Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= BRENDA::B1XNF8 (418 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 306 bits (784), Expect = 7e-88 Identities = 166/400 (41%), Positives = 241/400 (60%), Gaps = 13/400 (3%) Query: 21 DQYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQK 80 + + TYGR+P+++A+G+G RLWD +G+ Y+D ++GIA +LGH H L + +AQ +K Sbjct: 13 ESLLCRTYGRYPISVARGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARK 72 Query: 81 LHHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQP 140 L H+SNL+Y EQ LA+ ++ S K FFCNSGAEANEAAIKL R+Y V E Sbjct: 73 LVHVSNLFYQEEQLDLAERLLSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQG-REAY 131 Query: 141 VILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRR 200 I++ +FHGRTLAT+ ATGQ K+Q F P+P+GF VP DI AL AI + Sbjct: 132 EIITLTGAFHGRTLATVAATGQAKFQDGFYPMPEGFRQVPSGDIEALRAAI------GPQ 185 Query: 201 VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGI 260 A +++E +QGEGGV P D +Y +AV+ +C E G+L + DE+Q G+ RTG++W ++N G+ Sbjct: 186 TAGVLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYGL 245 Query: 261 EPDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQEN 319 EPDI + AK LA G+P+GAMM D A F G HA+TFG A A VE + +++ Sbjct: 246 EPDIVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFGAGALVSAVASRTVEIMLRDD 305 Query: 320 LLENVNARGEQLRAGLKTLAEKYPYFSD-VRGWGLINGMEIKADLELTSIEVVKAAMEKG 378 L G ++ + + +K P D VRG GL+ G+ L EV +A +++G Sbjct: 306 LAGRAATEGARIMDRFRAMGQKLPGTIDHVRGLGLMIGVV----LAFPGKEVWQALIDRG 361 Query: 379 LLLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLAAMAL 418 + VLR +P L + A+++ L+ L+A L Sbjct: 362 FICNLTQDCVLRLLPALTIPRADLDAFADALEDILSARTL 401 Lambda K H 0.319 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: 380 Number of extensions: 15 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: 418 Length of database: 402 Length adjustment: 31 Effective length of query: 387 Effective length of database: 371 Effective search space: 143577 Effective search space used: 143577 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 09 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