Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_900115975.1:WP_092482996.1 Length = 396 Score = 229 bits (583), Expect = 1e-64 Identities = 141/392 (35%), Positives = 216/392 (55%), Gaps = 38/392 (9%) Query: 30 RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89 R E + +WD +GRE++DF GGIAV + GH HP V+ A+QEQ +L H + EP Sbjct: 27 RGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVS-NLYYIEPQAR 85 Query: 90 LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIAFTGAYHGRT 143 LAE + + D + SG+EA E A+K+AR + +I ++HGRT Sbjct: 86 LAELLVQNSCCD---RVFFCNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGRT 142 Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203 + + TG+ Y G +P G V +D A +ER A A Sbjct: 143 LAAITATGQP-KYQQGFEPLPPGF---------KYVPFNDPDA-LER-----AIGPHTCA 186 Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263 +++EPVQGEGG Y + ++ +R LCD++G+LL+ DEVQ G GRTG F A + + PD Sbjct: 187 VMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEPD 246 Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323 + T AK++GGGFPI + K + A APG T+ G+P+ACAA LA ++ + +++ Sbjct: 247 IITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGDGVMQ 306 Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383 +AVG K L+++ K+ I +VRGLG ++ +EL ++P ++V+ R RE Sbjct: 307 NCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMEL------NRPGGDIVN----RCRE 356 Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415 KGL L++C NV+RF P+ I ++++ L Sbjct: 357 KGL-LINC-VNNNVLRFTPPLVIGTEEVDRAL 386 Lambda K H 0.319 0.137 0.393 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: 414 Number of extensions: 21 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: 426 Length of database: 396 Length adjustment: 31 Effective length of query: 395 Effective length of database: 365 Effective search space: 144175 Effective search space used: 144175 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