Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 202 bits (515), Expect = 2e-56 Identities = 123/356 (34%), Positives = 194/356 (54%), Gaps = 5/356 (1%) Query: 28 EDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYD 87 EDVI L++G PDF TP + AA A+ E T YT AG L LR+A+ + Sbjct: 32 EDVIILSVGDPDFPTPDFITDAAVDALREGDTHYTEIAGRLALREAIAARYSQLFGRELQ 91 Query: 88 AESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSH-G 146 A S +I GA A+ +L+ GDEV+ P+Y YE + GA V V + G Sbjct: 92 A-SNVINVAGAQNALFITSLCLLTAGDEVLALDPMYVTYEATLKASGATLVRVPCAADSG 150 Query: 147 FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSEL 206 F+L A ++ A+TP T+ + L P+NPTGV L+ EEL++IA L +++V+ DE+Y L Sbjct: 151 FRLDAAVLAKAITPRTRAIFLSNPNNPTGVVLNREELQAIADLAITHDLWVVVDEVYESL 210 Query: 207 TYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCA 264 ++R H S+A + ++ +VI LSKSH+MTGWRIG++ A + + H + + Sbjct: 211 AFEREHLSLAALPGMAERCVVIGSLSKSHAMTGWRIGWIVADETLVAHAETLMLSMLYGL 270 Query: 265 SSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSIKS 323 +AAL+AV + MRE Y++R D V L G+ V+ P ++ ++ Sbjct: 271 PGFVMEAALKAVQAHEEVTHGMREIYRRRRDLVVKGLSDCPGISVLTPDAGMFVLVDVRG 330 Query: 324 FGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFV 379 G++S +F+ LL +A V+++ ++F +G+VRLSF + L + R+ F+ Sbjct: 331 TGLSSLEFAWRLLREARVSVLDAAAFGEPAQGFVRLSFTLGEERLAQACQRIRDFI 386 Lambda K H 0.319 0.135 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 497 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 393 Length of database: 667 Length adjustment: 35 Effective length of query: 358 Effective length of database: 632 Effective search space: 226256 Effective search space used: 226256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory