Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012333639.1 M446_RS18530 aspartate aminotransferase family protein
Query= curated2:Q9CC12 (404 letters) >NCBI__GCF_000019365.1:WP_012333639.1 Length = 445 Score = 191 bits (485), Expect = 4e-53 Identities = 152/442 (34%), Positives = 211/442 (47%), Gaps = 53/442 (11%) Query: 2 TPTQTNTATMQQRWETVMMNN-YGTPPIVLASGNGAVVTDVDSNTYLDLLGGIAVNVLGH 60 TP + N + W N + P +L + G T D T LD G+ GH Sbjct: 3 TPLRANRPRLDAYWMPFTANRQFKAAPRLLVAAEGMHYTADDGRTVLDGTAGLWCVNAGH 62 Query: 61 RHPAVIEAVTHQITTLGHTSNLYATEP-SITLAEELVALL-GADTQT--RVFFCNSGTEA 116 ++EAV HQ++TL + + P + AE L A+ G D RVFF SG+E+ Sbjct: 63 GRRRIVEAVAHQLSTLDYAPSFQMGHPIAFDFAERLAAIAPGPDGSRLDRVFFTGSGSES 122 Query: 117 NELAFKLS----RLTG---RTKLVAAQAAFHGRTMGSLALTGQPAKQAAFEPLPG--HVT 167 + A K++ R G RT+L+ + +HG G +++ G + + F LPG H+ Sbjct: 123 VDTALKIALAYQRAVGQGTRTRLIGRERGYHGVGFGGISVGGLVSNRRMFPLLPGADHLR 182 Query: 168 HVP--------YGQVDALAAAVDN-----------DTAAVFLEPIMGESGVIVPPEGYLA 208 H GQ + A D+ AAV +EP+ G +GV+VPP+GYL Sbjct: 183 HTHDLARNAFVKGQPEHGAELADDLERMVALHGAETIAAVIVEPVAGSTGVLVPPKGYLE 242 Query: 209 AARDITTRHGALLVIDEVQTGIGRTGAFFAHQHDSITPDVVTLAKGL-GGGLPIGAFLAT 267 RDI TRHG LL+ DEV TG GR GA FA +TPD+VT AKGL G +P+GA A+ Sbjct: 243 RLRDIATRHGVLLIFDEVITGFGRLGAPFATDFFGVTPDLVTAAKGLTNGTVPMGAVFAS 302 Query: 268 GPAAELLTLG-------LHGSTFGGNPVCTAAALAVLRVLATQGLVRRAEVLGDSMRIGI 320 + L G HG T+ G+P AA LA L V +GL+ R L + + Sbjct: 303 RAVHDALMRGPQDAIELFHGYTYSGHPAGCAAGLATLDVYEEEGLLTRVAELQEFWHEAM 362 Query: 321 ESL--SHPLIDQVRGRGLLLGIVLTAPRAKDIEKAARDA-------GFLVNATAPEVIRL 371 L + +ID VR GL+ GI L APRA A DA G L+ T ++I L Sbjct: 363 HGLRAARNVID-VRTIGLIAGIEL-APRAGAPGARAYDAFVDCFEKGLLIRVTG-DIIAL 419 Query: 372 APPLIITESQIDSFITALPGIL 393 +PPLI +D ++ L L Sbjct: 420 SPPLIAERRHVDDMVSMLADAL 441 Lambda K H 0.318 0.135 0.385 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: 473 Number of extensions: 23 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: 404 Length of database: 445 Length adjustment: 32 Effective length of query: 372 Effective length of database: 413 Effective search space: 153636 Effective search space used: 153636 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: 51 (24.3 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