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_085771307.1 B1812_RS09075 ornithine--oxo-acid transaminase
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_002117405.1:WP_085771307.1 Length = 413 Score = 195 bits (495), Expect = 2e-54 Identities = 135/399 (33%), Positives = 195/399 (48%), Gaps = 41/399 (10%) Query: 32 ATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVT--LA 89 A L DV G YID + + ++ GH HP ++A + +Q + VP +Y L Sbjct: 28 AYLWDVAGRRYIDMMSAYSAVSLGHAHPRILAKLSEQAHRLA------VPSRAYYNDRLG 81 Query: 90 EKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGR------PGVIAFSGGFHGRTYM 143 + AL ++G +GAEAVE A+K AR R P +I G FHGRT Sbjct: 82 PFLEALCMLTGLDAALPMNSGAEAVETAIKAARRWGQRVKGVASPEIIVAEGNFHGRTTT 141 Query: 144 TMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAII 203 ++ + + Y+ GFGPF VP+ DL S ++ A++ Sbjct: 142 VISFSSE-QEYRDGFGPFTPGFRAVPF-GDLEATRAAIS--------------ERTVAVL 185 Query: 204 FEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLM 263 EP+QGE G V P+ +A +RRLCDE I+++ DE+QSG RTG FA H PD + Sbjct: 186 VEPIQGEAGVIVPPRGWLAGLRRLCDEARILLLLDEIQSGLGRTGAWFAYQHENVLPDGV 245 Query: 264 TMAKSLAGG-MPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCER 322 T+ K+L GG +P+S V +MD PG G T+ GN LA A LN+I +E+L ER Sbjct: 246 TLGKALGGGVLPVSAFVARREVMDVFTPGSHGSTFGGNALAAAVGLEALNVIREENLVER 305 Query: 323 ANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQG 382 + LG L + L K P +A VRGLG E +P + A+ +R L +G Sbjct: 306 SRTLGAHLFDRLHAIKS--PVLADVRGLGLWAGAEI------QPRFSSARTFCERLLEKG 357 Query: 383 LLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421 +L+ + V+R PL I A D A+ ++ L + Sbjct: 358 --VLSSATHHTVVRLAPPLVISKADLDWALDRFEEVLRE 394 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: 404 Number of extensions: 22 Number of successful extensions: 7 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: 413 Length adjustment: 31 Effective length of query: 390 Effective length of database: 382 Effective search space: 148980 Effective search space used: 148980 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 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