Gene T2H3.9
Putative Identification GTP pyrophosphokinase
Position 25585 - 30524, from within the CDS to the termination codon
Strand -
EST hits Z34769
Database match bacterial GTP pyrophosphokinases

 

CDS:  The table below lists the coordinates of the T2H3.9 exons and which exon prediction algorithms selected the 3' and 5' termini (GS = GenScan, Gr = GRAIL, M = MZEF, NPG = NetPlantGene - selects splice sites only, not exons). Splice sites delineated by identity to EST Z34769 are designated by EST and those suggested by similarity to EST N38487 are designated by est.

Exon Range 3' 5'
1 30336 - 30524 Gr, M, NPG Gr, M, NPG
2 29969 - 30151 GS, Gr, NPG Gr, M, NPG
3 29818 - 29883 GS, M, NPG GS, M, NPG
4 29357 - 29488 GS, Gr, M, NPG GS, Gr, M, NPG
5 29143 - 29244 GS, Gr, NPG GS, Gr, NPG
6 28990 - 29067 GS, Gr, NPG GS, Gr, NPG
7 28827 - 28898 GS, M, NPG see note below
8 28545 - 28652 GS, Gr, M, NPG GS, Gr, M
9 28268 - 28365 GS, Gr, M, NPG GS, Gr, M
10 28125 - 28185 GS, M, NPG GS, Gr, M, NPG
11 27947 - 28012 GS, NPG GS, M
12 27630 - 27731 est, GS, Gr, M, NPG est, GS, Gr, M
13 27319 - 27477 GS, Gr, NPG est, GS, Gr, NPG
14 27071 - 27202 GS, Gr, M, NPG GS, Gr, M, NPG
15 26897 - 26983 GS, Gr, M, NPG GS, Gr, M, NPG
16 26706 - 26777 Gr, NPG Gr, NPG
17 26490 - 26576 GS, Gr, M, NPG GS, Gr, M, NPG
18 25966 - 26413 EST, GS, Gr, M, NPG GS, Gr, M, NPG
19 25818 - 25879 EST, Gr, NPG EST, GS, Gr, NPG
20 25585 - 25731   EST, Gr, M, NPG

Note regarding exon 7:  GenScan predicts the 5' end of exon 7 at position 28952. This would make intron 6 38 nt in length. Although this splice site maintains the reading frame, the resulting intron is too short to be considered as more than purely conjectural. MZEF predicts the 5' end of exon 7 at 28908. Although the resulting intron 6 is 82 nt, the reading frame is not preserved. Neither NetPlantGene nor GRAIL predict splice acceptors in this region. I have chosen an AG "consensus" splice acceptor at 28898 in order that the reading frame be preserved and preserved in a manner that good similarity to other proteins is maintained. The 8 amino acids bridging this splice site are highlighted in blue in the multiple sequence alignment below. It should be noted though that this gene could be processed in a manner different to the model presented here or it could encode a pseudogene.

Alternate exons not used in building the gene model:   GenScan predicts that genes T2H3.9 and T2H3.J are joined as a single gene. Exons near T2H3.J are described. GenScan predicts exons from 29969 to 30021, from 28827 to 28952, from 27801 to 27857 and a terminal exon from 25773 to 25879. GRAIL predicts internal exons from 29571 to 29663, from 28088 to 28185, from 27801 to 27882 and from 25697 to 25731. MZEF predicts exon 2 from 30138 to 30151, from 28827 to 28909, from 27921 to 28102 and from 25663 to 25731. NetPlantGene predicts many splice sites in the region of T2H3.H. Notable splice sites include acceptors at 29681 (confidence score of 0.94), 29659 (0.97), 28009 (0.90) and donors at 30138 (0.92) and 25355 (0.96).

Complete CDS of T2H3.9

TGTCTGTGGAATGTGTGAACATATGTAATCTAACGAAAGGAGATGGGAATGCAAGAAGCG
ATTGCAGTGCTCTCTCCTGTGCTTGGAAAGCTCCAAGAGCGTTAACTGGGTTTCTAGCTA
GCACTGCTCATCCACCTGTGTGTTCTGTGTATTCATGTGGCAGAAATGGAAGAAAGAGCA
GAATGAAAGCTTGCGCCTGGCAGAGGTATGAATATGAAGTAGGCTTTTCTGAGGCTCCTT
ACTTTGTAAATGTGAGAAATATCTTGAAGTCCAGATTATCTTGTGGTGGTCATAAAAGAT
GGGAACTGTATTGCGTATCAGCTGAATCTTCTTCTGGTGCATCCAGTGATGTTACCGTCG
AAACATTGTGGGAGGACCTTTTCCCATCAATATCTTATCTACCCCGTAAAGAATTAGAAT
TTGTTCAAAAGGGCCTTAAGGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATG
ACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
CTGTGCGTCACATCGTAGAAGGGGAGACCAAGGTGTCAAAACTGGGAAAGTTAAAGTGTA
AAACGGAAAGTGAAACAATACAAGATGTAAAAGCAGATGATTTGCGGCAGATGTTTCTGG
CGATGACAGACGAGGTCCGCGTCATTATTGTCAAACTAGCTGACCGGTTGCATAATATGC
GAACTCTCTGCCACATGCCTCCCCATAAGCAGTCCAGCATTGCAGGGGAGACTTTGCAGG
TCTTTGCTCCTTTAGCAAAATTATTGGGAATGTATTCAATAAAGTCTGAACTGGAAAATC
TGTCTTTCATGTACGTAAGTGCTGAGGATTATGATAGAGTCACTAGCAGGATTGCTAACC
TCTACAAAGAGCATGAAAAAGAACTCACTGAGGCAAACAGAATTTTGGTGAAAAAGATTG
AAGATGATCAGTTTCTGGACCTTGTGACTGTGAATACTGATGTTCGATCTGTTTGCAAGG
AAACTTACAGCATCTACAAAGCTGCTCTCAAATCGAAAGGATCAATTAATGATTACAACC
AGATTGCTCAGCAGTTACGGATTGTTGTAAAGCCAAAACCATCTGTAGGGGTCGGGCCTT
TGTGCAGTCCACAACAGGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGA
GCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTCAGA
TCAGAACCGAGGAGATGGACTTGATTGCTGAAAGGGGCATTGCTGTTTACTACAATGGCA
AGTCTCTATCTACTGGATTAGTTGGAAACGCGGTTCCTTTAGGTAGAAATTCAAGGGGGA
AGACGGGTTGCCTCAACAATGCAGATTTTGCACTCAGGGTTGGGTGGCTAAATGCAATAA
GGGAATGGCAAGAGGAGTTTGTGGGTAACATGAGCTCTAGAGAATTTGTGGATACCATTA
CGAGGGATCTTTTAGGTAGTCGTGTGTTTGTATTCACACCTAAAGGAGAGATAAAGAACC
TCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACA
AGATGGTAGCAGCAAAGGTCAATGGTAATCTTGTTTCCCCAACTCACGTTCTTGAGAATG
CTGAGGTCGTGGAGATAGTCACCTACAACGCCCTCTCAAGTAAATCTGCTTTCCAAAGAC
ATAAACAGTGGTTGCAACATGCCAAAACAAGGAGTGCAAGACACAAGATTATGAGGTTCC
TAAGGGAGCAAGCTGCACAATGTGCTGCCGAAATTACCCAGGATCAAGTGAATGACTTTG
TGGCGGACTCTGATAGTGATGTGGAAGATCTCACAGAAGATTCAAGAAAGAGCCTACAAT
GGTGGGAGAAAATCCTCGTCAATGTTAAGCAATTCCAGTCACAAGACAAAAGTAGAGATA
CAACACCCGCTCCTCAAAACGGAAGCGTTTGGGCCCCAAAGGTGAATGGAAAACACAACA
AAGCCATAAAGAACTCGAGTTCTGATGAGCCAGAGTTCCTCCTACCTGGAGATGGAATTG
CCAGGATTTTACCTGCTAATATCCCTGCTTATAAGGAAGTGTTGCCCGGCTTAGACAGTT
GGCGAGACAGTAAAATTGCCACATGGCATCATCTCGAAGGTCAGTCCATCGAATGGTTAT
GTGTAGTATCCATGGATCGCAAAGGCATAATCGCAGAGGTTACAACAGTCCTCGCAGCTG
AAGGCATTGCATTATGTTCTTGCGTGGCCGAGATTGACAGAGGAAGAGGATTAGCAGTAA
TGTTATTTCAAATAGAAGCAAACATTGAAAGTTTGGTAATATGTCCTGTTGATCTAAACT
CTCTTTTAACTCTTGTTTTTGTTCTTTTTGGATCTTCGATCACTAAACACTAA

 

Protein translation of T2H3.9

SVECVNICNLTKGDGNARSDCSALSCAWKAPRALTGFLASTAHPPVCSVYSCGRNGRKSR
MKACAWQRYEYEVGFSEAPYFVNVRNILKSRLSCGGHKRWELYCVSAESSSGASSDVTVE
TLWEDLFPSISYLPRKELEFVQKGLKELDWESIVAGLLHDTVEDTNFITFEKIEEEFGAT
VRHIVEGETKVSKLGKLKCKTESETIQDVKADDLRQMFLAMTDEVRVIIVKLADRLHNMR
TLCHMPPHKQSSIAGETLQVFAPLAKLLGMYSIKSELENLSFMYVSAEDYDRVTSRIANL
YKEHEKELTEANRILVKKIEDDQFLDLVTVNTDVRSVCKETYSIYKAALKSKGSINDYNQ
IAQQLRIVVKPKPSVGVGPLCSPQQVKDYIATPKPNGYQSLHTTVIPFLYESMFRLEVQI
RTEEMDLIAERGIAVYYNGKSLSTGLVGNAVPLGRNSRGKTGCLNNADFALRVGWLNAIR
EWQEEFVGNMSSREFVDTITRDLLGSRVFVFTPKGEIKNLPKGATVVDYAYLIHTEIGNK
MVAAKVNGNLVSPTHVLENAEVVEIVTYNALSSKSAFQRHKQWLQHAKTRSARHKIMRFL
REQAAQCAAEITQDQVNDFVADSDSDVEDLTEDSRKSLQWWEKILVNVKQFQSQDKSRDT
TPAPQNGSVWAPKVNGKHNKAIKNSSSDEPEFLLPGDGIARILPANIPAYKEVLPGLDSW
RDSKIATWHHLEGQSIEWLCVVSMDRKGIIAEVTTVLAAEGIALCSCVAEIDRGRGLAVM
LFQIEANIESLVICPVDLNSLLTLVFVLFGSSITKH*

 

Multiple Sequence Analysis

T2H3.9 is aligned with bacterial GTP pyrophosphokinases (RelA gene products) from Bacillus subtilis, Staphylococcus aureus and Myxococcus xanthus. In B. subtilis this enzyme catalyzes the production of guanosine 3'-diphosphate 5'-triphosphate (EC 2.7.6.5) from ATP + GTP.

          1                                                         60
BsubRelA  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SaurRelA  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 MyxRelA  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  T2H3.H  SVECVNICNLTKGDGNARSDCSALSCAWKAPRALTGFLASTAHPPVCSVYSCGRNGRKSR

          61                                                       120
BsubRelA  ~~~~~~~~~~~~~~~~~~~~~~~~~MANEQVLTAEQVIDKARSYLSDEHIAFVEKAYLYA
SaurRelA  ~~~~~~~~~~~~~~~~~~MNGVYHIMNNEYPYSADEVLHKAKSYLSADEYEYVLKSYHIA
 MyxRelA  ~~~~~~~~~~~~MWGNVAPPLVQSYDCSSFDDSPERHPPTVSQYHPDPDLDIIKKAYVYS
  T2H3.9  MKACAWQRYEYEVGFSEAPYFVNVRNILKSRLSCGGH.KRWELYCVSAESSSGASSDVTV

          121                                                      180
BsubRelA  EDAHREQYRKSGEPYIIHPIQVAGILVDLEMDPSTIAGGFLHDVVEDTD.VTLDDLKEAF
SaurRelA  YEAHKGQFRKNGLPYIMHPIQVAGILTEMRLDGPTIVAGFLHDVIEDTP.YTFEDVKEMF
 MyxRelA  AKVHQGQLRKSGEPYLVHPLEVAGILGELKLDEASIVTGLLHDTIEDTL.ATEEELTELF
  T2H3.9  ETLWEDLF..PSISYLPRKELEFVQKGLKELDWESIVAGLLHDTVEDTNFITFEKIEEEF

          181                                                      240
BsubRelA  SEEVAMLVDG...VTKLGKIKYK....SQEEQQAENHRKMFVAMAQDIRVILIKLADRLH
SaurRelA  NEEVARIVDG...VTKLKKVKYR....SKEEQQAENHRKLFIAIAKDVRVILVKLADRLH
 MyxRelA  GSEVAHLVDG...VTKLSKFSASA.SLSQEEKQAENFRKMIIAMAQDIRVILVKLADRTH
  T2H3.9  GATVRHIVEGETKVSKLGKLKCKTESETIQDVKADDLRQMFLAMTDEVRVIIVKLADRLH

          241                                                      300
BsubRelA  NMRTLKHLPQEKQRRISNETLEIFAPLAHRLGISKIKWELEDTALRYLNPQQYYRIVNLM
SaurRelA  NMRTLKAMPREKQIRISRETLEIYAPLAHRLGINTIKWELEDTALRYIDNVQYFRIVNLM
 MyxRelA  NMRTLDHMSEEKQARIAQETLDIYAPLANRLGISWIKTELEDLSFRYVKPQEFFALQAKL
  T2H3.9  NMRTLCHMPPHKQSSIAGETLQVFAPLAKLLGMYSIKSELENLSFMYVSAEDYDRVTSRI

          301                                                      360
BsubRelA  KKKRAERELYVDEVVNEVKKRVEE......VNIKADFSGRPKHIYSIYRKMVLQNKQFNE
SaurRelA  KKKRSEREAYIETAIDRIRTEMDR......MNIEGDINGRPKHIYSIYRKMMKQKKQFDQ
 MyxRelA  NKRKKEREKYIEDTCDLIRSKLAE......RGLKGEVSGRFKHVYSIYKKIKSQGIDFDQ
  T2H3.9  ANLYKEHEKELTEANRILVKKIEDDQFLDLVTVNTDVRSVCKETYSIYKAALKSKGSIND

          361                                                      420
BsubRelA  IYDLL.AVRILVNSIKDCYAVLGIIHTCWKPMPGRFKDYIAMPKPNMYQSLHTTVIGPKA
SaurRelA  IFDLL.AIRVIVNSINDCYAILGLVHTLWKPMPGRFKDYIAMPKQNLYQSLHTTVVGPNG
 MyxRelA  IHDII.AFRIIAPTAPSCYEALGLVHEMWKPVPGRFKDFIAIPKPNMYQSLHTTIIGPLS
  T2H3.9  YNQIAQQLRIVVKPKPS....VGVGPLC...SPQQVKDYIATPKPNGYQSLHTTVIPFLY

          421                                                      480
BsubRelA  D...PLEVQIRTFEMHEIAEYGVAAHWAYK.................EGKAANE.GATFE
SaurRelA  D...PLEIQIRTFDMHEIAEHGVAAHWAYK.................EGKKVSEKDQTYQ
 MyxRelA  E...RVEVQIRTSEMHKIAEEGIAAHWKYK.................EGKAVISKD...D
  T2H3.9  ESMFRLEVQIRTEEMDLIAERGIAVYYNGKSLSTGLVGNAVPLGRNSRGKTGCLNNADFA

          481                                                      540
BsubRelA  KKLSWFREILEFQNE...STDAEEFMESLKIDLFSDMVYVFTPKGDVIELPSGSVPIDFS
SaurRelA  NKLNWLKELAEADHT...SSDAQEFMETLKYDLQSDKVYAFTPASDVIELPYGAVPIDFA
 MyxRelA  EKFAWLRQLMEWQQD...LKDPKEFLETVKVDLFTDEVFVFTPKGDVRSLPRGATPVDFA
  T2H3.9  LRVGWLNAIREWQEEFVGNMSSREFVDTITRDLLGSRVFVFTPKGEIKNLPKGATVVDYA

          541                                                      600
BsubRelA  YRIHSEIGNKTIGAKVNGKMVTLDHKLRTGDIVEILT.....SKHSYGPSQDWVKLAQTS
SaurRelA  YAIHSEVGNKMIGAKVNGKIVPIDYILQTGDIVEIRT.....SKHSYGPSRDWLKIVKSS
 MyxRelA  YAIHSDVGNRCVGAKVNGKIVPLRYKMKNGDTVEVLT.....SPQQH.PSKDWLTFVKTS
  T2H3.9  YLIHTEIGNKMVAAKVNGNLVSPTHVLENAEVVEIVTYNALSSKSAFQRHKQWLQHAKTR

          601                                                      660
BsubRelA  QAKHKIRQFFKKQRREENVEKGRELVEKEIKNLDFELKDVLTPENIQKVADKFNFSNEED
SaurRelA  SAKGKIKSFFKKQDRSSNIEKGRMMVEVEIKEQGFRVEDILTEKNIQVVNEKYNFANEDD
 MyxRelA  RAQQRIRGFIKQQQREKSLQLGRELADRELKRFQLNFNRLLKSGEMKKAAVDLGFRVEDD
  T2H3.9  SARHKIMRFLREQAAQCAAEITQDQVNDFVADSDSDVEDLTEDSRKSLQWWEKILVNVKQ

          661                                                      720
BsubRelA  MYAAVGYNGITALQVANRLTEKE..........RKQRDQEEQEKIVQEVTGEPKP....Y
SaurRelA  LFAAVGFGGVTSLQIVNKLTERQ...........RILDKQRALNEAQEVT.KSLP....I
 MyxRelA  MLVAIGYGKVTPQQLSHRLVPQE...KLNAAEAGGRADANPAATTSGGAGNSVLPGLSRV
  T2H3.9  FQSQDKSRDTTPAPQNGSVWAPKVNGKHNKAIKNSSSDEPEFLLPGDGIARILPANIPAY

          721                                                      780
BsubRelA  PQ......GRKREAGVRVKGIDNLLVRLSKCCNPVPGDDIVGFITKGRGVSVHREDCPNV
SaurRelA  KD......NIITDSGVYVEGLENVLIKLSKCCNPIPGDDIVGYITKGHGIKVHRTDCPNI
 MyxRelA  TDLAKRLVGRSNRSGVQIGGVDDVLVRFGRCCNPVPGDPIAGFITRGRGVTVHTVGCEKA
  T2H3.9  KEVLPGLDSWRDSKIATWHHLEGQSIEW.LCVVSMDRKGIIAEVTTVLAAEGIAL.CSCV

          781                                                      840
BsubRelA  KTNEAQERLIPVEWEHESQVQKRKEYNVEIEILGYDRRGLLNEVLQAVNETKTNISSVSG
SaurRelA  K.NET.ERLINVEWVKSKDATQK..YQVDLEVTAYDRNGLLNEVLQAVSSTAGNLIKVSG
 MyxRelA  LATD.PERRVDVSW....DVRGDFKRPVTLRVLTADRPGLLADITNTFSKKGVNISQANC
  T2H3.9  AEIDRGRGLAVMLFQIEANIESLVICPVDLNSLLTLVFVLFGSSITKH*~~~~~~~~~~~

          841                                     883
BsubRelA  KSDRNKVATIHMAIFIQNINHLHKVVERIKQIRDIYSVRRVMN*
SaurRelA  RSDIDKNAIINISVMVKNVNDVYRVVEKIKQLGDVYTVTRVWN*
 MyxRelA  RATGDDRAVNTFEVIISDLKQLTDLMRTIERLQGVYSVERI*~~
  T2H3.9  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

written 14 Sep 98
updated 15 Sep 98
Larry Parnell