Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__azobra:AZOBR_RS29185 Length = 478 Score = 253 bits (647), Expect = 8e-72 Identities = 157/459 (34%), Positives = 233/459 (50%), Gaps = 16/459 (3%) Query: 56 NPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115 NPAR +++G + A+ + AE+A+ +A A W NP+ R+++L + + R E Sbjct: 23 NPARPGEVIGHYAWASVEQAEEALGAAHAALPGWAASNPQTRSDVLRRVGDELNARAEEL 82 Query: 116 SAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILS--RPGEQNRYFYTPMG 173 A L E GK +E + + Y A + L +G E L R G P+G Sbjct: 83 GALLTREEGKTLREGIGEVRRSAQIFHYAAGE--PLRQGGEALPGLRDGTTAMVSREPVG 140 Query: 174 VTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINY 233 V V I+PWNF +A+ + GNTVVLKP+ TP A + ++L AGLP G N Sbjct: 141 VVVLITPWNFPMAVPAWKTAYALAFGNTVVLKPSEVTPACAWELADILHRAGLPAGAFNL 200 Query: 234 VPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTV 293 V G G +G LVD ++FTGS VG + ER+ + RV +E+GGK+ + Sbjct: 201 VVGDGRTLGPALVDG--ADAVSFTGSPGVGRAILERSVA------RMTRVQLELGGKNPL 252 Query: 294 VVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPT 353 VV DADL+LA + L AF +GQ+C+A SR ++ + V+D +E+ V L VGDP Sbjct: 253 VVHDDADLELAVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRIAALRVGDPM 312 Query: 354 NRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGDSSTGFFIQPTIIADLDPEAVI 412 + MGPV+ E K + I + EG L GG G+F++PT+ D I Sbjct: 313 DAATDMGPVVSEAQLAKDLHCIADARSEGAELAFGGGRMDGDGYFLEPTLFVGTDNAMRI 372 Query: 413 MQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNR 472 ++E+FGPV A+ DHA+ IAN++++ L+ ++TR A E +R G + N Sbjct: 373 NRDEVFGPVACVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFRRRSRAGLVMVNA 432 Query: 473 NCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510 G + YH PFGG SG + G + + KT Sbjct: 433 PTAG--IDYHVPFGGRGPSGYGGREQGSAAVEFFTEGKT 469 Lambda K H 0.316 0.134 0.388 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: 596 Number of extensions: 29 Number of successful extensions: 5 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: 515 Length of database: 478 Length adjustment: 34 Effective length of query: 481 Effective length of database: 444 Effective search space: 213564 Effective search space used: 213564 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 (21.6 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