Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= curated2:Q9K8V5 (384 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 261 bits (668), Expect = 2e-74 Identities = 158/380 (41%), Positives = 222/380 (58%), Gaps = 13/380 (3%) Query: 5 FPTYAKWDVTITSGKGTKLYDNQGNEYLDFVSGIAVCNLGHCHPKVVAAVEEQLHSFWHV 64 F Y DVT G+ ++D+QGNEYLD G AV ++GH HP ++EQL + Sbjct: 4 FDVYPLIDVTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFY 63 Query: 65 SNLFHIPIQENVAALLTEQSGMD--AVFFCNSGAEANEAAIKLARKATGKHEIVTFTQSF 122 SN IPIQ+ +A L + SG +F CNSGAEANE A+KLA TGK + FT+ F Sbjct: 64 SNSVQIPIQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGF 123 Query: 123 HGRTLGTMSATGQDKIKTGFGPMLETFHHVPFNDIAAL-KQVVNEQTAAIVLEVIQGEGG 181 HGRT G ++ T KI F E H +PFND+ A+ KQ+ A +++E IQG GG Sbjct: 124 HGRTSGAVALTDNPKIIAPFNAH-EGVHILPFNDLEAVEKQLATGTIAGVIVEGIQGVGG 182 Query: 182 VNLIDPEFAASVNHVCQEHGILLIIDEIQTGIGRTGTAFAFQQYE-LTPDIITVAKGLGN 240 + + DP F ++ + +++G LI+DE+Q+G R+G FA Q E L PD+ITVAKG+GN Sbjct: 183 IQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGN 242 Query: 241 GFPVGAMLGKQHLIDAFSAGSHGSTFGGNPLAMAAAQAVLTEVFQPNFLQAVQEKGKQLL 300 GFP+G +L S G G+TFGGN LA AAA AVL + + N + A E GK ++ Sbjct: 243 GFPIGGVLISPEF--KASHGLLGTTFGGNHLACAAALAVLEVIDEENLITAAAENGKAIM 300 Query: 301 SGLNEALSGLEIVKEIRGNGLLVGIELQEEGAPFIKQLREKGLLVLNA--GPNVIRLLPP 358 + L E ++G V E+RG GL++G +L E P L + + + G + IRLLPP Sbjct: 301 AAL-EKVAG---VTEVRGKGLMIGFDLATEAGPVRAALIHEHKIFTGSAGGKHTIRLLPP 356 Query: 359 LVVTSEELHEAVTQLKEVLD 378 L + + L + +L+ VL+ Sbjct: 357 LNIEPKALTLFLEKLETVLN 376 Lambda K H 0.318 0.135 0.391 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: 419 Number of extensions: 31 Number of successful extensions: 8 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: 384 Length of database: 381 Length adjustment: 30 Effective length of query: 354 Effective length of database: 351 Effective search space: 124254 Effective search space used: 124254 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