Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate GFF3775 PGA1_262p01790 aldehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Phaeo:GFF3775 Length = 483 Score = 227 bits (578), Expect = 9e-64 Identities = 149/461 (32%), Positives = 229/461 (49%), Gaps = 11/461 (2%) Query: 57 GSWGGRGEVITTYCPAN-NEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVR 115 G W I P++ N+ I QAS + T+++A+ A WA ++ ++ Sbjct: 11 GDWVAGATEIENRNPSDLNDLIGMFAQASPDQLDATLEQAQRAQVEWAGYGIERKYNVLM 70 Query: 116 QIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSG 175 IG + + + LG+L++ E GK L EG GEV Y + G S R G Sbjct: 71 AIGTEMMTRAEELGTLLAREEGKPLAEGKGEVYRAGQFFTYYAAETLRQMGDTADSVRDG 130 Query: 176 HALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIA 235 + + PVG+V +I+ +NFP A W A A+ GN +WK A T +VA+ +IIA Sbjct: 131 IEIDVRREPVGVVVVISPWNFPTATASWKIAPALCYGNAVVWKPANVTPASAVALVEIIA 190 Query: 236 KVLEDNKLPGAICSLTCG-GADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSL 294 + +P + SL G G+ IG + + +VN +SFTGS VGK + + R Sbjct: 191 R----QDIPKGLVSLVMGAGSSIGQRLVESPKVNAISFTGSVPVGKGIAACAIQNLTRVQ 246 Query: 295 LELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAY 354 +E+G NA+ +DAD+ L V AL A G +GQ+CT + RL +H+SIHD+ V +L Sbjct: 247 MEMGSKNALAVMDDADIDLAVSLALGGAFGGSGQKCTASSRLVVHQSIHDQFVEKLVMGA 306 Query: 355 AQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGK--VMDRPGNYVEPT 412 ++VG+ + GP+ ++Q ++ L V+ A EG ++ GG+ M G YV P Sbjct: 307 KAMKVGHALEAGTQMGPVVSEQQLNENLAYVDLAASEGAELLCGGQRLEMATDGYYVSPG 366 Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472 I G +D I E FAP+ V + +E N+ GL++ I T +L R + Sbjct: 367 IFVGTNNDMRINREEMFAPLACVIPVASYDEALHVVNDTNFGLTAGIVTTNLARATHF-- 424 Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTG-GGRESGSDA 512 + + G V VN+PT+G + FGG + G RE G A Sbjct: 425 RRNAQSGCVMVNLPTAGTDYHVPFGGRGDSSYGPREQGQTA 465 Lambda K H 0.318 0.136 0.417 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: 631 Number of extensions: 40 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: 539 Length of database: 483 Length adjustment: 34 Effective length of query: 505 Effective length of database: 449 Effective search space: 226745 Effective search space used: 226745 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 (21.7 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