Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 240 bits (612), Expect = 1e-67 Identities = 144/441 (32%), Positives = 235/441 (53%), Gaps = 15/441 (3%) Query: 56 NPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115 +PA ++ V + A D + A+ +A EAF W P +R++ L + A ++ R +F Sbjct: 42 DPATGEE-VHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDF 100 Query: 116 SAWLVHEAGKPWK-EADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYT-PMG 173 + + GKP K + D ID ++A L +G+ G+ Y P+G Sbjct: 101 ARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHL-QGQSAGEYSGDHTSYVRREPIG 159 Query: 174 VTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINY 233 V +I+PWN+ L + + I GNT+VLKPA TP+ + F + +AG+P GVIN Sbjct: 160 VVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINI 219 Query: 234 VPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTV 293 V G+G E G++LV HP ++++FTGS VG R+ E A +KR+ +E+GGK Sbjct: 220 VTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATA------SVKRLHLELGGKAPF 273 Query: 294 VVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPT 353 VV DADL+ A + A +GQ C+A +RA + + +Y+E + +T AL + + +GDP Sbjct: 274 VVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLGDPF 333 Query: 354 NRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGGE---GDSSTGFFIQPTIIADLDPEA 410 +GP+I +++ +++ + R++TGGE G+ G + +PT+IA ++ Sbjct: 334 APGTDLGPLISHVHRDRVAGFVDRARAYARVVTGGEAPQGELKNGAYYRPTLIAGAAQDS 393 Query: 411 VIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYF 470 I+Q EIFGPV+ + D + +AN+T YGL + +R+ +A RE G ++ Sbjct: 394 EIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGCVWV 453 Query: 471 NRNCTGAIVGYHPFGGFKMSG 491 N + I+ P GG K SG Sbjct: 454 NDHI--PIISEMPHGGSKQSG 472 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: 670 Number of extensions: 28 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: 511 Length adjustment: 35 Effective length of query: 480 Effective length of database: 476 Effective search space: 228480 Effective search space used: 228480 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