Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 210 bits (534), Expect = 7e-59 Identities = 142/401 (35%), Positives = 203/401 (50%), Gaps = 46/401 (11%) Query: 27 VAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEP 86 V R S VWD GRE +DFAGGIAV GH HP ++AA+ EQ GKL H + EP Sbjct: 27 VPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHIS-NIYTNEP 85 Query: 87 YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIAFTGAYH 140 + LA+++ V F + SG+EA E A K+AR + +I+ ++H Sbjct: 86 ALRLAKKL---VAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKFEIISALNSFH 142 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQD 200 GRT+ T+ + G+ YS G G I I + ND + Sbjct: 143 GRTLFTVTVGGQS-KYSDGFG---------------------PKIEGITHVPYNDLEALK 180 Query: 201 IA------AIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFA 254 A A+++EP+QGE G +++++ R LC++H LLI DEVQTG GRTG FA Sbjct: 181 AAISDKTCAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFA 240 Query: 255 TEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLK 314 GI PD+ T AKS+GGGFPI + EI ++ G G TY G+P+ACA A AV+ Sbjct: 241 YMHYGITPDILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVD 300 Query: 315 VFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELV 374 + ++LE +A ER KA L +I ++ V VRG G ++ L D K A Sbjct: 301 IVNTPEVLEGVKAKHERFKARLTQIGERYGVFSLVRGRGLLIGCVL---SDAWKGKA--- 354 Query: 375 SKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415 A ++ L++L G +V+R + I A +++GL Sbjct: 355 GAFCAAAEKEALMVLQAGP--DVVRLAPSLVIDQADIDEGL 393 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: 402 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: 426 Length of database: 406 Length adjustment: 31 Effective length of query: 395 Effective length of database: 375 Effective search space: 148125 Effective search space used: 148125 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