Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PfGW456L13_805 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_805 Length = 497 Score = 986 bits (2550), Expect = 0.0 Identities = 497/497 (100%), Positives = 497/497 (100%) Query: 1 MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQ 60 MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQ Sbjct: 1 MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQ 60 Query: 61 RAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYID 120 RAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYID Sbjct: 61 RAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYID 120 Query: 121 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP Sbjct: 121 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180 Query: 181 ALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTL 240 ALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTL Sbjct: 181 ALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTL 240 Query: 241 VFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGE 300 VFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGE Sbjct: 241 VFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGE 300 Query: 301 VCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESG 360 VCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESG Sbjct: 301 VCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESG 360 Query: 361 HADGARLVAGGKRTLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIA 420 HADGARLVAGGKRTLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIA Sbjct: 361 HADGARLVAGGKRTLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIA 420 Query: 421 IANDTPYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480 IANDTPYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS Sbjct: 421 IANDTPYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480 Query: 481 LHAFDKYTELKATWIKL 497 LHAFDKYTELKATWIKL Sbjct: 481 LHAFDKYTELKATWIKL 497 Lambda K H 0.316 0.132 0.390 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: 1014 Number of extensions: 34 Number of successful extensions: 1 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: 497 Length of database: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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