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_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_001592305.1:WP_068170823.1 Length = 428 Score = 518 bits (1334), Expect = e-151 Identities = 256/420 (60%), Positives = 322/420 (76%), Gaps = 3/420 (0%) Query: 2 SNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDL 61 +N +HQRRL ATPRGVGVM +FF A+NA L D+EG +IDFA GIAVLNTGH HP + Sbjct: 9 TNAAWHQRRLDATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKV 68 Query: 62 VAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIA 121 AA+ QLQ+FTH+ YQ+VPY YV+LAE+INA+ P+ G+AKTAFF+TGAEA+ENA+KIA Sbjct: 69 QAAIAAQLQRFTHSCYQVVPYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIA 128 Query: 122 RAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQD 181 R+ TGR GVIAF G FHGR+ ++LTGKV PYK GFGPFP +YHVP+P++ G S + Sbjct: 129 RSSTGRSGVIAFGGAFHGRSLFAVSLTGKVQPYKAGFGPFPPEIYHVPFPAE--GASLDE 186 Query: 182 SLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQ 241 + A++ +FK DIE +VAAI+FEPVQGEGGFN K+ V +R LCD+HGI++IADEVQ Sbjct: 187 TKRAMDHVFKCDIEPSRVAAIVFEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQ 246 Query: 242 SGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNP 301 +GFARTG++FAM+HY PDLMTMAKS+AGG LS V G A IMD PAPGGLGGTYAGNP Sbjct: 247 TGFARTGRMFAMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNP 306 Query: 302 LAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP 361 LA+AA+HAVL+++ +E L ERA +LG +L L AK P I VRGLG+M+A EF D Sbjct: 307 LAIAASHAVLDVMAEEKLPERAQRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVD- 365 Query: 362 QTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421 G P A +++Q AL +GLLLLTCG YGNVIR+L+PLTI D+ F A+ +L A+++ Sbjct: 366 AAGAPDADTTKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAE 425 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: 621 Number of extensions: 26 Number of successful extensions: 3 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: 428 Length adjustment: 32 Effective length of query: 389 Effective length of database: 396 Effective search space: 154044 Effective search space used: 154044 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 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