Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase
Query= curated2:P94427 (436 letters) >FitnessBrowser__Cola:Echvi_0577 Length = 413 Score = 199 bits (506), Expect = 1e-55 Identities = 125/408 (30%), Positives = 215/408 (52%), Gaps = 45/408 (11%) Query: 35 KGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELI--HPGFNVMMYPTY 92 +GEG ++D++G ++ DF + +N GH HP++++ + QA L F+ + + Sbjct: 32 RGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRAFHNDVLGPF 91 Query: 93 IELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKY-------TKRQGVVSFTRG-F 144 + + G K + +N+GAE VE A+KIARK+ + +G + + F Sbjct: 92 EKFLTEYFGY------DKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNF 145 Query: 145 HGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFF 204 HGRT +S ++ K FGP+ P P +DD I A D Sbjct: 146 HGRTTTVISFSNDETARK-NFGPYTPGFVTIP---------------HDD--IDALKDVL 187 Query: 205 IASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTY 264 S + + ++EP+QGE G +P + +++ VA+ CK+HG++F+ADEIQTG ARTG Sbjct: 188 SQS---KNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKL 244 Query: 265 FAIEHFDVVPDLITVSKSLAAGL-PLSGVIGRAEMLDAAAPGELGGTYAGSPLGCAAALA 323 A +H V PD++ + K+++ G P+S V+ +++ PG+ G T+ G+PLG A+ Sbjct: 245 LACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMT 304 Query: 324 VLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKDPDTREPDK 383 L+++++E L E ++++GK+ ++ + + + +R G + AI I DT + D Sbjct: 305 ALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVI---NDTEDSDT 361 Query: 384 TKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILE 431 +A +NG LL +GNIIRF PLVI++ L++ I+E Sbjct: 362 AWRLCLA--LKENG--LLAKPTHGNIIRFAPPLVITEEQLHDCCDIIE 405 Lambda K H 0.319 0.136 0.393 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: 473 Number of extensions: 23 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: 436 Length of database: 413 Length adjustment: 32 Effective length of query: 404 Effective length of database: 381 Effective search space: 153924 Effective search space used: 153924 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 (21.7 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