Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 176 bits (445), Expect = 2e-48 Identities = 125/372 (33%), Positives = 183/372 (49%), Gaps = 42/372 (11%) Query: 91 LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHAIADFSEALAS 150 ++D+ G YLD + G AV++ GH HP + + Q+ + Y N + LA+ Sbjct: 22 IWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNI----AFYSNSVQIPIQKELAT 77 Query: 151 KLPGDLKV-----VFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQ 205 KL G L +F NSG EANE AL +A TG + +A G+HG + + T Sbjct: 78 KL-GQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHGRTSGAVALTDN 136 Query: 206 SMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFICEAIQGVG 265 + + H ++ P+ DL+ + + TG IAG I E IQGVG Sbjct: 137 PKI---IAPFNAHEGVHILPFN------------DLEAVEKQLATGTIAGVIVEGIQGVG 181 Query: 266 GIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFE-AHNVVPDIVTMAKGIG 324 GI P +L K+ G I DEVQSG+AR+G F+ + + PD++T+AKG+G Sbjct: 182 GIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMG 241 Query: 325 NGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYL 384 NGFP+G V+ +PE + TFGGN ++ A LAVL VI++E L AA G + Sbjct: 242 NGFPIGGVLISPEFKA--SHGLLGTTFGGNHLACAAALAVLEVIDEENLITAAAENGKAI 299 Query: 385 KEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGG 444 L EK + +VRG+GLM+G +L ++ P A +H E + G G Sbjct: 300 MAAL----EKVAGVTEVRGKGLMIGFDLATE---AGPVRAALIH------EHKIFTGSAG 346 Query: 445 YFGNVFRITPPL 456 + R+ PPL Sbjct: 347 -GKHTIRLLPPL 357 Lambda K H 0.320 0.136 0.403 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: 469 Number of extensions: 29 Number of successful extensions: 6 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: 477 Length of database: 381 Length adjustment: 32 Effective length of query: 445 Effective length of database: 349 Effective search space: 155305 Effective search space used: 155305 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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