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 GFF3619 PGA1_262p00230 betaine aldehyde dehydrogenase BetB
Query= SwissProt::Q8CHT0 (562 letters) >FitnessBrowser__Phaeo:GFF3619 Length = 494 Score = 150 bits (379), Expect = 1e-40 Identities = 134/449 (29%), Positives = 212/449 (47%), Gaps = 32/449 (7%) Query: 93 FCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKT-MVGQG 151 F D A ++ A+ +A+A + W P A R + +AA ++ AE LA V G Sbjct: 52 FAAGDAADVDHAVTSAVAGFEIWSATPPARRCAILNEAARLMR--HEAEHLAVVECVDSG 109 Query: 152 KTVIQAEIDAA--AELIDFFRFNAKFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPF 209 KT+ +A D A A L++++ A A +L+G +++ R G A I P+ Sbjct: 110 KTLAEARGDIAGSARLLEYY---AGAADKLDGRS-VNLGNDNAAFTLREPVGVTAHIVPW 165 Query: 210 NFTAIGGNLAGAPALM-GNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTF 268 N+ + APAL G + KP++T + + +L AGLP ++ V G Sbjct: 166 NYPSSTLVRGIAPALAAGCSAVVKPAETTPFTALMIADLLIRAGLPAGVVNVVTGTGIAA 225 Query: 269 GDTVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADV 328 G + + + FTGSV T + + VA N+ L E GGK+ A+V Sbjct: 226 GAPLVRDPRVRHVTFTGSVATGVGVMQSVAPNVTG------LTLELGGKSPLVAFGDANV 279 Query: 329 DSVVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFS 388 D+VV G L + F GQ CSA SRL + +SL +++ +L+ R++VG G Sbjct: 280 DAVVEGALWAIFSNAGQICSAGSRLVIHRSLHAEVRDKLVARAQRLRVGHGLR--GPDIG 337 Query: 389 AVIDAKAFARIKKWLEHARSSPSLSILAGGQCNESV----GYYVEPCIIESKDPQEPIMK 444 AV A+ A+I + AR+ + I+ GG+ V G++ P I++ + + Sbjct: 338 AVNSARHLAQIDDHVSRARTR-GVEIVTGGEILTDVESGKGWFYAPTILDDLAANDDAVL 396 Query: 445 EEIFGPVLTVYVYPDDKYRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNA-AGNF 503 +EIFGPVL + V+ D+ E L L + T + L ++ +D + A RM R AG Sbjct: 397 QEIFGPVLAIQVFEDE--AEALALANG-TEFALAAGIYTRD---IATALRMARRVDAGQV 450 Query: 504 YINDKSTGSVVGQQPFGGARASGTNDKPG 532 +ND G + + PFGG R SG + G Sbjct: 451 TVNDYWAGGI--ELPFGGNRKSGFGREKG 477 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: 586 Number of extensions: 29 Number of successful extensions: 3 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: 494 Length adjustment: 35 Effective length of query: 527 Effective length of database: 459 Effective search space: 241893 Effective search space used: 241893 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 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