Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_054255500.1 BN2503_RS04745 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_001298675.1:WP_054255500.1 Length = 436 Score = 169 bits (428), Expect = 2e-46 Identities = 124/352 (35%), Positives = 172/352 (48%), Gaps = 35/352 (9%) Query: 5 NESLLKRRQAAVPRGVGQI---------HPVVAERAENSTVWDVEGREYIDFAGGIAVLN 55 N SL +R +A +P GV P RA+ + +WD G+ +ID+ G + Sbjct: 8 NLSLFERAKALIPGGVNSPVRAFRAVGGTPRFIARAQGAYMWDANGQRFIDYIGSWGPMI 67 Query: 56 TGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEA 115 GH HP V+ AVQ+ L F E +ELAEEI + VP + LV+SG+EA Sbjct: 68 LGHGHPAVLEAVQK--AALEGFSFGAPT-EREVELAEEIIRHVPS--MEMIRLVSSGTEA 122 Query: 116 VENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMP-GGIFRALAPC 174 +A+++AR ATGR+ +I F G YHG L AG GL G A P Sbjct: 123 GMSAIRLARGATGRSKIIKFNGCYHGHADSLL--------VKAGSGLATFGHATSAGVPA 174 Query: 175 ELHG---VSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCD 231 E+ V E + +A +E F +++A +I+EP+ G F S FM+R R LC Sbjct: 175 EVVQHTLVLEYNDVAQLEEAFA--LHGKEVACVIMEPIAGNMNFVRASVPFMRRARELCT 232 Query: 232 QHGILLIADEVQT----GAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIM 287 QHG LL+ DEV T G G +A + G PDLT K +GGG P++ G IM Sbjct: 233 QHGALLVIDEVMTGFRVGLGSAQGLYAQQIPGFAPDLTVLGKVIGGGMPLAAFGGPRAIM 292 Query: 288 DAIAPGG---LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGL 336 + +AP G GT +G+P+A A LA L+ + E+ A L GL Sbjct: 293 EQLAPLGPVYQAGTLSGNPVATACGLATLREIAKPGFYEQLAARTRALIDGL 344 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: 482 Number of extensions: 27 Number of successful extensions: 6 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: 436 Length adjustment: 32 Effective length of query: 394 Effective length of database: 404 Effective search space: 159176 Effective search space used: 159176 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. 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