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 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 171 bits (433), Expect = 4e-47 Identities = 126/405 (31%), Positives = 191/405 (47%), Gaps = 52/405 (12%) Query: 30 ENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLA 89 + + L DV+G EY+D +GIAV + GH H +L Q ++ H + + E + LA Sbjct: 31 QGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVS-NLFYQEEQLDLA 89 Query: 90 EKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPG------VIAFSGGFHGRTYM 143 E+ L S K F +GAEA E A+K+AR + R +I +G FHGRT Sbjct: 90 ER---LLSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEIITLTGAFHGRTLA 146 Query: 144 TMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEA------K 197 T+A TG+ A ++ GF P P VP DIEA Sbjct: 147 TVAATGQ-AKFQDGFYPMPEGFRQVP---------------------SGDIEALRAAIGP 184 Query: 198 QVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYA 257 Q A ++ E VQGEGG + A++ LC E G++ + DE+Q+G RTG+ ++ +Y Sbjct: 185 QTAGVLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYG 244 Query: 258 DKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKE 317 +PD+++ AK+LA G+P+ ++ + G T+ L A A + I+ ++ Sbjct: 245 LEPDIVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFGAGALVSAVASRTVEIMLRD 304 Query: 318 SLCERANQLGQRLKNTLIDAKESVP-AIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQ 376 L RA G R+ + + +P I VRGLG MI V P +++ Q Sbjct: 305 DLAGRAATEGARIMDRFRAMGQKLPGTIDHVRGLGLMIGVVLAFP---------GKEVWQ 355 Query: 377 RALAQGLLLLTCGAYGN-VIRFLYPLTIPDAQFDAAMKILQDALS 420 + +G + C + V+R L LTIP A DA L+D LS Sbjct: 356 ALIDRGFI---CNLTQDCVLRLLPALTIPRADLDAFADALEDILS 397 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: 401 Number of extensions: 20 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: 402 Length adjustment: 31 Effective length of query: 390 Effective length of database: 371 Effective search space: 144690 Effective search space used: 144690 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 17 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