Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF3555 PS417_18205 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__WCS417:GFF3555 Length = 492 Score = 243 bits (620), Expect = 1e-68 Identities = 152/444 (34%), Positives = 242/444 (54%), Gaps = 13/444 (2%) Query: 51 KIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRR 110 ++ NP ++L+ + DL + A Q+A A W ++P +R+ L K A +I+ Sbjct: 29 RLDDRNPFNGERLLEMPLASVVDL-DDAYQAAQRAQTDWAALHPTQRSAQLEKLAQVIQD 87 Query: 111 RKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILS-RPGEQNRYFY 169 R E WL+ E+G +A + ++ + A +++ G+ + S +PGEQ+ F Sbjct: 88 RSEEIIDWLIRESGSTRIKAGMEWQFTLNLVRECATLPMQVE-GRILSSYKPGEQSFVFR 146 Query: 170 TPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFV-EVLEDAGLPK 228 P+GV ISPWNF L + + + V + GNTVVLKPAS T V + + E+AG P Sbjct: 147 EPLGVVGVISPWNFPLYLSMRSVVPALALGNTVVLKPASDTAVTGGLLIAHLFEEAGFPA 206 Query: 229 GVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMG 288 G +N V G+G+E+GD V+HP SLI+FTGS DVG R R A+ G H+KRV +E+G Sbjct: 207 GALNVVVGAGSEIGDAFVEHPIPSLISFTGSTDVG-RNVGRIAI---GGKHIKRVALELG 262 Query: 289 GKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLT 348 G +VV DAD+++AA + +V F GQ C + +R ++ + +Y + V NL Sbjct: 263 GNAPLVVLDDADIEIAAHAAVVGRFLHQGQICMSVNRVIVDRSLYADFAALVVERVLNLK 322 Query: 349 VGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGDSSTGFFIQPTIIADLD 407 GDP D +GPV+++ + ++ I+ ++ G + + GG+ + G + + ++ Sbjct: 323 TGDPAKPDTVIGPVVNQSQLDGLLGKIDAAERAGLKQLCGGQ---AQGLVLPAHVFGEVG 379 Query: 408 PEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGN 467 PE + ++E FGP++ A++ HALE+AN +EYGL+ AV TR+ A R G Sbjct: 380 PEQALARDETFGPLLPLMIAHNQAHALELANASEYGLSSAVFTRDMARGLSFARGIVAGM 439 Query: 468 LYFNRNCTGAIVGYHPFGGFKMSG 491 + N + T PFGG K SG Sbjct: 440 THIN-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: 602 Number of extensions: 33 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: 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