Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 222 bits (566), Expect = 1e-62 Identities = 127/355 (35%), Positives = 199/355 (56%), Gaps = 4/355 (1%) Query: 28 EDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYD 87 EDVI L++G PDF TP V+ AA A+ T YTP G ELR A+ + ++ + Sbjct: 32 EDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAALARDVARRTGLPVE 91 Query: 88 AESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSHGF 147 E+ +I+ GA + A ++ GDEV++P P+Y YE + GA V V + Sbjct: 92 PEN-VIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVAPDAATL 150 Query: 148 KLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSELT 207 +L + A+TP T+ + L P+NPTG+ +S EEL+++A L + +++V++DE+Y+ LT Sbjct: 151 RLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVADEVYASLT 210 Query: 208 YDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCAS 265 +DRPH IAT + ++T+ IN LSKSH+MTGWR G++ AP + H+ + + Sbjct: 211 FDRPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLALCMLYGLP 270 Query: 266 SISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSIKSF 324 Q+AAL AV G + MRE Y++R D + L S+ GL +KP ++ ++ Sbjct: 271 GFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMFMLVDVRGT 330 Query: 325 GMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFV 379 G+ + +F+ L + GV+++ +F G VRLSFA S L E R+ FV Sbjct: 331 GLPTMEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAELAEACRRIAAFV 385 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: 311 Number of extensions: 17 Number of successful extensions: 5 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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: 50 (23.9 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