Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_014026152.1 PYRFU_RS02975 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000223395.1:WP_014026152.1 Length = 401 Score = 147 bits (370), Expect = 7e-40 Identities = 110/368 (29%), Positives = 178/368 (48%), Gaps = 19/368 (5%) Query: 25 AQHEDVISLTIGQPDFFTPHH-VKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKAD 83 A+ + VI LT+GQPD P V+ A +A + Y P G E R+AV YM+ Sbjct: 28 AKRKPVIDLTLGQPDVTPPQTLVELLATEARGVGASRYPPPQGLAEYREAVASYMRDF-- 85 Query: 84 FNYDAESE-IIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 + DAE E ++ GA I AA ++ GD +++ P + Y + G KPV+ Sbjct: 86 YGVDAEPERVVALAGAKPGIAAAIYSVCDHGDAMLVLTPHFYAYVNAARMLGVKPVMARL 145 Query: 143 TSHGFKL--TARLIEDALTPNTKC-VVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLS 199 G +L ++ A + C V++ P NPTG+ L E LK I L N VLS Sbjct: 146 RWDGGRLFIDEDEVKKAFEEHKPCLVIVNTPHNPTGLHLDRETLKLIGDLASEHNTLVLS 205 Query: 200 DEIYSELTYDRPHYSIATYLRDQTIV-INGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQ 258 DE+YS L + H + L ++ ++ + SK+ ++ GWR+GFL+AP+++ K + + Sbjct: 206 DEVYSWLVFRGEHVPLLRLLGEERVIHLESFSKTLAIPGWRVGFLYAPREVVKATVFFNS 265 Query: 259 YNVSCASSISQKAALEAVTNGFDDALIMREQYKK---RLDYVYDRLVSM---GLDVVKPS 312 + Q A + +T +D + E+ +K R V+ +S +DV +P+ Sbjct: 266 NVYTGIPRFIQLAVAKYITAYREDMVEYVERVRKLYGRRARVFTEALSQLEDLIDVYEPA 325 Query: 313 GAFYIFPS----IKSFGMTSFDFSMALL-EDAGVALVPGSSFSTYGEGYVRLSFACSMDT 367 F++FP I+ G+ S + + L+ + GV VPG+ F GY+R+S Sbjct: 326 AGFFLFPRVERLIEKLGVGSAERLVELMAREVGVLAVPGTVFGEEWRGYIRVSLTAPESR 385 Query: 368 LREGLDRL 375 LRE R+ Sbjct: 386 LREAAARI 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: 311 Number of extensions: 19 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: 401 Length adjustment: 31 Effective length of query: 362 Effective length of database: 370 Effective search space: 133940 Effective search space used: 133940 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