Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate AO356_12620 AO356_12620 amino acid dehydrogenase
Query= reanno::psRCH2:GFF3724 (432 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12620 AO356_12620 amino acid dehydrogenase Length = 434 Score = 751 bits (1938), Expect = 0.0 Identities = 370/433 (85%), Positives = 400/433 (92%), Gaps = 1/433 (0%) Query: 1 MRVLVLGSGVVGTASAYYLARAGFEVVVVDRQPAVAMETSFANAGQVSPGYASPWAAPGV 60 MRVLVLGSGV+GT SAYYLARAGFEVVVVDRQPA AMETSFANAGQVSPGYASPWAAPGV Sbjct: 1 MRVLVLGSGVIGTVSAYYLARAGFEVVVVDRQPAPAMETSFANAGQVSPGYASPWAAPGV 60 Query: 61 PLKAMKWLLQRHAPLAIKLTGDVDQYLWMAQMLRNCTAARYAVNKERMVRLSEYSRDCLD 120 PLKA+KWLLQRHAPLAIK T D+DQYLWMAQMLRNCTA+RYA+NKERMVRLSEYSRDCLD Sbjct: 61 PLKAIKWLLQRHAPLAIKATADIDQYLWMAQMLRNCTASRYAINKERMVRLSEYSRDCLD 120 Query: 121 ELRAETGIAYEGRQLGTTQLFRTQAQLDAAAKDIAVLERSGVPYELLDRAAIGRVEPALA 180 ELRAETGIAYEGR LGTTQLFRTQAQLD AAKDIAVL+ SGVP+E+LDR I RVEPALA Sbjct: 121 ELRAETGIAYEGRSLGTTQLFRTQAQLDGAAKDIAVLKESGVPFEVLDREGIARVEPALA 180 Query: 181 KVAHKLSGALRLPNDQTGDCQMFTSRLAEMALALGVEFRFGQNIQRLEHAGDRIAGVWID 240 V L+GALRLPNDQTGDCQMFT+RLAEMA+ LGV+FRFGQ+IQRL+ AGDRI GVWID Sbjct: 181 NVTDILAGALRLPNDQTGDCQMFTTRLAEMAVKLGVQFRFGQDIQRLDFAGDRINGVWID 240 Query: 241 GKLETADRYVLALGSYSPQMLKPLGIRAPVYPLKGYSLTVPISDPAMAPQSTVLDETYKV 300 GKLETADRYVLALGSYSPQ+LKPLGIRAPVYPLKGYSLTVPI++PAMAP ST+LDETYKV Sbjct: 241 GKLETADRYVLALGSYSPQLLKPLGIRAPVYPLKGYSLTVPITNPAMAPTSTILDETYKV 300 Query: 301 AITRFDQRIRVGGMAEIAGHDLSLNPRRRETLEMVVGDLYPQGGDPAEAVFWTGLRPATP 360 AITRFD RIRVGGMAEIAG DLSLNPRRRETLEM+V DLYPQGGD AEA FWTGLRP TP Sbjct: 301 AITRFDNRIRVGGMAEIAGFDLSLNPRRRETLEMIVNDLYPQGGDLAEASFWTGLRPTTP 360 Query: 361 DGTPIIGATAYRNLYLNTGHGTLGWTMACGSGRVLADLLASKRPQISTDGLDIFRYG-KH 419 DGTPI+GAT ++NL+LNTGHGTLGWTMACGSGR+LADL+A K+PQIS +GLDI RYG K Sbjct: 361 DGTPIVGATPFKNLFLNTGHGTLGWTMACGSGRLLADLMAKKKPQISAEGLDISRYGSKT 420 Query: 420 KETRKHAHPAAAH 432 +E+ KH +PA AH Sbjct: 421 QESAKHVNPAPAH 433 Lambda K H 0.320 0.135 0.405 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: 720 Number of extensions: 16 Number of successful extensions: 2 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: 432 Length of database: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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