Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_089323505.1 CHB58_RS07585 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_900188395.1:WP_089323505.1 Length = 395 Score = 212 bits (539), Expect = 2e-59 Identities = 134/405 (33%), Positives = 209/405 (51%), Gaps = 35/405 (8%) Query: 78 RKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYL 137 R P++ V G+ YL+DE+G++YLD AGIAV N GH H ++ E + Q K L H + L+ Sbjct: 17 RYPISFVKGEGCYLYDENGKKYLDFLAGIAVCNLGHSHKEIAETICKQAKTLIHTSNLFH 76 Query: 138 NHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQ-----DIVAVRNGY 192 A+ ++ + G VFF NSG EANE A+ +A+ Y + +I+A +N + Sbjct: 77 IKPQAELAKLICENSFGSK--VFFCNSGAEANEGAIKLARRYAFERGKKGYEIIAFKNSF 134 Query: 193 HGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGH 252 HG A++ TGQ + G SD + + D ++ + Sbjct: 135 HGRTFASVSVTGQGKYNEGF---------------GPMLSDVKFAEFNNIDSVKKIISKK 179 Query: 253 IAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNV 312 G I E IQG GGI+ +L + + I DEVQ+G RTG + ++ + V Sbjct: 180 TCGIIVEPIQGEGGIIPAEKEFLKELRNLANNYDAVLIFDEVQTGIGRTGKLFAYQHYGV 239 Query: 313 VPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEK 372 PD++T+AK +GNG P+GA+VT + +L + +TFGGN +ST AG+ V+ +I EK Sbjct: 240 EPDVMTLAKALGNGVPIGAIVTNERTSQILKPGLHASTFGGNFLSTAAGVKVMEIISDEK 299 Query: 373 LQENAAMVGSYLKEKLTQLK-EKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMD 431 +N G YL EKL ++K E I ++RG GLM+G L D K +++ Sbjct: 300 FLKNVEAKGKYLTEKLKEIKNELQGTISEIRGIGLMIGAILKIDGK----------KLVE 349 Query: 432 QMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAMDYSMSK 476 + + G++I G NV R+ PPL T+ + D +E + S+ + Sbjct: 350 KALKNGLIINVTG--ENVLRLVPPLTITQQEIDEGIEILKESIKE 392 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: 444 Number of extensions: 21 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: 395 Length adjustment: 32 Effective length of query: 445 Effective length of database: 363 Effective search space: 161535 Effective search space used: 161535 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 10 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