Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Ac3H11_3991 Glutamate-1-semialdehyde aminotransferase (EC 5.4.3.8)
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3991 Length = 434 Score = 156 bits (395), Expect = 1e-42 Identities = 122/361 (33%), Positives = 171/361 (47%), Gaps = 35/361 (9%) Query: 5 NESLLKRRQAAVPRGVGQI---------HPVVAERAENSTVWDVEGREYIDFAGGIAVLN 55 N L +R +A +P GV P +RA+ + WD + +ID+ G + Sbjct: 8 NIPLFERAKALIPGGVNSPVRAFKAVGGTPRFVKRAQGAYFWDANDQRFIDYIGSWGPMI 67 Query: 56 TGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEA 115 GH HP V+ AVQ L F E +ELAEEI VP + LV+SG+EA Sbjct: 68 LGHGHPAVLEAVQS--AALEGFSFGAPT-EREVELAEEILGLVPS--MEMIRLVSSGTEA 122 Query: 116 VENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMP-GGIFRALAPC 174 +A+++AR ATGR+ I F G YHG L AG GL G A P Sbjct: 123 GMSAIRLARGATGRSKFIKFEGCYHGHADSLL--------VKAGSGLATFGNATSAGVPP 174 Query: 175 ELHG---VSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCD 231 E+ V E +++A +E F +++A ++IEP+ G S FM+R R LC Sbjct: 175 EVVQHTIVLEYNNVAQLEEAFA--LHGKELACVMIEPIAGNMNLVRASVPFMKRCRELCT 232 Query: 232 QHGILLIADEVQTG----AGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIM 287 +HG LL+ DEV TG G + +A G PDLT K +GGG P++ G IM Sbjct: 233 EHGALLVLDEVMTGFRVALGSAQSVYAKSIPGFKPDLTVLGKVIGGGMPLAAFGGPRAIM 292 Query: 288 DAIAP-GGL--GGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHK 344 + +AP GG+ GT +G+P+A A LA L+ ++ + A L GL A Sbjct: 293 EHLAPLGGVYQAGTLSGNPVATACGLATLREIKKPGFFDALSARTRSLVDGLAAAAAAEG 352 Query: 345 V 345 V Sbjct: 353 V 353 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: 472 Number of extensions: 32 Number of successful extensions: 5 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: 434 Length adjustment: 32 Effective length of query: 394 Effective length of database: 402 Effective search space: 158388 Effective search space used: 158388 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 17 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