Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__WCS417:GFF1577 Length = 389 Score = 199 bits (506), Expect = 1e-55 Identities = 135/399 (33%), Positives = 199/399 (49%), Gaps = 38/399 (9%) Query: 81 LNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHA 140 L+ G L+D+ GR YLDA AG+AV N GH HP +V + Q L H + LY Sbjct: 15 LSFTRGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNLYS--- 71 Query: 141 IADFSEALASKLP--GDLKVVFFTNSGTEANELALMMAKLYTGCQDI-----VAVRNGYH 193 D+ + LA +L L FF NSG EANE AL +A+L+ + I V + N +H Sbjct: 72 -IDWQQRLAQRLTQLSGLDRAFFNNSGAEANETALKLARLHGWKKGIEAPLVVVMENAFH 130 Query: 194 GNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDL--IQYGTTG 251 G T+ A+ + Q L D + FG DL L I Sbjct: 131 GRTLGTLAASDGPSVRLGFQQ------LPGDFLKVRFG--------DLAALEAITKAFGP 176 Query: 252 HIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHN 311 I + E IQG G++ GYL A D + G L + DE+Q+G RTG ++ F+ Sbjct: 177 RITAVLLEPIQGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEG 236 Query: 312 VVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKE 371 +VPD++T+AKG+GNG P+GA + +A + T S+ +TFGGN ++ G VL++IE++ Sbjct: 237 IVPDVMTLAKGLGNGVPIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQ 296 Query: 372 KLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMD 431 L +NAA G L +L +H + +RG+GLM+G+EL S + A+ Sbjct: 297 GLLQNAAQQGERLLARLRVELNEHAQVVAIRGQGLMIGIELASPCRDLAQRAAQ------ 350 Query: 432 QMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAM 470 E G+LI G + R+ PPL + + +V A+ Sbjct: 351 ---EHGLLINVTR--GKIIRLLPPLTLDTQEVEMIVRAI 384 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: 397 Number of extensions: 18 Number of successful extensions: 3 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: 389 Length adjustment: 32 Effective length of query: 445 Effective length of database: 357 Effective search space: 158865 Effective search space used: 158865 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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