Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_017751028.1 PN53_RS06660 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q8R7C1 (393 letters) >NCBI__GCF_000816635.1:WP_017751028.1 Length = 454 Score = 196 bits (497), Expect = 1e-54 Identities = 135/439 (30%), Positives = 221/439 (50%), Gaps = 62/439 (14%) Query: 4 YEKKYLMDTYNRY----PIMLVKGEGTRVWDSEGNAYLDFVAGIAVNSLGHCHPALVEAI 59 Y++KY + +++ P+++ K EG WDS G Y D + + ++GH + ++EAI Sbjct: 19 YDRKYNLHSWSAQKKIDPLVITKAEGIYFWDSTGKKYFDMSSQLVNLNIGHGNRKVIEAI 78 Query: 60 KKQAETLIHCSNLYWNEKQIELARMISENSFGG--KVFFANSGAEANEGAIKLARKYASL 117 K+QA+ + Y + + +LA + E + KVFF GA+ANE AIK+A+ Y Sbjct: 79 KEQADKMPFMGPGYAVDVRAKLAERVIEKAPDNMDKVFFTLGGADANENAIKIAKMYTG- 137 Query: 118 KYGGKRYKIITAKNSFHGRTFGALTATGQEKYH----------KGFGPLLAGFK------ 161 ++KI + S+HG +FGA +G+ + + K F P + K Sbjct: 138 -----KFKIFSRYRSYHGASFGAANLSGEPRRYTCEPGIPGFVKFFDPYIYREKIKFESE 192 Query: 162 ------YVPLNDIEALYEAVDDEVCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLF 215 Y+ + + +YE D +V A+ +E I G G+ Y++ +R++CD+ +L Sbjct: 193 EKATEFYLGKLEEQLIYEGTD-KVAAVFIETITGSNGVIIPPKGYLQGIRRLCDKYGILM 251 Query: 216 ILDEVQTGIGRTGKLFGYEHYGVVPDIMTLAKGLGGGF-PIGAIVAKEDKAVFKPGDH-- 272 I DEV G GRTG+ F ++ V PDI+T AKG+ G+ P+G ++ DK + + D Sbjct: 252 ICDEVMAGWGRTGEWFACNNWNVKPDIITFAKGITCGYVPLGGVLV--DKKIAEYFDDNV 309 Query: 273 ---ASTFGGNPLACAAGIAVLNEVTKDGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGK 329 T+ +PLACAAG A L ++ +E G E LE L++KH V ++R Sbjct: 310 LMCGLTYNAHPLACAAGCATLEVYEEEKLIENSRNMGAILGEKLEELKEKHSSVGDVRYI 369 Query: 330 GLMVGCEVDLED----------------ASEIVLKALEKGLLINSVSH-NVLRFVPPLIV 372 GL E+ + ++I+ EKG ++ SH N + PPLI+ Sbjct: 370 GLFSAVELVKDKNTREALVPYGKDPEGRMTKIIGMLKEKG--FSTYSHENSIMIAPPLII 427 Query: 373 TEEEIDEALQILDDVLSEI 391 +EE++EAL ILDDV+ + Sbjct: 428 NKEELEEALDILDDVMDSV 446 Lambda K H 0.319 0.139 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: 528 Number of extensions: 27 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: 393 Length of database: 454 Length adjustment: 32 Effective length of query: 361 Effective length of database: 422 Effective search space: 152342 Effective search space used: 152342 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 (21.7 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