Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_013643724.1 METBO_RS00600 acetylornithine transaminase
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000191585.1:WP_013643724.1 Length = 390 Score = 219 bits (559), Expect = 1e-61 Identities = 134/401 (33%), Positives = 212/401 (52%), Gaps = 33/401 (8%) Query: 78 RKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYL 137 R + +V GK ++D G Y+D AGIAV N GH +P V E + NQ+K+L H + LY Sbjct: 20 RHKIALVKGKDTTVWDADGNSYIDCVAGIAVNNVGHSNPKVGEAICNQVKKLIHTSNLYY 79 Query: 138 NHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAA 197 ++ L P + FF NSG EANE A+ +A+ ++G +I+ + N +HG Sbjct: 80 TEEQVTLAKLLVDVSPH--QKAFFCNSGAEANEGAIKLARKHSGKGEIITMINSFHGRTI 137 Query: 198 ATMGATGQSMWK--FNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAG 255 T+ ATGQ ++ F + +A PY + + ++++I T A Sbjct: 138 TTITATGQPKYQKGFEPLTPGFKYA----PYGDI---------EAVKEMISPST----AA 180 Query: 256 FICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPD 315 + E +QG G++ GYL + + + L I DEVQ+GF RTG + + V PD Sbjct: 181 VLVEPVQGESGVIVPPEGYLKQLKEVCEDSNVLLIFDEVQTGFGRTGEMFASQTFGVTPD 240 Query: 316 IVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQE 375 I ++AK I GFP+GAV+ ++A + TFGGN + A A +N I +EKL + Sbjct: 241 ITSLAKAIAGGFPMGAVLANNDVAESFVPGDHAATFGGNPLGCAAAKASINFILEEKLLD 300 Query: 376 NAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKE 435 + GSY EKL +L+ +HE+I +VRG+GLM+GVE+ +D ++D++ + Sbjct: 301 KSKENGSYFVEKLLKLQNQHELINEVRGKGLMVGVEMKTDCGC----------MVDELFK 350 Query: 436 LGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAMDYSMSK 476 G+++ GNV R PPL TK+ D + A++ +S+ Sbjct: 351 EGIIVNCAA--GNVLRFVPPLTITKEQIDTVTAALNNVLSR 389 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: 473 Number of extensions: 16 Number of successful extensions: 4 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: 390 Length adjustment: 32 Effective length of query: 445 Effective length of database: 358 Effective search space: 159310 Effective search space used: 159310 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