Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 194 bits (494), Expect = 5e-54 Identities = 138/441 (31%), Positives = 221/441 (50%), Gaps = 14/441 (3%) Query: 21 RAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAP 80 R I+G++ ++ + + ++P +L ++ ++ AV A+ F + W + Sbjct: 9 RLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKT--WRKTPI 66 Query: 81 TKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDKIYD 140 R +++ L++++ ELA + + GK + D+ DV + + + + Sbjct: 67 GTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEG-DVFRGLEVVEHAAAIGNLQLG 125 Query: 141 EVAATPHDQLGLVT-REPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLT 199 E+A + + T +P+GV I P+NFP M+ W A++TGN+ +LKPSE+ P+ Sbjct: 126 ELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 185 Query: 200 AIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGES 259 +R+ ELA+EAGIPKGVLNV+ G G V A+ H D+ + F GST++ +Y+ S Sbjct: 186 TMRLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGSTRVGTH--VYNRAS 242 Query: 260 NM-KRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKF 318 KRV G K+ +V DA N + A GA G+ C A S L++ + + Sbjct: 243 LAGKRVQCMMGAKNHAVVLPDA-NKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEAR-SW 300 Query: 319 LPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGKRTLQET 378 +P ++ K K T+VG ++ V I SG GA L G R Q Sbjct: 301 VPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDG-RNPQVD 359 Query: 379 G---GTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWT 435 G G +V PTIF GV+ M+I QEEIFGPVL ++E ++ E+AIA+ N P G AV+T Sbjct: 360 GFEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFT 419 Query: 436 ADISKAHLTARALRAGSVWVN 456 + A + G V +N Sbjct: 420 QSGAAARKFQEDIDVGQVGIN 440 Lambda K H 0.316 0.132 0.390 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: 569 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: 497 Length of database: 501 Length adjustment: 34 Effective length of query: 463 Effective length of database: 467 Effective search space: 216221 Effective search space used: 216221 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 Apr 09 2024. 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