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_050465856.1 AKL27_RS26225 aldehyde dehydrogenase
Query= SwissProt::Q8CHT0 (562 letters) >NCBI__GCF_001189915.1:WP_050465856.1 Length = 477 Score = 155 bits (393), Expect = 3e-42 Identities = 131/440 (29%), Positives = 210/440 (47%), Gaps = 29/440 (6%) Query: 101 LNRAIDAALAARK-EWDLKPMADRAQVFLKAADMLSGPRRAEVLAKTMVGQ-GKTVIQAE 158 ++RA+ AA AA + EW A+R+++ + A L AEVLA+ GK + QA Sbjct: 41 IDRAVQAARAAYEGEWGRLSAAERSRLLYRLALRLQD--NAEVLAQLEAADCGKPLKQAR 98 Query: 159 IDAAAELIDFFRFNAKFAVELEGEQPISVPPSTNHTV--YRGLEGFVAAISPFNFTA-IG 215 DAAA + +F F A A +L GE ++P + ++V +R G I P+N+ I Sbjct: 99 ADAAA-IARYFEFYAGAADKLHGE---TIPYQSGYSVLTWREAHGVTGHIVPWNYPMQIF 154 Query: 216 GNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSS 275 G A GN KP++ A L+ V + EAG P + V G GD + S Sbjct: 155 GRCVAAALAAGNTCAVKPAEDACLSLLKVAELAAEAGFPAGALNLVTGYGHEAGDALVSH 214 Query: 276 EHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGT 335 + ++FTGS K + R A++ + E GGK+ V + AD +VV Sbjct: 215 PGIDHVSFTGSPNVGKIVVRAAAEH------HTPVTLELGGKSPQIVFADADFSAVVPTV 268 Query: 336 LRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKA 395 + + + GQ CSA SRL V + ++ Q+ + R++VG D +I Sbjct: 269 VNAIVQNAGQTCSAGSRLLVQREVYDQVIELVAAAFGRLRVGSSQMDLDC--GPLIRQTQ 326 Query: 396 FARIKKWLEHARSSPSLSILAGGQCNESV---GYYVEPCIIESKDPQEPIMKEEIFGPVL 452 R++K+L AR + I GQ + + G+Y P + + PQ + ++EIFGPVL Sbjct: 327 LQRVQKFLADARQD-GIPIAGQGQIDAAAPKGGFYQAPVLFKDVPPQHALAQQEIFGPVL 385 Query: 453 TVYVYPDDKYRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGS 512 + + D+ + +++ + T +GL +V+ +D R +R AG YIN+ G Sbjct: 386 SAMPFDDE--ADAVRIANG-TDFGLVSSVWTRDGGRQLRLARKIR--AGQVYINNYGAGG 440 Query: 513 VVGQQPFGGARASGTNDKPG 532 + + PFGG +ASG + G Sbjct: 441 GI-ELPFGGVKASGHGREKG 459 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: 609 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 562 Length of database: 477 Length adjustment: 35 Effective length of query: 527 Effective length of database: 442 Effective search space: 232934 Effective search space used: 232934 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