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_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_000566685.1:WP_025763135.1 Length = 384 Score = 177 bits (449), Expect = 5e-49 Identities = 126/337 (37%), Positives = 171/337 (50%), Gaps = 33/337 (9%) Query: 29 AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQ--FTHTAYQIVPYESYV 86 A+ + L D G EY+D G AV++ GH HPD VA + +QL + F + QI E Sbjct: 18 AQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSVQIPQQEELA 77 Query: 87 TLAEKINALAPVSGQAKTAFF--TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMT 144 T L +SG F +GAEA ENA+K+A HTGR V+AF+ FHGRT Sbjct: 78 T------KLGTLSGYPDYKLFLCNSGAEANENALKLASFHTGRKKVVAFTKAFHGRTAGA 131 Query: 145 MALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAIIF 204 +A T P V V Y + + D IE L E +VAA+I Sbjct: 132 VAATDN-----------PSIVAPVNYNEHVSFLPFND----IEALQAGITE--EVAAVIV 174 Query: 205 EPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLMT 264 E +QG GG V E + A+R+ CDE G +I D VQ G+ RTGK F+ PD+MT Sbjct: 175 EGIQGVGGIQVCSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHPDMMT 234 Query: 265 MAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERAN 324 MAK + G P++GV+ + G LG T+ GN LA AA AVL+I+ E L + A Sbjct: 235 MAKGMGNGFPIAGVLIAPQF--KASFGLLGTTFGGNHLACAAGIAVLDIMKDEQLLDNAT 292 Query: 325 QLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP 361 ++G L + + E + +RG G MI +EF+ P Sbjct: 293 KIGAYLFHEI----EELGGYKDLRGRGLMIGIEFDFP 325 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: 433 Number of extensions: 25 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: 421 Length of database: 384 Length adjustment: 31 Effective length of query: 390 Effective length of database: 353 Effective search space: 137670 Effective search space used: 137670 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: 50 (23.9 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