Subject: Another new peptidase gene in Drosophila
I believe I have discovered a second previously unannotated gene in the
Drosophila genome. Sequence similarity was detected by a TBlastN search of
the NR database at NCBI using the sequence of the Thermoplasma proteasome
beta component (peptidase family T1) as a probe. A match was found with
GenBank entry AE003657, section 50 of 63 of the genomic scaffold
142000013386055 of Drosophila. The Drosophila homologue occupies bases
100613-101452 and is a continuous open reading frame from initiation
methionine to stop codon: there are no introns. I attach a file
(AE003657.Ret) showing a TFastX-derived alignment between this Drosophila
sequence and CG12323 protein (AAF58748 \- another Drosophila proteasome beta
subunit), and a file containing the complete amino acid sequence of the
newly identified gene (AE003657.AA).
In GenBank entry AE003657 the region 100613-101452 has not been defined as
containing a gene/
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Dr Neil D. Rawlings
MRC Molecular Enzymology Laboratory
Babraham Institute
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Please visit the MEROPS database, the URL is:
http://WWW.MEROPS.CO.UK/merops/Merops.htm
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AE003657.Ret:
TFASTXY compares a protein to a translated DNA data bank
version 3.2t06 July 29, 1999
Please cite:
Pearson et al, Genomics (1997)  46:24-36 
aaseq\AAF58748.aa, 282 aa
vs AE003657.dna library
256010 residues in 1 sequences
TFASTX (3.26 July 1999) function <up>optimized, BL50 matrix ( 15:-5 )</up> ktup: 2
join: 36, opt: 24, gap-pen: \-15/ \-2 shift: \-20, width: 16 reg.-scaled
The best scores are: initn init1 opt
AE003657 \- DNA sequence (99702) f 949 886 1006
AE003657 \- DNA sequence (99702) r 118 49 57
AE003657 \- DNA sequence (58298) r 94 44 57
AE003657 \- DNA sequence (99702) r 115 52 52
AE003657 \- DNA sequence (58298) f 70 47 51
AE003657 \- DNA sequence (99702) f 89 45 48
>>AE003657 \- DNA sequence (99702 aa)
Frame: f initn: 949 init1: 886 opt: 1006
Smith-Waterman score: 1006; 51.786% identity in 280 aa overlap
(1- 279:100613-101443 )
10 20 30 40 50
gi|730 MALAEICKISNAPYMRPNAW-SSADVEEEQKGLMCNLANPYTLAAPPFENPLHNLNQIQA
 ::: :: ... :.:. .. .: .. :: . :. :: .. :::.::: .......:
AE0036 MALESICGMDKLPFMKSFGYRTSKQTIEEIRVASSNMDNPLAIMAPPYENPRESVKKLNA
100640 100670 100700 100730 100760 100790
60 70 80 90 100 110
gi|730 NGDKTGVKINFDHGTTTLGFKFKGGVLLAVDSRATGGSYIGSQSMKKIVEINQFMLGTLA
.. :.:.:::::::.:: ..::..: ::::::.:. :::::..:.:..::...:: :
AE0036 LSE---VQIDFDHGTTTVGFVYQGGIILCVDSRATSGKLIGSQSIHKVVQVNQYIMGTTA
100820 100850 100880 100910 100940
120 130 140 150 160 170
gi|730 GGAADCVYWDRVLSKECRLHELRNKERISVAAASKIMANIAHEYKGMGLSMGMMLAGYDK
 ::::::.::::.:..:::::::: :::. : .:.: ..:.: ::::::: :::::::..
AE0036 GGAADCTYWDRALTRECRLHELRYKERLPVQSAAKYISNVAAEYKGMGLCMGMMLAGWSP
100970 101000 101030 101060 101090 101120
180 190 200 210 220 230
gi|730 RGPGLYYVDSEGSRTPGNLFSVGSGSLYAYGVLDSGYHWDLEDKEAQELGRRAIYHATFR
.::.: ::::.: : :.::.::::. : :.::: :. :: :.:: .:. :.::::.
AE0036 EGPSLVYVDSNGLRIHGKLFAVGSGAPNALGILDSDYRLDLSDNEAYDLAFLAVYHATMT
101150 101180 101210 101240 101270 101300
240 250 260 270
gi|730 DAYSGGIIRVYHIKEDGWVNISNTDCMELHYMYQEQLKQQ
 : .:::..:.::. . .: :..: ::.::: .:. .::
AE0036 DIFSGGVVRLYHMDQGNWRNVANKDCQELHEQYSGVGNQQ
101330 101360 101390 101420
>>AE003657 \- DNA sequence (99702 aa)
Frame: r initn: 118 init1: 49 opt: 57
Smith-Waterman score: 58; 33.333% identity in 27 aa overlap (68- 94:63554-63474 )
70 80 90
gi|730 INFDHGTTTLGFKFKGGVLLAVDSRAT
.....:: .. . :::..: .::. :
AE0036 VSMQNGTMYISENCKGGTFLPLDSHPT
63540 63510 63480
>>AE003657 \- DNA sequence (58298 aa)
Frame: r initn: 94 init1: 44 opt: 57
Smith-Waterman score: 58; 29.268% identity in 41 aa overlap
(14- 51:252897-252775 )
20 30 40 50
gi|730 YMRPNAWSSADVEE---EQKGLMCNLANPYTLAAPPFENPL
 : : ::. ..:. .. .: ..: .:: : ..: :
AE0036 YGRVRAWQPLNIEQIRGTWNNKICPISNXGNLAFPXIRNXL
252880 252850 252820 252790
>>AE003657 \- DNA sequence (99702 aa)
Frame: r initn: 115 init1: 52 opt: 52
Smith-Waterman score: 61; 32.653% identity in 49 aa overlap
(49- 96:142982-142839 )
50 60 70 80 90
gi|730 NPLH-NLNQIQANGDKTGVKINFDHGTTTLGFKFKGGVLLAVDSRATGG
 : :: : :: ...: .:. . : .:.::.. . :.: .: :
AE0036 NGLHXNXNQTKTQG-XNGITTTVTHQATALGYSNHTEDLIASXLKARRG
142980 142950 142920 142890 142860
>>AE003657 \- DNA sequence (58298 aa)
Frame: f initn: 70 init1: 47 opt: 51
Smith-Waterman score: 69; 20.548% identity in 73 aa overlap
(6- 74:198602-198820 )
10 20 30 40 50 60
gi|730 ICKISNAPYMRPNAWSSADVE----EEQKGLMCNLANPYTLAAPPFENPLHNLNQIQANG
.:.:. .: .:. ::. .. . :.: :.. ..: : . . . . :
AE0036 MCSINXIAKIRTSAFVSAEYVXMFIDQPSHLLCALSTIFALKPQKFCXIFIKNTWLGNCG
198620 198650 198680 198710 198740 198770
70
gi|730 DKTGVKINFDHGT
. .:.:... :.
AE0036 SCVGIKMSLRSGS
198800
>>AE003657 \- DNA sequence (99702 aa)
Frame: f initn: 89 init1: 45 opt: 48
Smith-Waterman score: 60; 26.087% identity in 46 aa overlap (23- 68:80498-80635 )
30 40 50 60
gi|730 ADVEEEQKGLMCNLANPYTLAAPPFENPLHNLNQIQANGDKTGVKI
 ::: . . : . .: .: :..:: .. .. :.:. .. :.
AE0036 ADVLQIDPGPSSIFRSPEVLFQKRFQSPLDDFXHVLAGGSGNSHKL
80510 80540 80570 80600 80630
282 residues in 1 query sequences
256010 residues in 1 library sequences
Scomplib <up>version 3.2t06 July 29, 1999</up>
start: Fri Feb 09  14:55:45  2001 done: Fri Feb 09  14:56:32  2001
Scan time: 0.000 Display time: 47.000
Function used was TFASTXY
============================================================================
AE003657.AA:
>AE003657 \- proteasome beta subunit, Drosophila melanogaster
MALESICGMDKLPFMKSFGYRTSKQTIEEIRVASSNMDNPLAIMAPPYENPRESVKKLNA
LSEVQIDFDHGTTTVGFVYQGGIILCVDSRATSGKLIGSQSIHKVVQVNQYIMGTTA
GGAADCTYWDRALTRECRLHELRYKERLPVQSAAKYISNVAAEYKGMGLCMGMMLAGWSP
EGPSLVYVDSNGLRIHGKLFAVGSGAPNALGILDSDYRLDLSDNEAYDLAFLAVYHATMT
DIFSGGVVRLYHMDQGNWRNVANKDCQELHEQYSGVGNQQ
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