Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012403978.1 BPHY_RS23615 betaine-aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000020045.1:WP_012403978.1 Length = 483 Score = 274 bits (701), Expect = 5e-78 Identities = 166/471 (35%), Positives = 253/471 (53%), Gaps = 22/471 (4%) Query: 35 KEYPLIINGERVT--TEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNV 92 + + L+I+G+R+ T + + NPA ++ + + QD+ + A+++A A + W + Sbjct: 8 RRHDLLIDGKRLPPGTGEYSVNLNPATEEPIALVAQGSAQDV-DTAVKAARAALKVWNAM 66 Query: 93 NPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIEL 151 ER IL++ ++R + E A +AGKP D AID L YYA ++ Sbjct: 67 RAAERGRILMRFCEVLREHQDEIVALESLDAGKPLAAVKRQDVPAAIDTLAYYAGWCDKI 126 Query: 152 NRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTP 211 N G+ + RP P+GV I PWNF L I + + G T+V+KPA TP Sbjct: 127 N-GQVVPVRPDALTYTIREPVGVVGAIVPWNFPLMIGMWKIAPALACGCTMVVKPAEITP 185 Query: 212 VVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAA 271 + A + E+ +AG+P GV+N V G G VGD +V HP +TFTGS VG + + AA Sbjct: 186 LSALRVAELALEAGVPPGVLNIVTGKGRVVGDAIVAHPDIDKVTFTGSPSVGRGILQGAA 245 Query: 272 VVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKD 331 + KRV +E+GGK V+ DA++D A + F +GQ CSAGSR + H+D Sbjct: 246 ------GNFKRVTLELGGKSANVIFADANIDNAVRAAASGIFFNTGQVCSAGSRILAHRD 299 Query: 332 VYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEG 390 VYDEV+E+ VA AK + VGDP R+ MGP++ + ++ Y+++G+KEG ++TGG Sbjct: 300 VYDEVVERLVARAKGIKVGDPAERETTMGPLVSAAQMKTVLDYVDVGRKEGASIVTGGAR 359 Query: 391 DSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVIT 450 GFF++PT+ A+++ E I QEEIFGPV + + ND + A+ IAN T Y L V + Sbjct: 360 IGQKGFFVEPTVFANVEHEMRISQEEIFGPVASVVRFNDEEDAVRIANGTAYSLAAGVWS 419 Query: 451 RNRAHIEQAKREFHVGNLYFNRNCTGAIVGYH----PFGGFKMSGTDSKAG 497 + + + G ++ N GY P+GG SG + G Sbjct: 420 ADIGRVHRVAHALKAGTVWIN------TYGYTDVRLPWGGSGDSGFGREHG 464 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: 585 Number of extensions: 24 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: 515 Length of database: 483 Length adjustment: 34 Effective length of query: 481 Effective length of database: 449 Effective search space: 215969 Effective search space used: 215969 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 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