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_110806203.1 C8J30_RS11905 aspartate aminotransferase family protein
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_003217355.1:WP_110806203.1 Length = 393 Score = 182 bits (461), Expect = 2e-50 Identities = 140/402 (34%), Positives = 196/402 (48%), Gaps = 50/402 (12%) Query: 30 ENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTA--YQIVPYESYVT 87 E + L +G+ Y+D AGIAV GH P+LVA + +Q + H + Y+I E Sbjct: 20 EGSWLWTEDGSRYLDLGAGIAVNALGHAAPELVATLTEQAGKLWHVSNLYRIPEQER--- 76 Query: 88 LAEKINALAPVSGQAKTAFFT-TGAEAVENAVKIARAH---TGRP---GVIAFSGGFHGR 140 LA+ + A + A T FFT +G EA E AVK+ R + G+P ++ FSG FHGR Sbjct: 77 LADMLVA----NTFADTVFFTNSGTEACELAVKMVRKYFYEKGQPERSDILTFSGAFHGR 132 Query: 141 TYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVA 200 + +A G K GFGP H+P+ L+A++ A Sbjct: 133 SSAAIAAAGTEKMVK-GFGPLLPGFKHLPW----------GDLEAVKAAVTDT-----TA 176 Query: 201 AIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKP 260 AI+ EP+QGEGG AP+ + A+R +CD G +++ DEVQ G ARTG+LFA + P Sbjct: 177 AILIEPIQGEGGIRPAPEGFLKALREICDATGTLLVFDEVQCGVARTGRLFAHEWAGVTP 236 Query: 261 DLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDK---- 316 D+M +AK + GG PL V+ AN G G TY GNPL A ++ I+ Sbjct: 237 DVMMVAKGIGGGFPLGAVLATANAASGMTAGTHGSTYGGNPLGCAIGAKMIEIVTAPGFL 296 Query: 317 ESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQ 376 E + +A L QRL+ L+ A + VRG G M+ + P AA AQ Sbjct: 297 EEVSRKAGFLRQRLEG-LVAAHPDI--FEEVRGQGLMLGLRCKLPPGDVVKAAYAQN--- 350 Query: 377 RALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDA 418 LLT A NV+R L LTI + A++ L+ A Sbjct: 351 --------LLTVPAADNVLRLLPALTITEDDMAEAVRRLEAA 384 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: 423 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: 393 Length adjustment: 31 Effective length of query: 390 Effective length of database: 362 Effective search space: 141180 Effective search space used: 141180 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