Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_067912849.1 AQZ52_RS15205 aldehyde dehydrogenase family protein
Query= SwissProt::Q8CHT0 (562 letters) >NCBI__GCF_001519075.1:WP_067912849.1 Length = 474 Score = 120 bits (302), Expect = 9e-32 Identities = 106/359 (29%), Positives = 166/359 (46%), Gaps = 22/359 (6%) Query: 179 LEGEQPISVPPSTNHTVYRGLEGFVAAISPFNFTAIGGNLAGAPALM-GNVVLWKPSDTA 237 LEG + + P N G VAAI+P+N+ AP + GN V+ KPS+ Sbjct: 118 LEGFEWEAPVPGANARFVHEPIGVVAAITPWNWPLNQICAKIAPCIAAGNTVVLKPSEEC 177 Query: 238 MLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSSEHLCGINFTGSVPTFKHLWRQV 297 + + ++ AG+P + V DGP G +T + ++FTGS + + Sbjct: 178 PSNAVIMAEVMHAAGVPAGVFNLVQGDGPGVGVALTVHPDVDMVSFTGSTRAGIQIAKNA 237 Query: 298 AQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGTLRSAFEYGGQKCSACSRLYVPK 357 A T R+ E GGK+ + V AD + + GTL+ GQ C A +R+ VPK Sbjct: 238 AD------TVKRVHQELGGKSPNLVLEDADFAATLPGTLQGIVANTGQSCIAPTRILVPK 291 Query: 358 SLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKAFARIKKWLEHARSSPSLSILAG 417 S + + + + +KVG P E+ G V++ +++++ ++ + S+L G Sbjct: 292 SRKEEAETFVKNYFAAVKVGSPEEE-GMHIGPVVNKAQWSKVQSLID-TSIAEGASLLEG 349 Query: 418 G---QCNESVGYYVEPCIIESKDPQEPIMKEEIFGPVLTVYVYPDDKYRETLQLVDSTTS 474 G N + GYY+ P + P I +EE FGPV T+ Y D + ++L + T+ Sbjct: 350 GPGLPDNVNRGYYIRPTVFSDVTPDMTIFREETFGPVATITTY--DGIEDGIELA-NRTA 406 Query: 475 YGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGSVVGQQPFGGARASGTNDKPGG 533 YGL+ AV D + LR AG +N G V G FGG + SG N + GG Sbjct: 407 YGLS-AVVTGDVETAKGIVGRLR--AGLVAVN--QWGGVKG-GAFGGYKQSG-NGREGG 458 Lambda K H 0.319 0.135 0.411 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: 606 Number of extensions: 27 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: 562 Length of database: 474 Length adjustment: 35 Effective length of query: 527 Effective length of database: 439 Effective search space: 231353 Effective search space used: 231353 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: 52 (24.6 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