Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AO356_00680 AO356_00680 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00680 Length = 492 Score = 245 bits (626), Expect = 2e-69 Identities = 151/465 (32%), Positives = 246/465 (52%), Gaps = 21/465 (4%) Query: 38 PLIINGERVT--------TEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTW 89 P ING++ + ++ NP +QL+ + DL + A Q+A +A W Sbjct: 8 PYAINGDQYINGTWRAGRSARRLDDRNPFNGEQLLEMPLASIADL-DDAYQAAQKAQAPW 66 Query: 90 RNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMI 149 ++P +R L K A +I+ R+ E WL+HE+G +A + ++ + + Sbjct: 67 AQLHPTQRGAQLEKLAKVIQNRREEIIDWLIHESGSTRIKASMEWQFTLNLVRECTTMPM 126 Query: 150 ELNRGKEILS-RPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPAS 208 ++ G+ + S +PGEQ+ F P+GV ISPWNF L + + + V + GNT+VLKPAS Sbjct: 127 QVE-GRILTSYKPGEQSFVFREPLGVVGVISPWNFPLYLSMRSVVPALALGNTIVLKPAS 185 Query: 209 TTPVVAAKFV-EVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLY 267 T V + + E+AG P+G +N V G+G+E+GD V+HP SLI+FTGS DVG Sbjct: 186 DTAVTGGLLIAHLFEEAGFPEGSLNVVVGAGSEIGDAFVEHPVPSLISFTGSTDVG---- 241 Query: 268 ERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAV 327 + G H+KRV +E+GG +VV DAD+D+AA + +V F GQ C + +R + Sbjct: 242 RNVGRIATGGKHIKRVALELGGNAPLVVLDDADIDVAAHAAVVGRFLHQGQICMSVNRVI 301 Query: 328 IHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMT 386 + + +Y + V +NL GDPT D +GPV+++ + ++ ++ + G + + Sbjct: 302 VDRSLYADFASLVVERVRNLKTGDPTKADTVIGPVVNQSQLDGLLRKLDGARSAGLKQLC 361 Query: 387 GGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTG 446 GG ++G + + ++ + + ++E FGP++ A + HAL +AN +EYGL+ Sbjct: 362 GG---PASGLVLPAHVFGEVGADQELARDETFGPLLPLLVAENQTHALALANASEYGLSS 418 Query: 447 AVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 AV TR+ A R G + N + T PFGG K SG Sbjct: 419 AVFTRDMARGLNFARGIVAGMTHIN-DITVDDQPNAPFGGEKNSG 462 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: 633 Number of extensions: 32 Number of successful extensions: 6 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: 492 Length adjustment: 34 Effective length of query: 481 Effective length of database: 458 Effective search space: 220298 Effective search space used: 220298 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