Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= curated2:P30900 (393 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 206 bits (525), Expect = 8e-58 Identities = 142/436 (32%), Positives = 223/436 (51%), Gaps = 55/436 (12%) Query: 2 IASVLPTYTRAPL-AFVRGEGSWLWTADGSRYLDLGAGIAVNALGHAAPDLVATLTEQAG 60 ++ V P +T+A L V G+G +L A+G RYLD G AV+ LGH+ +++A + EQ G Sbjct: 1 MSHVFPRHTKADLPTAVAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVG 60 Query: 61 KLWHVSNLYRIPEQ-ERLADMLVAKTFADT--VFFTNSGTEACELAVKMVRKHFYDKGQP 117 KL + E E LAD+L+++ D V+F + G+EA E A+K+ R++ ++G Sbjct: 61 KLAFAHTGFLTSEPAEALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDT 120 Query: 118 ERTEILTFSGAFHGRSSAAIAAAGTEKMVKGFGPLL-------PGFVHLPWGDLDA---- 166 R ++ ++HG + A+AA G + F PLL P + ++ GD ++ Sbjct: 121 TRRHVIARRQSYHGNTLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDY 180 Query: 167 -------VKAAVT----ETTAAILIEPIQGE-GGIRPAPEGFLRALREICDETGTLLVFD 214 ++A + ET A + EP+ G G PA EG+ + +REICD+ G LL+ D Sbjct: 181 GQRVANELEAEILRLGPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILD 240 Query: 215 EVQCGVARTGKLFAHEWAGVTPDVMMVAKGIGGGF-PLGAVLATEDAASGMIAGT----H 269 EV CG+ RTG LFA E GV PD++ +AKG+G G+ P+GA+L + + G+ H Sbjct: 241 EVMCGMGRTGHLFACEADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQH 300 Query: 270 GSTYGGNPLGCAIGAKMIEIVTAPGFLDEVSRKAGFLRQWLEGLVAAHPDIFEEVRGQGL 329 G TY G+P+ A G ++ + G + + L L HP + ++RG+GL Sbjct: 301 GHTYIGHPVATAAGLAVVRALLDRGLVQRSAEMGETLHAALVARFGQHPHV-GDLRGRGL 359 Query: 330 MLGLRL------KLP-------PGDVVKAAYAQNLLTVPAA--------DNVLRLLPALT 368 G+ L K P G + KAA+ L+ P A D++L L P Sbjct: 360 FRGIELVADRESKTPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHIL-LAPPFI 418 Query: 369 ISEDDMAEAVRRLDAA 384 +SED + E +L+ A Sbjct: 419 LSEDQIGEITDKLEVA 434 Lambda K H 0.320 0.136 0.409 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: 443 Number of extensions: 16 Number of successful extensions: 4 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: 440 Length adjustment: 31 Effective length of query: 362 Effective length of database: 409 Effective search space: 148058 Effective search space used: 148058 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 (21.8 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