Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_900115975.1:WP_092482996.1 Length = 396 Score = 209 bits (533), Expect = 9e-59 Identities = 136/403 (33%), Positives = 202/403 (50%), Gaps = 48/403 (11%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA--FNAAPHGPYL 78 G A +WD DG+ ++DFVGGI V +LGHC+PAVV AIQ QA RL H + + P Sbjct: 28 GEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVSNLYYIEPQARLA 87 Query: 79 ALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGR 132 L+ Q S V + NSGAEA E A+K+AR K II + FHGR Sbjct: 88 ELLVQNSCCDRVFF------CNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGR 141 Query: 133 TLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVA 192 TLA + G+ Y+Q LP ++P+ D A++R Sbjct: 142 TLAAITATGQ-PKYQQGFEPLPPGFKYVPFNDPD----------ALERAIGPH-----TC 185 Query: 193 AFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEP 252 A + EPVQGEGG A + +R CD G+L++ DE+Q G GRTG+ A+ +EP Sbjct: 186 AVMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEP 245 Query: 253 DLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLA 312 D++ LAK++ GG P+GA++ ++ + AA G T+ GNP++CAA LA++ M + Sbjct: 246 DIITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGD--- 302 Query: 313 TWGERQEQAIVSRYERWKASGLS---PYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369 G Q V Y + K L+ +I + G+G + G+E G ++ Sbjct: 303 --GVMQNCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRPGGD--------IVN 352 Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 R +GLL+ + +++R PL I E ++ L+ +E L Sbjct: 353 RCREKGLLI--NCVNNNVLRFTPPLVIGTEEVDRALETVEAVL 393 Lambda K H 0.320 0.137 0.402 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: 418 Number of extensions: 15 Number of successful extensions: 4 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: 416 Length of database: 396 Length adjustment: 31 Effective length of query: 385 Effective length of database: 365 Effective search space: 140525 Effective search space used: 140525 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 Sep 17 2021.
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