Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000504245.1:WP_034272173.1 Length = 393 Score = 197 bits (502), Expect = 4e-55 Identities = 138/400 (34%), Positives = 199/400 (49%), Gaps = 37/400 (9%) Query: 75 ALFHFYNTP-LNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLIN 133 A+ Y TP L +V VFD +G YLD GGIA + GH HP VV +V +Q+ + Sbjct: 10 AMMDNYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLG 69 Query: 134 HSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLYTGCNDIVSLRN 193 H++ LY+N AE L+ + G V F NSG EA E A+ + RL TG + +V+ Sbjct: 70 HTSNLYINPVALSLAETLLD-IAGLSGKVLFCNSGAEAVEAAIKITRL-TGKSKLVACDG 127 Query: 194 SYHGNAAATMGATAQSNWK--FNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFG 251 +HG + T Q + + F + GV H P+ G+ A ++ Sbjct: 128 GFHGRTMGALSVTGQPSKREPFEPLLPGVTHV----PF-------GDTAA------LESA 170 Query: 252 TSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGF 311 G A E + G GG+V G+L AA +I AG + + DEVQ+G R G+ F F Sbjct: 171 VDGDTAAVFVEPVLGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWF-AF 229 Query: 312 QSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRV 371 Q GV PD++T+AKG+G G+PLGAV+ + +L + TFGGNP+ AAGHAV+R Sbjct: 230 QQAGVTPDVITLAKGLGGGLPLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRT 289 Query: 372 LHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETL 431 + E+ L ++ +G L + K + L+ +VRG GL+ G+ K P A Sbjct: 290 IREQGLLDHVETLGKDLAAGVR--KLDHPLVSEVRGAGLLQGIGLTKP---VAPTVATA- 343 Query: 432 HLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSD-ADFL 470 + G L+ +V R+ PPL T ADFL Sbjct: 344 -----AQRAGYLINP--VQPDVIRLAPPLIITERQVADFL 376 Lambda K H 0.320 0.136 0.406 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: 513 Number of extensions: 33 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: 481 Length of database: 393 Length adjustment: 32 Effective length of query: 449 Effective length of database: 361 Effective search space: 162089 Effective search space used: 162089 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 Jul 26 2024. The underlying query database was built on Jul 25 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