Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_008991607.1 I215_RS08785 aldehyde dehydrogenase family protein
Query= SwissProt::Q9DBF1 (539 letters) >NCBI__GCF_000300875.1:WP_008991607.1 Length = 517 Score = 497 bits (1279), Expect = e-145 Identities = 260/503 (51%), Positives = 341/503 (67%), Gaps = 7/503 (1%) Query: 42 LQDLGLREDNEGVYNGS-WGGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWN 100 L+ LG+ +N+G G+ W GE I P + +A+V+ +S +DY + I A A+ Sbjct: 14 LEILGIAGENKGSSTGTNWFSSGEWIDVVSPVDGNLMAKVQTSSKEDYNKVIETATAAFE 73 Query: 101 IWADIPAPKRGEIVRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGL 160 W +PAP+RGEIVR+ D R LG LVS EMGK EG+GEVQE +D+CD+A GL Sbjct: 74 KWKKVPAPQRGEIVRQFADKLRANKTALGELVSYEMGKSFQEGLGEVQEMIDICDFAVGL 133 Query: 161 SRMIGGPTLPSERPGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGA 220 SR + G T+ SERPGH + E W+PLG+VGII+AFNFPVAV+ WN+A+AL+ G+VC+WK + Sbjct: 134 SRQLHGLTMHSERPGHRMYEQWHPLGIVGIISAFNFPVAVWSWNSALALVCGDVCVWKPS 193 Query: 221 PTTSLVSVAVTKIIAQVLEDNLLPGAICSLVCGGADIGTTMARDERVNLLSFTGSTQVGK 280 T L +VA K+++QVL DN LP I LV G + +G +++D R+ L+S TGST++GK Sbjct: 194 EKTPLTAVACQKLLSQVLSDNSLPEGISCLVTGDSRVGELLSKDTRIPLVSATGSTRMGK 253 Query: 281 EVALMVQERFGKSLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHE 340 VA V R GKSLLELGGNNAII DAD+ + V +F AVGT GQRCT+ RRL +H+ Sbjct: 254 IVAKAVASRLGKSLLELGGNNAIIVTPDADIKMTVIGAVFGAVGTCGQRCTSTRRLIVHQ 313 Query: 341 SIHNEVVDRLRSAYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGK 400 ++++V D L AY Q+++G+P + GPL AV M++ A+E+AK+QG V+ Sbjct: 314 KVYDQVKDALVEAYGQLKIGDPLNEANHVGPLIDTDAVKMYLDALEKAKEQGAVVLTESG 373 Query: 401 VMD----HPGNYVEPTIVTGLAHDAPIVHQETFAPILYVFKFQ-DEEEVFEWNNEVKQGL 455 ++ G YV P +V ++D IV QETFAPILY+ K+ D E N V QGL Sbjct: 374 RLEGNEYQSGCYVRPAVVEA-SNDFNIVQQETFAPILYLIKYDGDLENAIAMQNGVVQGL 432 Query: 456 SSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQ 515 SS+I T +L +L +GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK Sbjct: 433 SSAIMTNNLREAELFLSNQGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKV 492 Query: 516 YMRRSTCTINYSTSLPLAQGIKF 538 YMRR T TINY+T++PLAQGIKF Sbjct: 493 YMRRQTNTINYTTTIPLAQGIKF 515 Lambda K H 0.319 0.137 0.421 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: 798 Number of extensions: 32 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: 539 Length of database: 517 Length adjustment: 35 Effective length of query: 504 Effective length of database: 482 Effective search space: 242928 Effective search space used: 242928 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 (21.7 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