Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_011996059.1 XAUT_RS02030 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000017645.1:WP_011996059.1 Length = 395 Score = 212 bits (539), Expect = 2e-59 Identities = 130/369 (35%), Positives = 202/369 (54%), Gaps = 8/369 (2%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L Q +++L IGQPDF TP H+ AA KA+ + YTP+ G L LR+AV + ++ Sbjct: 26 LAGQGRSILNLGIGQPDFRTPDHIVEAAVKALRDGQHGYTPSVGILPLREAVAADLNRRY 85 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVD- 141 D + ++I G + AA R PG E++ P P +P Y +I GA PV V Sbjct: 86 GVEVDPDL-VMIMPGGKVTMYAAIRLFGEPGAEILYPDPGFPIYRSMIEHTGATPVPVPI 144 Query: 142 TTSHGFKLTARLIEDALTPNTKCVVLPYPSNPT-GVTLSEEELKSIAALLKGRNVFVLSD 200 +GF +A +TP T+ +++ P+NPT GVT + E K + L +V ++SD Sbjct: 145 REENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPAAEIDKLVKGLAAHPHVALMSD 204 Query: 201 EIYSELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVH 257 EIY +D H ++ Y +RD+ I++NG SK+++MTGWR+G+ PKD+ + K+ Sbjct: 205 EIYDRFLFDGEEHRTLLAYPQIRDRLILLNGWSKTYAMTGWRLGYSIWPKDLYDKVRKLA 264 Query: 258 QYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFY 316 SC ++ +Q A + A+ D M ++ R V D L ++ G+ P GAFY Sbjct: 265 VNCWSCVNAATQYAGIAALEGPQDAVDAMTAEFDARRRIVVDGLNALPGVRCATPKGAFY 324 Query: 317 IFPSIKSFGMT-SFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRL 375 FP++ G + + + ALLE+AGVA++ G F YGEGY+RLS+A S + + L R+ Sbjct: 325 AFPNVSGTGWSEAKKLASALLEEAGVAVIGGPDFGVYGEGYLRLSYATSRENIAAALARM 384 Query: 376 ELFVLKKRE 384 F+ R+ Sbjct: 385 GDFLAANRK 393 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: 400 Number of extensions: 25 Number of successful extensions: 7 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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 Jul 25 2024. The underlying query database was built on Jul 25 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