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JOURNAL Unpublished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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