Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_015799315.1 AFER_RS10005 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000023265.1:WP_015799315.1 Length = 383 Score = 167 bits (424), Expect = 4e-46 Identities = 110/361 (30%), Positives = 182/361 (50%), Gaps = 8/361 (2%) Query: 21 SNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKK 80 S L +H + I+L G PD P A +++ Y P G ELR V + Sbjct: 11 SRLATEH-NAINLGQGFPDTPGPALAIEAGVRSLRAGHNQYAPAGGVPELRTRVASIWSQ 69 Query: 81 KADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIV 140 + D ++ IT GA++AI AA L PGDE I+ P Y Y + + GA PV V Sbjct: 70 RLGRPIDPLRDVTITVGATEAIAAACLAWLEPGDEAIVLEPAYDAYLWAVRMAGATPVGV 129 Query: 141 DTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSD 200 D S +L A +E A+TP T+ +++ P NP+G+ +S+EEL +I+A+ ++ VLSD Sbjct: 130 DLGST-MRLDAERLEQAITPRTRMLIVNSPHNPSGMVVSDEELAAISAVATRHDLRVLSD 188 Query: 201 EIYSELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQ 258 E+Y L Y+ H SIAT+ + D+T+V++ +K+ +TGW++G+ P D+ + Q Sbjct: 189 EVYEFLVYEGSHRSIATFDAMADRTVVVSSAAKTFGLTGWKVGWAIGPADLVSEVRSQAQ 248 Query: 259 YNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIF 318 Y ++ Q A +A+ N ++R+ ++ D + D L +G + +++ Sbjct: 249 YLTYAGATPLQHAVADALGNLDLIVPLVRDPLARQRDVLVDGLAKLGFTPLATQAGYFVL 308 Query: 319 PSIKSF-GMTSFDFSMALLEDAGVALVPGSSFSTYGEG---YVRLSFACSMDTLREGLDR 374 + T+ + ++ L E AG+ +P F E +R SFA TLR+ L + Sbjct: 309 TDLGPVEAETATEAALILAERAGIVTIPIEPFYVEPERAPLVLRWSFARQATTLRDALAQ 368 Query: 375 L 375 L Sbjct: 369 L 369 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: 298 Number of extensions: 16 Number of successful extensions: 3 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: 383 Length adjustment: 30 Effective length of query: 363 Effective length of database: 353 Effective search space: 128139 Effective search space used: 128139 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 10 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