Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012333042.1 M446_RS15500 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000019365.1:WP_012333042.1 Length = 451 Score = 192 bits (488), Expect = 2e-53 Identities = 137/418 (32%), Positives = 206/418 (49%), Gaps = 46/418 (11%) Query: 15 YSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL 74 + R P + + + +G +D VAG+ GH +V A++ Q L Sbjct: 33 FKRKPRMVARAKDMHYYTPDGRAILDGVAGLWCCNAGHNRDPIVAAIQAQAAELDFSPAF 92 Query: 75 YYNEPQAEA-ARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFT------GCTKFIAF 127 + A A +A AP DL+ VFFCNSG+E+V+ A+K+A + G T+ I Sbjct: 93 QFGHAGGFALASRIAALAPGDLDHVFFCNSGSEAVDTALKVALAYWNARGQGGRTRLIGR 152 Query: 128 EGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPY---------------------GDV 166 E G+HG G +S R F L+ +H+P+ D+ Sbjct: 153 ERGYHGVGFGGISVGGIVTNRRMFGTLLAGVDHLPHTYAREHQAFTVGEPEWGAHLADDL 212 Query: 167 NAVEKAIDDDT-AAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRT 225 + D T AAVIVEP+ G GV PP+G+L+ LR++CD HG+LLI DEV SG GR Sbjct: 213 ERIVALHDASTIAAVIVEPMAGSTGVLPPPKGYLQRLRQICDRHGILLIFDEVISGFGRL 272 Query: 226 GQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD-------HGSTFGG 277 G FA E V+PD++ AK + G VP+G + R+ + +AF G HG T+ Sbjct: 273 GHAFAAERYGVVPDMITFAKAVNSGTVPMGGVLVRKGIYDAFMQGPERTIELFHGYTYSA 332 Query: 278 NPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSEAEDV--VEEVRGRGLMMGVEVGD 335 +PLACAA A + +E+L A R + L D+ V ++R GL+ +++ Sbjct: 333 HPLACAAALATLDLYRDEDLFARARRLEPVLAEGLMSLRDLPNVLDIRALGLVGAIDLAS 392 Query: 336 -DERAKDVAREMLDR-----GALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387 + A A E +DR G +V +T G+ I + PPLVIGED++ + + +L +RA Sbjct: 393 RPDAAGARAFEAMDRAFQEFGLMVRIT-GETIAVTPPLVIGEDQIGELVDKLGRVIRA 449 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: 415 Number of extensions: 22 Number of successful extensions: 7 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: 451 Length adjustment: 32 Effective length of query: 357 Effective length of database: 419 Effective search space: 149583 Effective search space used: 149583 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 Jul 25 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