Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_046010019.1 OLEAN_RS15795 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_000967895.1:WP_046010019.1 Length = 430 Score = 168 bits (426), Expect = 3e-46 Identities = 125/407 (30%), Positives = 206/407 (50%), Gaps = 32/407 (7%) Query: 29 AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQ--FTH--TAYQIVPYES 84 A++ + D EGN Y+DF AG LN GH + L A + + + + TH + + Sbjct: 25 AKDEFMWDEEGNRYLDFLAGAGTLNYGHNNDHLKANLMKYIMEDGITHGLDMHTKAKGDF 84 Query: 85 YVTLAEKINALAPVSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYM 143 T EKI L P + F TG AVE A+K+AR TG+ ++ F+ GFHG + Sbjct: 85 LNTFNEKI--LKPRDMEYMVQFTGPTGTNAVEAAMKLARNVTGQQNIVTFTNGFHGVSLG 142 Query: 144 TMALTGKVAPYKIGFGPFPGSVYHVPYPSDL-HGISTQDSLDAIERLFKSDIEAKQVAAI 202 ++ TG + ++ G ++ +P+ L GI T + LD + L S AA+ Sbjct: 143 ALSATGN-SHHRDAAGVSLNGIHRMPFDGYLGDGIDTTEYLDKV--LSDSSSGINSPAAV 199 Query: 203 IFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDL 262 + E VQGEGG NVA E + + ++C +HG+++I D++Q+G RTG F+ + KPD+ Sbjct: 200 LLETVQGEGGVNVASIEWLQNLEKVCRKHGLLLIVDDIQAGCGRTGTFFSFEESGIKPDI 259 Query: 263 MTMAKSLAG-GMPLSGVVGNANIMDAPAPGGLGGTYAGNPLA-VAAAHAVLNIIDKESLC 320 +TM+KS++G G+P + V+ +D PG GT+ GN LA V A A+ + + Sbjct: 260 ITMSKSISGYGLPFAVVLMKPE-LDQWKPGEHNGTFRGNNLAFVTAKDAIDHYWSDDVFS 318 Query: 321 ERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGE------PSAAIAQKI 374 G+ +K LID I G G+ F + G + IA KI Sbjct: 319 NEVKAKGEYVKEQLID-------IVGQYGEGN-----FTNKGRGMFQGINCVNGEIAAKI 366 Query: 375 QQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421 ++A ++G+++ T GA +++ PLTI + ++IL++++ + Sbjct: 367 TKKAFSKGMIIETSGADDQIVKLFCPLTITQENLEKGIEILRESIKE 413 Lambda K H 0.319 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: 424 Number of extensions: 17 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: 421 Length of database: 430 Length adjustment: 32 Effective length of query: 389 Effective length of database: 398 Effective search space: 154822 Effective search space used: 154822 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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