Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_043743690.1 AMB_RS07030 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000009985.1:WP_043743690.1 Length = 384 Score = 154 bits (388), Expect = 5e-42 Identities = 111/352 (31%), Positives = 171/352 (48%), Gaps = 7/352 (1%) Query: 29 DVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYDA 88 DVI L +GQP P V AA +A+ YT G LR+ + + + + Sbjct: 32 DVIHLEVGQPSGQAPPKVLDAAARAVRTEPLGYTLALGRDSLRERIARHYHQAYGVSVVP 91 Query: 89 ESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-TSHGF 147 E + +TTG+S A AF PGD V + P YP Y I+ G + V+V S + Sbjct: 92 E-RVCVTTGSSAAFLLAFLAAFEPGDRVAVAAPGYPAYRNILESLGVECVLVPVGPSSRW 150 Query: 148 KLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSELT 207 ++TA ++ + VV+ PSNPTG LS E+ +A + + ++SDEIY +T Sbjct: 151 QITAEVLA-GVEGRLDGVVVASPSNPTGSMLSAHEVAELAGWCELHGIRLISDEIYHGIT 209 Query: 208 YDRPHYSIATYLR-DQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASS 266 Y R + A +VIN SK ++MTGWR+G++ P+D+A+ + + Q + Sbjct: 210 YGRAAATAAGMAAAPHAVVINSFSKYYAMTGWRLGWMVLPEDLARSVECLTQNLYISPPT 269 Query: 267 ISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPS-GAFYIFPSIKSFG 325 +SQ AA E+V + D+ Y+ D + L G D + PS GAFY++ + Sbjct: 270 LSQVAA-ESVFDCIDELEARVAAYRANRDILVAELPKAGFDRLAPSDGAFYLYADVSEMT 328 Query: 326 MTSFDFSMALLEDAGVALVPGSSFSTY-GEGYVRLSFACSMDTLREGLDRLE 376 S +F +L + GVA PG F G +R S+A S + + E RL+ Sbjct: 329 NDSREFCARMLAETGVACTPGVDFDPIEGHRTLRFSYAGSAEHMAEAARRLK 380 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: 310 Number of extensions: 20 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: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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