Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 166 bits (420), Expect = 1e-45 Identities = 124/395 (31%), Positives = 185/395 (46%), Gaps = 38/395 (9%) Query: 78 RKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYL 137 R L G+ YLF GRRYLD AG+AV GHCHP +V+ + Q ++ H + LY Sbjct: 6 RADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTSNLYR 65 Query: 138 NHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQD------IVAVRNG 191 + L + D VFF NSG EA E ++ MA+ + I+ Sbjct: 66 VAGQESVAAKLVERSFAD--TVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICAEGA 123 Query: 192 YHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTG 251 +HG AT+ A GQ H P V G D Y + ++ T Sbjct: 124 FHGRTLATVAAGGQKK-----------HLEGFAP--AVDGFDHVPYGN--LNALRASITE 168 Query: 252 HIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHN 311 A + E +QG GGIV P YL T + G L I DEVQ+G RTG + E Sbjct: 169 ETAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAG 228 Query: 312 VVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKE 371 + PDI+ +AKG+G GFP+GA + T + A + ++ +TFGGN ++ VL+++ + Sbjct: 229 IAPDIMGVAKGLGGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEP 288 Query: 372 KLQENAAMVGSYLKEKLTQLKEKHE-IIGDVRGRGLMLGVELVSDRKLKTPATAETLHIM 430 E+ + + L+ K+ + ++ +VRG GLMLG+ K + P T ++ Sbjct: 289 GFLEHVQAMAALLRSKVEDTAARFPGVVEEVRGLGLMLGI------KPRMPNT----EMV 338 Query: 431 DQMKELGVL-IGKGGYFGNVFRITPPLCFTKDDAD 464 ++ E G+L +G G N+ R+ PPL D Sbjct: 339 ARLAEGGLLTVGAG---DNIVRLLPPLIINDAQVD 370 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: 441 Number of extensions: 18 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: 477 Length of database: 384 Length adjustment: 32 Effective length of query: 445 Effective length of database: 352 Effective search space: 156640 Effective search space used: 156640 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