Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_005457886.1 SACCYDRAFT_RS16640 acetylornithine transaminase
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000244975.1:WP_005457886.1 Length = 395 Score = 193 bits (491), Expect = 8e-54 Identities = 136/401 (33%), Positives = 192/401 (47%), Gaps = 35/401 (8%) Query: 80 YNTP-LNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTIL 138 Y TP +N+V + V+D +GRRYLD GIA + GH HP VV++V +Q+ I H++ L Sbjct: 18 YGTPAVNLVRGEGAVVWDADGRRYLDFVTGIAVNALGHAHPAVVSAVTRQIATIGHTSNL 77 Query: 139 YLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLYTGCNDIVSLRNSYHGN 198 YLN AE L+ V F NSG EA E A +AR TG + +V+ +HG Sbjct: 78 YLNEPALTLAERLLELSGAGDGKVLFCNSGAEAVEAAFKLAR-RTGRSTVVATEGGFHGR 136 Query: 199 AAATMGATAQ--SNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFGTSGQV 256 + T Q F + GV H P+ + ++ Sbjct: 137 TMGALALTGQPAKRAPFEPLVPGVRHV----PFGDV-------------PALERAIDSDT 179 Query: 257 AGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGV 316 A F+ E +QG G+V YL AA +I R+ G + + DEVQ+G R G+ F +Q G+ Sbjct: 180 AAFVVEPVQGENGVVVPGDDYLRAAREITRRHGVLLVVDEVQTGVGRLGSWF-AYQQTGI 238 Query: 317 IPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEK 376 PD+VT+AKG+G G+PLGA + E A + + TFGGNP+C AAG AVL + Sbjct: 239 QPDVVTLAKGLGGGLPLGACLAFGEAATLFEPGQHGTTFGGNPVCCAAGLAVLDTIAANG 298 Query: 377 LQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQ 436 L E+ +G + L L + L+ VRG GL+LGV A A+ Sbjct: 299 LLEHTAALGKEISAGLERL--DHPLVRTVRGAGLLLGVVLNSAVSAGVAAAAQ------- 349 Query: 437 MKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVMDHA 477 G LV +V R+ PPL + AD L+ + A Sbjct: 350 --RAGFLVNP--VQPDVVRLAPPLVVSQEQADALLAALPAA 386 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: 472 Number of extensions: 23 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: 481 Length of database: 395 Length adjustment: 32 Effective length of query: 449 Effective length of database: 363 Effective search space: 162987 Effective search space used: 162987 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