Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_044410795.1 NA59_RS08125 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000934765.1:WP_044410795.1 Length = 392 Score = 328 bits (841), Expect = 2e-94 Identities = 176/392 (44%), Positives = 249/392 (63%), Gaps = 26/392 (6%) Query: 35 VMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLHH 94 +MNTY R PI G+G+TL+D +G++YLD V+GIA C+LGHAHP + A+ +Q +KL H Sbjct: 5 LMNTYARLPITFVEGEGATLYDEQGRAYLDAVSGIAVCSLGHAHPEIAHALCEQSKKLIH 64 Query: 95 VSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVIL 154 SNLY++ Q LA ++ S D+VFF NSGAEANE AIK+ RKY + P IL Sbjct: 65 TSNLYHVVNQQLLADELIRLSGMDKVFFGNSGAEANEGAIKIARKYGND--QGKTNPEIL 122 Query: 155 TAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRVAA 214 + SFHGRT+AT++ATG K Q+ F PLV GF VP++DI ++E K+A + + A Sbjct: 123 VMENSFHGRTMATLSATGSQKVQEGFHPLVSGFVRVPFDDIAAVEQKIA----SHPNLVA 178 Query: 215 IFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVEPD 274 I +EP+QGEGGV Y K +R +CDQ+++LL+ DE+Q GVGRTGK + ++H + PD Sbjct: 179 ILVEPVQGEGGVHVPKDGYLKALRALCDQHNLLLMIDEIQTGVGRTGKWFAFQHEDILPD 238 Query: 275 IFTSAKGLAGGVPIGAMMCK-KFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLLD 333 + + AK L GVPIGA + + K +V PGNH +TFGGNPLACAAGLAV+KTIE +D Sbjct: 239 VLSLAKALGNGVPIGACLARGKAAEVLAPGNHGTTFGGNPLACAAGLAVIKTIEHHNFID 298 Query: 334 NVQARGEQLRS-------GLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAA 386 V +GE + S G+ ++K +VRG G + G+++ E+VK A Sbjct: 299 YVAKQGEIMISDFKARLAGIEQVK--------QVRGKGYMIGIQLDRPCG----ELVKRA 346 Query: 387 MEQGLLLAPAGPKVLRFVPPLVVTEAEIAQAV 418 +++ LL+ +R +PP V++ + Q V Sbjct: 347 LDKNLLINVTRGDTIRLLPPFVMSHTQQEQLV 378 Lambda K H 0.320 0.137 0.405 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: 468 Number of extensions: 30 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: 429 Length of database: 392 Length adjustment: 31 Effective length of query: 398 Effective length of database: 361 Effective search space: 143678 Effective search space used: 143678 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: 50 (23.9 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