Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012330737.1 M446_RS03720 aspartate aminotransferase family protein
Query= curated2:Q9CC12 (404 letters) >NCBI__GCF_000019365.1:WP_012330737.1 Length = 445 Score = 182 bits (462), Expect = 2e-50 Identities = 145/439 (33%), Positives = 210/439 (47%), Gaps = 53/439 (12%) Query: 1 MTPTQTNTATMQQRWETVMMNN-YGTPPIVLASGNGAVVTDVDSNTYLDLLGGIAVNVLG 59 +T + N ++ W N + P +L + G T D T LD G+ G Sbjct: 2 ITQPRANRPSLDAYWMPFTANRQFKAAPRLLVAAEGMHYTADDGRTVLDGTAGLWCVNAG 61 Query: 60 HRHPAVIEAVTHQITTLGHTSNLYATEP-SITLAEELVALLGADTQTR---VFFCNSGTE 115 H ++EAV HQ++TL + + P + AE L A+ +R VFF SG+E Sbjct: 62 HGRRHIVEAVAHQLSTLDYAPSFQMGHPIAFDFAERLAAIAPGPEGSRLDRVFFTGSGSE 121 Query: 116 ANELAFKLS----RLTG---RTKLVAAQAAFHGRTMGSLALTGQPAKQAAFEPLPG--HV 166 + + A K++ R G RT+L+ + +HG G +++ G + F LPG H+ Sbjct: 122 SVDTALKIALAYQRAVGQGTRTRLIGRERGYHGVGFGGISVGGLVNNRRMFPLLPGADHL 181 Query: 167 THVP--------YGQVDALAAAVDN-----------DTAAVFLEPIMGESGVIVPPEGYL 207 H GQ + A D+ AAV +EP+ G +GV+VPP+GYL Sbjct: 182 RHTHDLSRNAFVKGQPEHGADLADDLERLVTLHGAETIAAVIVEPVAGSTGVLVPPKGYL 241 Query: 208 AAARDITTRHGALLVIDEVQTGIGRTGAFFAHQHDSITPDVVTLAKGL-GGGLPIGAFLA 266 R+I TRHG LL+ DEV TG GR GA FA +TPD+VT AKGL G +P+GA A Sbjct: 242 ERLREIATRHGILLIFDEVITGFGRLGAPFATDFFGVTPDLVTTAKGLTNGTIPMGAVFA 301 Query: 267 TGPAAELLTLG-------LHGSTFGGNPVCTAAALAVLRVLATQGLVRRAEVLGDSMRIG 319 + + L G HG T+ G+P AA LA L + + L+ RA L + Sbjct: 302 SRAVHDALMRGPQDAIELFHGYTYSGHPAGCAAGLATLDIYEEEDLLTRAAGLQEYWHEA 361 Query: 320 IESL--SHPLIDQVRGRGLLLGIVLTAPRAKDIEKAARDA-------GFLVNATAPEVIR 370 + +L + +ID VR G++ GI L APRA A DA G L+ T ++I Sbjct: 362 MHTLRAARNVID-VRTIGMIAGIEL-APRAGAPGARAYDAFVDCFEKGLLIRVTG-DIIA 418 Query: 371 LAPPLIITESQIDSFITAL 389 L+PPLI +D ++ L Sbjct: 419 LSPPLIAERRHVDDMVSML 437 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: 462 Number of extensions: 24 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