTCGCCGAGGTCAGCGCGCGC 
TTTTCCCTGGATGCCATGCCGGGCAAGCAGATGAGCATCGACGGCGACATGCGTGCCGGCGTGATCGATGTC 
AACGAGGCGCGGGCGCGGCGCGCGGTGATCGAAAAGGAAAGCCAGATGTTCGGCTCTATGGACGGCGCGATG 
AAATTCGTCAAGGGCGACGCCATCGCCGGGCTGATCATTATCGTCGTCAACATCCTCGGCGGCATCGCCATC 
GGCGTCACGCAGAAGGGCCTGAGCACCGCCGACGCGCTGCAACTGTACGCGGTGCTGACCGTCGGCGATGGC 
ATGGTCTCGCAGGTGCCGGCGTTGCTGATCGCCATCACCGCCGGGATCATCGTCACGCGGGTGTCTTCCGAC 
GAATCGGCGGACCTCGGCAGCGACATCGGCGAACAGGTGGTGGCGCAGCCCAAGGCGCTGCTGATCGGCGGC 
CTGTTGCTGGTGCTGTTCGGCCTGATTCCCGGTTTCCCGACCCTGACCTTCCTGGCTCTCGCGCTGCTGGTC 
GGCGGCGGCGGCTACTTCATGCTCTGGCGCCAGCGGCTCCAGGCCAGCGCCGGTTCCCGCGACCTGCCGGCG 
CTGCTCGCGCAGGGCGCCGGAGCGCCATCGGCCAAGGCGCGCGGCAAGGCTGGCGGCGGCAAGCCGAAGGCC 
GGGCGTCTCGCCGAGCAGGAAGAATTCGCCCTCACCGTGCCGTTGCTGATCGACGTCGATGCCAGCCTCCAG 
GAACGTCTGGAGGCGATGTCGCTGAACGAGGAACTGGTGCGGGTACGACGCGCGCTGTACCTGGATTTCGGC 
GTGCCGTTCCCGGGTATCCACTTGCGCTTCAACGAAGCGATGGGCGATGGCGAATACCTGGTGCAGCTACAG 
GAGGTCCCGGTCGCGCGCGGATGCCTGCGGCCGGGCTGGTTGCTGGTGCGCGAACGCGCCGCGCAGCTGGAA 
TTGCTCGCGGTCCCCCACGAGCCGGCGGAGCTGCAGGTGCCGGGAGAGGAAGCGAGCTGGGTGGAGCAGGCG 
CATCAGGATCGCCTGGAGCGTTCCGGCTGTGCCTGCCTGGGCCTGGAGCAGGTGCTCACCTGGCACCTGTCC 
CATGTGCTGCGGGAGTACGCCGAGGATTTCATCGGCATCCAGGAGACGCGCTACCTGCTGGAGCAGATGGAG 
CAGGGTTACGGCGAGCTGGTGAAGGAGGCACAGCGGATCGTTCCCCTGCAGCGGATGACCGAGATTCTCCAG 
CGCCTGGTCGGCGAGGACATCTCGATCCGCAACATGCGGGCGATCCTCGAGGCGATGGTGGAGTGGGGGCAG 
AAGGAGAAGGACGTGGTGCAGCTCACCGAGTACATCCGCAGCAGCCTCAAGCGCTACATCTGCTACAAGTAC 
TCCAGCGGCAACAACATCCTTCCCGCCTATCTGCTGGACCAGGCGGTGGAGGAGCAGATCCGCGGTGGCATC 
CGCCAGACCAGCGCCGGCAGCTACCTGGCCCTCGACCCGGCGATAACCCAGGCCTTCCTCGAGCGCGTGCGG 
CAGACCGTCGGCGATCTCGCGCAGATGCAGAACCGGCCGGTGCTGATCGTTTCCATGGATATCCGCCGCTAC 
GTGCGCAAGCTGGTGGAGAGCGACTATGCCGGGCTGCCGGTGCTGTCCTACCAGGAGCTGACCCAGCAGATC 
AACATCCAGCCGCTTGGCAGGATCGTGTTGTGA