Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Keio:17148 Length = 459 Score = 317 bits (812), Expect = 4e-91 Identities = 175/374 (46%), Positives = 240/374 (64%), Gaps = 18/374 (4%) Query: 32 DDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNEPQAEAARLLAEAA 91 D +G E+ID + G + +GH +P VV AV+ Q+ + S + +A A+ LA Sbjct: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 Query: 92 PKDLNKVFFCNSGTESVECAIKLARKFT---GCTKFIAFEGGFHGRTMGALSATWKPEFR 148 P L FFCNSGTESVE A+KLA+ + G FIA G FHG+++GALSAT K FR Sbjct: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFR 197 Query: 149 EPFEPLVPEFEHVPYGDVNAVEKAID------DDTAAVIVEPVQGEAGVRIPPEGFLREL 202 +PF PL+P F HVP+G++ A+ A++ DD AAVI+EP+QGE GV +PP G+L + Sbjct: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257 Query: 203 RELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGGV-PVGATIAREE 261 R+LCDE G L+I+DEVQ+GMGRTG+ FA EHE+V PDI+CLAK LGGGV P+GATIA EE Sbjct: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEE 317 Query: 262 VAEAF--EPGDHGSTFGGNPLACAAVCAAVSTVLEENLPEAAERKGKLAM----RILSEA 315 V P H +TFGGNPLACAA A ++ +LE+NLP AE+KG + + ++ E Sbjct: 318 VFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREY 377 Query: 316 EDVVEEVRGRGLMMGVEVGDDERAKDVAREMLDRGALV--NVTSGDVIRLVPPLVIGEDE 373 D+V+E RG+G++M +E D+E + A EM + LV + + IR+ PPL + ++ Sbjct: 378 PDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQ 437 Query: 374 LEKALAELADALRA 387 E + AL A Sbjct: 438 CELVIKAARKALAA 451 Lambda K H 0.318 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: 447 Number of extensions: 28 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: 389 Length of database: 459 Length adjustment: 32 Effective length of query: 357 Effective length of database: 427 Effective search space: 152439 Effective search space used: 152439 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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