Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF4018 Psest_4091 diaminobutyrate--2-oxoglutarate aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__psRCH2:GFF4018 Length = 425 Score = 205 bits (521), Expect = 2e-57 Identities = 142/414 (34%), Positives = 219/414 (52%), Gaps = 38/414 (9%) Query: 7 IDKYHMNTYSR-FPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQV 65 +++ + +Y R FPV +GA + +G YID +AG GH HP + +A+ E + Sbjct: 6 LNESKVRSYCRSFPVVFNQAQGAELVTQDGKRYIDFLAGAGTLNYGHNHPVLKQALLEYI 65 Query: 66 ER--LIHCSNLYYNEPQAEAA---RLLAEAAPK-DLNKVFFCNSGTESVECAIKLARKFT 119 E + H ++Y + RL+ E D F +GT +VE A+KLARK T Sbjct: 66 ENDGITHGLDMYTAAKERFLETFNRLILEPRGMGDYRMQFTGPTGTNAVEAAMKLARKVT 125 Query: 120 GCTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYGD--------VNAVEK 171 G I+F GFHG ++GAL+AT R + + +PY + + ++K Sbjct: 126 GRNNIISFTNGFHGCSIGALAATGNQHHRGGSGISLTDVSRMPYANYFGDKTNTIGMMDK 185 Query: 172 AIDDDT------AAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRT 225 + D + AAVIVE VQGE G+ ++R+L +LC +H +LLIVD++Q+G GRT Sbjct: 186 LLSDPSSGIDKPAAVIVEVVQGEGGLNTASTEWMRKLEKLCRKHEMLLIVDDIQAGCGRT 245 Query: 226 GQFFAFEHEDVLPDIVCLAKGLGG-GVPVGATIAREEVAEAFEPGDHGSTFGGNPLACAA 284 G FF+FE + PDIV L+K L G G+P + R+E+ + ++PG+H TF GN A Sbjct: 246 GTFFSFEEMGIQPDIVTLSKSLSGYGLPFAMVLLRQEL-DQWKPGEHNGTFRGNNHAFVT 304 Query: 285 VCAAVSTVLEEN-LPEAAERKGKLAMRILSEAEDVVEE-------VRGRGLMMGVEVGDD 336 AAV + + + + KGK RI + ++ ++GRG+M+G+ D Sbjct: 305 AAAAVEHFWQNDAFANSVKAKGK---RIADGMQRIIRRHGPDSLYLKGRGMMIGISCPDG 361 Query: 337 ERAKDVAREMLDRGALVNVTSG---DVIRLVPPLVIGEDELEKALAELADALRA 387 E A V R + G LV TSG +V++ + PL+I E++++KALA L A A Sbjct: 362 EIAAAVCRHAFENG-LVIETSGAHSEVVKCLCPLIISEEQIDKALAILDKAFAA 414 Lambda K H 0.318 0.137 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: 381 Number of extensions: 18 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: 389 Length of database: 425 Length adjustment: 31 Effective length of query: 358 Effective length of database: 394 Effective search space: 141052 Effective search space used: 141052 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