Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_010936947.1 DET_RS06460 acetylornithine transaminase
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000011905.1:WP_010936947.1 Length = 398 Score = 193 bits (491), Expect = 8e-54 Identities = 136/409 (33%), Positives = 207/409 (50%), Gaps = 39/409 (9%) Query: 79 FYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQL-KLINHSTI 137 FY P+ IV+ + V+D+ G+ YLD G A S GHCHP VV +V +Q LI S Sbjct: 16 FYRAPITIVKGQGAKVWDDKGKEYLDFVAGWAVNSLGHCHPAVVKAVSEQAGTLIQTSNN 75 Query: 138 LYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLY-----TGCNDIVSLR 192 Y TI A + L +FF NSGTEA E A+ +AR Y G ++++ Sbjct: 76 FY---TIPQLKLAKLLVDNSVLDRIFFCNSGTEATEGAVKLARRYGKLKLKGAYEVITAT 132 Query: 193 NSYHGNAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGI-FGSDGEKYASDVHDLIQFG 251 S+HG A + A+ QS ++ +PY + G +Y + I+ Sbjct: 133 GSFHGRTLAMVSASGQSKYQ--------------EPYTPLPTGFINVEYNNP--QAIKTA 176 Query: 252 TSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGF 311 + + + E IQG G+ GYL A I +AG + I DE+Q+G RTG F + Sbjct: 177 ITDKTCAVMLEPIQGESGVNVPDKGYLKAVRQICDEAGILLILDEIQTGIGRTGKLF-AY 235 Query: 312 QSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRV 371 + G+ PDI+T+AKG+ GIP+GA + E A V ++ + +TFGGNP+ AAG+A ++ Sbjct: 236 EHSGIEPDIITLAKGLAGGIPIGAFMAK-ESASVFAKGEHGSTFGGNPLACAAGYAAMKF 294 Query: 372 LHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETL 431 + + + ENA +GS+L L LK K+ LI RG GL++ ++F KT E Sbjct: 295 ILDNHISENAGSMGSYLAEGLEKLKIKHSLIQGCRGCGLLMALDF------KTNIAKE-- 346 Query: 432 HLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVMDHAMSK 480 +++ E G+L+ N R PPL T +D D + +D +++ Sbjct: 347 -IVESCLEEGLLL--NAVKPNALRFMPPLNITQADIDAAIAKLDSVLTR 392 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: 416 Number of extensions: 25 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: 481 Length of database: 398 Length adjustment: 32 Effective length of query: 449 Effective length of database: 366 Effective search space: 164334 Effective search space used: 164334 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