Flagellin and Tubulin Genes

Brian Foley btf at t10.lanl.gov
Wed Oct 8 18:26:36 EST 1997


Bob Cooper wrote:
> 
> Hi
> 
> I had a student question about genes that code for tubulin and
> flagellin.  The flagella of prokaryotes and eukaryotes are analogous
> structures.  Prokaryotic flagella are composed of flagellin subunits
> while the microtubules that make up the eukaryotic flagellum
> (undulopodium) are composed of tubulin.  Does anybody know if the genes
> that code for these protein subunits (i.e., flagellin and tubulin) are
> at all homologous?
> 
> Bob Cooper
> rac7 at erols.co

	First of all, the word "homologous" is supposed to mean
"derived from a common ancestor".  And this is usually a yes or
no answer.  There are not supposed to be differeing levels of
"homology".  However, people mis-use these terms in place of 
"similar" and and "similarity" so much, that I suppose we need 
to give up on the orignal definition.

	Two genes can be derived from a common ancestor
and not show much similarity (divergent evolution).  Conversely 
two genes which did not share a common ancestor can show some 
similarity (convergent evolution).  

	There is a huge grey area where the % similarity is
too low to prove that a pair of genes shared a common ancestor.
Any two genes should be about 25% similar by chance (there
are only 4 bases to choose from at each position) and if
we allow some gaps, it is easy to increase that value a bit.

	If one compares the prokaryotic EF-G protein or gene to
the eukaryotic EF-2 protein or gene, the degree of conservation
is great enough to infer that they are homologous as well as
similar.

	I do not see enough similarity between tubulin and
flagellin to infer a common ancestor:

LOCUS       CSFALAAB     4057 bp    DNA             BCT      
12-MAR-1997
DEFINITION  Campylobacter sp. flaA and flaB genes.
ACCESSION   Y11762
NID         g1888388
KEYWORDS    flaA gene; flaB gene; flagellin.
SOURCE      Campylobacter sp.
  ORGANISM  Campylobacter sp.
            Eubacteria; Proteobacteria; epsilon subdivision;
Campylobacter.
REFERENCE   1  (bases 1 to 4057)
  AUTHORS   Linton,D., Hurtado,A., Clewley,J.P., Chart,H., Owen,R.J. and
            Stanley,J.
  TITLE     A Campylobacter group from fresh water with enlarged
flagellin
            genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4057)
  AUTHORS   Stanley,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-MAR-1997) J. Stanley, Central Public Health
            Laboratory, Virus Reference Division, 61 Colindale Avenue,
NW9 5HT,
            UK
FEATURES             Location/Qualifiers
     source          1..4057
                     /organism="Campylobacter sp."
                     /strain="NCTC 13006"
     gene            1..1881
                     /gene="flaA"
     CDS             <1..1881
                     /gene="flaA"
                     /codon_start=1
                     /product="flagellin"
                     /db_xref="PID:e307462"
                     /db_xref="PID:g1888389"
                     /transl_table=11
                    
/translation="FRINTHVAALNAKANSDLNSKALDQSLARLSSGLRINSAADDAS
                    
GMAIADSLRTQASTLGQAINNGNDAASILQTADKAMDEQLKILDTIKVKATQAAQDGQ
                    
SAKTRNMLQADINRLMEELDNIANTTSFNGKQLLSGGFINQEFQIGAQSNQTIKASIG
                    
ATQSSKIGVTRFETGANVTSSSIASMTIKNYNGIDDFKIQNVVISTSVGTGLGALAEE
                    
INRVADRTGVRASFNVQTVGGAPVLKGSTSDDFTINGVKIGKIDYESGDANGSLVSSI
                    
NAVKDTTGVEAALNENGQLVLTSREGRGIKIEGDMGSGAGIAVNMRENYGRLSLVKND
                    
GRDIAISGTGFGFDNEKLVSQNSVSLRDTKGQISQEIADAMGFNSSNKVASIRIGVTA
                    
MSVLAGTGLSKETSLLYTAGSGFSAFTISAKSQLNMVGQVIDLGPKHSAFSGGYTALG
                    
FTAGSGFSAINSALSMLMYSKMYGTQTGAAKFSVAVAMSTADIKFVSTISTGGLSGLY
                    
NDGLKSGETRTENIGQEQTAGVTTLKGAMAVMDVAETAITNLDTIRADLGSIQNQISA
                    
TINNITVTQVNVKSAESTIRDVDFASESANYSKANILAQSGSYAMAQANASQQNVLRL
                     LQ"
     gene            2049..3941
                     /gene="flaB"
     CDS             2049..3941
                     /gene="flaB"
                     /codon_start=1
                     /product="flagellin"
                     /db_xref="PID:e307463"
                     /db_xref="PID:g1888390"
                     /transl_table=11
                    
/translation="MGFRINTNIGALNAHANSVVNANALDKSLNRLSSGLRINSAADD
                    
ASGMAIADSLRSQAATLGQAINNGNDAIGILQTADKAMDEQLKILDTIKVKATQAAQD
                    
GQSTKTRNMLQADINRLMEELDNIANTTSFNGKQLLSGGFINQEFQIGAQSNQTIKAS
                    
IGATQSSKIGVTRFETGANVVQSGIASLTIKNYNGLEDFKFRDIVISTSVGTGLGALA
                    
EEINRVADKTGVRASFNVQTTGGAPIIAGVTGEDFSINGVIIGKIEYQAGDANGALVS
                    
SINAVKDTTGVEAALDENGHLVLTSREGRGIKIEGDMGSGAGIAVNMRENYGRLSLVK
                    
NDGRDIAISGTGFGFDNEKLVSQNSVSLRDTKGQISQEIADAMGFNSSNKVASIRIGV
                    
TAMSVLAGTGLSKETSLLYTAGSGFSAFTISAKSQLNMVGQVIDLGPKHSAFSGGYTA
                    
LGFTAGSGFSAINSALSMLMYSKMYGTQTGAAKFSVAIAMSTTNIQINSAVSGTNGIS
                    
GLYQTLGLEFGEKRIENIGQEQTAGVTTLKGAMAVMDIAETATINLDQIRADIGSVQN
                    
QLQVTINNITVTQVNVKAAESTIRDVDFAAESANFSKYNILAQSGSYAMSQANAVQQN
                     VLKLLQ"
BASE COUNT     1365 a    655 c    840 g   1192 t      5 others
ORIGIN      
        1 tttcgtatta acacacacgt tgcagcatta aatgctaaag caaactcgga
tctaaatagc
       61 aaagcattgg atcaatcgct tgcaagactt agttcaggtc ttagaatcaa
ttctgcagca
      121 gatgatgctt cagggatggc gatagcagat agcttaagaa ctcaagcttc
aactttgggt
      181 caagctataa acaatggtaa cgatgcagca agtatcttac aaactgcaga
taaggctatg
      241 gatgagcagc ttaaaatctt agataccatt aaagttaaag caactcaagc
agcacaagat
      301 ggacaaagtg caaaaacaag aaatatgctt caagcagata tcaatcgttt
aatggaagaa
      361 cttgataata tcgcaaatac aacttcattt aacggtaaac aacttttaag
tggtggtttt
      421 atcaatcaag aattccaaat cggtgcacag tctaatcaaa ccatcaaagc
ttcaatcgga
      481 gcgactcagt catcaaaaat cggtgtaaca agatttgaaa caggagcgaa
tgtaactagt
      541 tctagtattg cttctatgac tattaaaaat tacaacggta tagatgattt
taaaattcaa
      601 aatgtagtta tctctacttc agtaggaaca ggacttggag ctttagctga
agagatcaac
      661 cgtgtggctg atagaacagg tgttagagct agctttaatg tgcaaactgt
aggtggngca
      721 cctgtgctta aaggttctac aagtgatgat tttacaatca atggcgtaaa
aatcggtaaa
      781 attgattacg aatcagggga tgcaaatggt tctttggttt catctatcaa
tgctgtaaaa
      841 gatactacag gggttgaagc tgctttgaat gaaaatggac aacttgttct
tacttcaaga
      901 gagggtagag gcattaaaat cgaaggtgat atgggttcag gagcaggcat
agctgttaat
      961 atgagagaaa actatggccg tttatctttg gtaaaaaatg acggtagaga
tatagcgatt
     1021 tcaggaacag gttttggttt tgataatgaa aaacttgttt ctcaaaactc
agtttcttta
     1081 agagatacca aaggacaaat ttctcaagaa attgccgatg ctatgggctt
taactcaagc
     1141 aataaagtgg caagtataag aataggggtg actgctatgt ctgtacttgc
tggaacaggt
     1201 ttaagtaagg aaacttcttt actttatact gcaggtagcg gttttagtgc
atttacaatt
     1261 tctgccaaaa gtcaacttaa tatggtaggt caagtaattg atctaggtcc
aaaacatagc
     1321 gcattctctg gtggttatac agctttaggt tttacagcag gcagtggttt
ttcagcgatt
     1381 aatagtgctt tatctatgtt aatgtattct aaaatgtatg gtactcaaac
tggtgctgct
     1441 aaattttctg tagctgtagc gatgagtaca gctgatatta agtttgtaag
cactataagt
     1501 actggcggtc tttctggttt gtataatgat ggattaaaat caggtgaaac
aagaactgaa
     1561 aacataggac aagaacaaac cgcaggggtt acaactctaa aaggcgctat
ggctgtgatg
     1621 gatgtagctg aaacagctat taccaatctt gataccatta gagcagatct
tggttctata
     1681 caaaatcaga tttcagcaac tatcaacaac attactgtaa ctcaagtaaa
tgttaaatcc
     1741 gctgaatcga ccatcagaga tgtagacttt gcaagcgaga gtgcaaacta
ctctaaagct
     1801 aatatcctag ctcaaagtgg atcttatgcg atggcgcaag ctaatgcttc
tcagcaaaat
     1861 gttttaagat tgctccagta gtaaacccaa atcatctcat cctttgnagg
gacgctacaa
     1921 tttntacaaa tccaagccta gtagaaatac taggcttttt ttattttaga
ataattttaa
     1981 atcataaata aaacttggaa cacttcttgc tttagtcctt ttgatgcaat
attttgaaag
     2041 gatttaaaat gggttttaga ataaacacca acatcggtgc gttaaatgca
catgcaaatt
     2101 cagttgttaa tgctaatgca cttgataagt ctttaaatag actgagttca
ggtcttagaa
     2161 tcaactccgc agcagatgat gcttcaggga tggcgatagc agattctttg
cgttcacaag
     2221 cagcaacttt gggtcaagct ataaacaatg gtaatgatgc cataggtatc
ttgcaaactg
     2281 cagataaggc tatggatgag cagcttaaaa tcttagatac catcaaagtt
aaagcaactc
     2341 aagcagcaca agatggacaa agcactaaaa caagaaatat gcttcaagca
gatatcaatc
     2401 gtttgatgga agaacttgat aatatcgcaa atacaacttc atttaacggt
aaacaacttt
     2461 taagtggtgg ttttatcaat caagaattcc aaatcggtgc acagtctaat
caaaccatca
     2521 aagcttcaat cggagcaacc cagtcatcaa aaatcggtgt aacaagattt
gaaacagggg
     2581 cgaatgtcgt gcaatctggc attgcttctt tgactattaa aaattataat
ggtttagagg
     2641 attttaaatt tagagatata gttatctcna cttcagtagg aacaggactt
ggagctttag
     2701 ctgaagaaat caaccgtgta gctgataaaa caggtgttag agctagtttt
aatgtgcaaa
     2761 cnacaggggg agcgccaatc atagcaggtg tgactggaga ggatttttct
atcaatggcg
     2821 tgattatcgg taaaattgag tatcaagcag gggatgcaaa cggtgctttg
gtttcatcta
     2881 tcaatgctgt aaaagatact acaggggttg aagctgcctt ggatgaaaat
ggtcatcttg
     2941 ttcttacttc aagagagggt agaggcatta aaatcgaagg tgatatgggt
tcaggagcag
     3001 gcatagctgt taatatgaga gaaaactatg gccgtttatc tttggtaaaa
aatgacggta
     3061 gagatatagc gatttcagga acaggttttg gttttgataa tgaaaaactt
gtttctcaaa
     3121 actcagtttc tttaagagat accaaaggac aaatttctca agaaattgcc
gatgctatgg
     3181 gctttaactc aagcaataaa gtggcaagta taagaatagg ggtgactgct
atgtctgtac
     3241 ttgctggaac aggtttaagt aaggaaactt ctttacttta tactgcaggt
agcggtttta
     3301 gtgcatttac aatttctgca aaaagtcaac ttaatatggt aggtcaagta
attgatctag
     3361 gtccaaaaca tagcgcattc tctggtggtt atacagcttt aggttttaca
gcaggcagtg
     3421 gtttttcagc gattaatagt gctttatcta tgttaatgta ttctaaaatg
tatggtactc
     3481 aaactggtgc tgctaaattt tctgtagcta ttgctatgag cactacaaat
attcaaataa
     3541 atagtgctgt tagtggaaca aatggaattt caggtttgta tcaaactctt
ggtttagaat
     3601 ttggtgaaaa aagaattgaa aacataggac aagagcaaac cgcaggggtt
acaactctaa
     3661 aaggtgctat ggctgtgatg gatatagcag aaactgctac aatcaacctt
gatcaaatca
     3721 gagcagatat aggttcagtg caaaaccaac ttcaagtgac tatcaacaat
atcactgtaa
     3781 ctcaagtcaa tgttaaagcc gctgaatcaa ccatcagaga tgtagacttt
gctgcagaaa
     3841 gtgcaaattt ttctaaatac aacatcctag ctcaaagtgg atcttatgcg
atgagtcagg
     3901 ccaatgctgt gcagcaaaat gttttaaaac tcttacaata aaaatcgctc
tttttagagc
     3961 gattatacaa gttttctttt ttctaccata tcccttaaag gtataatggc
gctttttaaa
     4021 ataccatttt gcaagatgat taaattatgt acttcat
//



LOCUS       PFU58642     1706 bp    mRNA            PLN      
29-AUG-1997
DEFINITION  Pelvetia fastigiata alpha-tubulin mRNA, clone PTalpha2,
complete
            cds.
ACCESSION   U58642
NID         g1381655
KEYWORDS    brown algae; cDNA.
SOURCE      Pelvetia fastigiata.
  ORGANISM  Pelvetia fastigiata
            Eukaryotae; stramenopiles; Phaeophyceae/Xanthophyceae group;
            Phaeophyceae; Fucales; Fucaceae; Pelvetia.
REFERENCE   1  (bases 1 to 1706)
  AUTHORS   Coffman,H.R. and Kropf,D.L.
  TITLE     The brown alga Pelvetia fastigiata, expresses two
alpha-tubulin
            sequences (Accession Nos. U58641 and U58642) (PGR97-019)
  JOURNAL   Plant Physiol. 113, 663 (1997)
REFERENCE   2  (bases 1 to 1706)
  AUTHORS   Coffman,H.R. and Kropf,D.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-1996) H.R. Coffman, Biology, University of
Utah,
            Salt Lake City, UT 84112, USA
FEATURES             Location/Qualifiers
     source          1..1706
                     /organism="Pelvetia fastigiata"
                     /dev_stage="24h zygotes"
                     /clone="PTalpha2"
     CDS             71..1432
                     /note="cytoskeletal protein"
                     /codon_start=1
                     /product="alpha-tubulin"
                     /db_xref="PID:g1381656"
                    
/translation="MRECISIHIGQAGIQTGNACWELYCLEHGIQPDGQMPSDKTIGG
                    
GDDAFNTFFSETGAGKHVPRAVYVDLEPTVCDEVRTGTYRQLYHPEQIISGKEDAANN
                    
YARGHYTIGKEIVDLVLDRIRKLADNCTGLQGFLVFHATGGGTGSGLGSLLLERLSVD
                    
YGRKSKLSFAITPAPQVATAVVEPYNSVLSTHALLEHTDCTFCLDNEALYDVCRRNLD
                    
IERPTYTNLNRLVAQVISSLTASLRFDGALNVDVTEFQTNLVPYPRIHFMLTSYAPII
                    
SAEKAYHEQLSVAEITNSVFEPAGMMTNCDPRHGKYMACCLMYRGDVVPKDVNAAVAT
                    
IKTKRTIQFVDWCPTGFKCGINYQPPTVVPGGDLARVQRAVCMVANTTAIAEALSRID
                    
HKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGAETAEGEGEEEDFG
                     EEY"
BASE COUNT      380 a    505 c    475 g    346 t
ORIGIN      
        1 ccgatatctt gaatcgtagc cacccacaac ccaatcttcc tctttttacg
actcccacct
       61 ttcttcaact atgcgtgagt gcatctctat ccacatcggc caggccggca
tccagaccgg
      121 taacgcatgc tgggagctgt actgtcttga gcacggcatc cagcccgacg
gtcagatgcc
      181 ctcggacaag accatcggtg gtggtgacga cgctttcaac acattctttt
cggagaccgg
      241 cgctggcaag cacgtacccc gcgcggtata cgtggacctg gagcccacgg
tttgcgacga
      301 ggtgcgcacc ggcacgtacc gccagctata ccacccggag cagatcatct
cgggcaagga
      361 agacgcggct aacaactacg cccgcggcca ttacactatc ggcaaggaga
tagtggacct
      421 cgtcctcgac cgcatccgta agctagccga caactgcact gggctccagg
gcttcctggt
      481 gttccacgcc accggcggtg ggaccggatc cggactgggc tccctgctct
tggagcgcct
      541 gtccgtggac tacggccgca agtcgaagct gtcgtttgcc atcacgcccg
cgccacaggt
      601 ggcaacggcc gtggttgagc cgtacaactc ggtgctgtcg acccacgcgc
tgctggagca
      661 cacggactgc accttctgcc tcgacaacga ggcgctgtac gacgtttgcc
gccgcaacct
      721 ggacattgag cgccccacgt acaccaacct gaaccggcta gtggctcagg
tgatctcgtc
      781 gctgaccgcc tcgctgcgct tcgacggcgc gctgaacgtg gacgtgacgg
agttccagac
      841 caacctggtg ccctacccgc ggatccactt catgctcaca tcgtacgcgc
ccatcatctc
      901 tgccgaaaag gcgtaccacg aacaactctc ggtggccgag atcacgaact
ctgtgttcga
      961 gccggcaggc atgatgacaa attgcgaccc taggcacggc aaatacatgg
cgtgctgcct
     1021 catgtaccgt ggcgacgttg tgcccaaaga cgtgaacgct gccgtggcca
ccatcaagac
     1081 caagcgcaca atccagttcg tggattggtg ccccacaggc ttcaagtgcg
gcatcaacta
     1141 ccagccgccc accgtcgtgc ctggcggtga ccttgcccgc gttcagcgcg
ctgtgtgcat
     1201 ggtggccaac accacggcca tcgccgaggc tctatcgcgc atcgaccaca
agttcgacct
     1261 catgtacgcc aagcgtgctt tcgtgcactg gtacgtgggt gagggcatgg
aagagggtga
     1321 gttctcggag gctcgtgagg atcttgctgc gctggagaag gactacgaag
aggttggagc
     1381 tgagaccgct gagggcgagg gcgaggagga ggacttcgga gaggagtact
aagtctcaat
     1441 atcagcatcc catcgccatg ttgtcccctg aaagcgaaca ttttctgttg
ggccagagta
     1501 aaatgcccct tcaaaagggt tatttgtcta ttctatgcct agattgtagt
gtcgagtctg
     1561 ctgacctaca gttttcggtt cagggcaaaa gagcaagatt ttgatagaaa
tgggatggga
     1621 gaaaagcgga agcggtgctt ttttgcgccg taattataaa tataaatata
tatgttatat
     1681 tcaatccaaa aaaaaaaaaa aaaaaa
//


-- 
 ____________________________________________________________________
|Brian T. Foley               btf at t10.lanl.gov                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos National Lab      http://hiv-web.lanl.gov/index.html     |
|Los Alamos, NM 87544  U.S.A. http://www.t10.lanl.gov/~btf/home.html |
|____________________________________________________________________|




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