Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_010530243.1 ON01_RS06680 acetylornithine transaminase
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000224785.1:WP_010530243.1 Length = 385 Score = 347 bits (891), Expect = e-100 Identities = 183/395 (46%), Positives = 252/395 (63%), Gaps = 19/395 (4%) Query: 33 TYVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKL 92 T + TY RF +++ R G+T+ DT+GKSYLDF AGI C+LGH HP++ A+ Q+ Sbjct: 2 TALFPTYKRFNLSVERASGTTVEDTDGKSYLDFGAGIGVCSLGHRHPSVQEALQTQLNAY 61 Query: 93 HHVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPV 152 HVSNLY+ P Q +A + ++S D+VFFCNSG EANEAAIKL RK + Sbjct: 62 WHVSNLYHNPVQENVANLLTQYSSGDQVFFCNSGTEANEAAIKLARKAT-------GKHK 114 Query: 153 ILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRV 212 ++T SFHGRTL + ATGQ K F P++ F YVP+ND +L+ + + Sbjct: 115 MITFNQSFHGRTLGAMAATGQEKIHNGFGPMLETFQYVPFNDNETLKQVI------DGET 168 Query: 213 AAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVE 272 AA+ LE +QGEGG+ P D + + + +C +ND+LL+ DEVQ G+GRTGK + Y+H G+ Sbjct: 169 AAVMLEVVQGEGGINPADTDFVQELERVCQENDVLLIVDEVQTGIGRTGKPFAYQHYGIS 228 Query: 273 PDIFTSAKGLAGGVPIGAMMCK-KFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRL 331 PDI TSAKGLA GVP+GAM+ K K D F PG+HA+TFGGNPLA AA AVLK + D Sbjct: 229 PDIITSAKGLADGVPVGAMIAKDKLRDAFGPGSHAATFGGNPLAMAAAEAVLKHVFQDGF 288 Query: 332 LDNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGL 391 L V + L L E+ P + + +RG GL+ G+E S S +V+A +E+GL Sbjct: 289 LQEVTDKSNYLMDCLNELIKPLPVV-SSIRGKGLMIGIECSQNVS----HLVEALIEKGL 343 Query: 392 LLAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAIA 426 L+ AGP VLR +PPL+V++ EI QAV++L + ++ Sbjct: 344 LVLSAGPNVLRLLPPLIVSKEEIDQAVDLLSEVLS 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: 386 Number of extensions: 17 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: 385 Length adjustment: 31 Effective length of query: 398 Effective length of database: 354 Effective search space: 140892 Effective search space used: 140892 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 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