Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AMB_RS19600 AMB_RS19600 succinyl-diaminopimelate desuccinylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Magneto:AMB_RS19600 Length = 379 Score = 94.7 bits (234), Expect = 4e-24 Identities = 107/362 (29%), Positives = 158/362 (43%), Gaps = 29/362 (8%) Query: 28 IRGYLESHGIAVDVLPGPEG--DRSNIFATIGPKEARGYIISGHMDVVPAAETGWTSDPF 85 + G LE G A + G + N++A +G EA +GH DVVP + GWT +PF Sbjct: 30 LAGALEELGFACHHIRSATGGPEIRNLYARLGT-EAPNLCFAGHTDVVPPGK-GWTVEPF 87 Query: 86 RLRVEADRLYGRGTTDMKGFLAAVLAAVPKLA--AMPLRRPLHLALSYDEEA-GCRGVPH 142 ++ RL+GRG+ DMKG +A +AAV +L P + L L ++ DEE G Sbjct: 88 AAGIDQGRLFGRGSADMKGAIACFVAAVARLLEDGAP-KGSLSLLITGDEEGPAVDGTVK 146 Query: 143 MIARLPELCRQPLGAIIGEPTGMRAIR-----AHKGKAAARLTVRGRSGHSSRPDQGLNA 197 ++ L + I+GEPT R + +G RLTV G GHS+ P N Sbjct: 147 VLDWLAARGERIDCCIVGEPTNPRKLGDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNP 206 Query: 198 IHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVK-GGQAVNIIPDSCEVEFEAR 256 I + +L + + EA G P S+L + TV G A N+IP F R Sbjct: 207 IPRLLDIL-RRLTEAPLDEGTPHFQA-----STLALTTVDVGNPATNVIPAEARAGFNIR 260 Query: 257 AISGVDPAELLAPVRKTAEALTTLGFEVEWQELSAYPALSLEPDAPLAALLE---ELTGR 313 A L +R T + G EVE + + + P A AL E E+TG Sbjct: 261 FNDLHSGASLERWIRDT---VAQAGGEVEIKVEVSGESFLTPPGALSDALAEAAFEVTGL 317 Query: 314 EALPAVSYGTEAGLFQRAGIDAIICGPGDIGRA-HKPDEYILIDELMACRAMVEALGARC 372 + S GT F + + G +G+ HK DE++ + ++ A + + R Sbjct: 318 RPELSTSGGTSDARFIKNHCPVVEFGL--VGQTMHKSDEHVSVADMEALTEIYRRVLVRL 375 Query: 373 TA 374 A Sbjct: 376 AA 377 Lambda K H 0.319 0.137 0.410 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: 349 Number of extensions: 18 Number of successful extensions: 2 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: 374 Length of database: 379 Length adjustment: 30 Effective length of query: 344 Effective length of database: 349 Effective search space: 120056 Effective search space used: 120056 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 (21.7 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