Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate GFF49 HP15_49 acetyl-CoA acetyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >FitnessBrowser__Marino:GFF49 Length = 391 Score = 360 bits (924), Expect = e-104 Identities = 205/403 (50%), Positives = 261/403 (64%), Gaps = 24/403 (5%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60 M+ VIVDA+R+P+GR + + + A L A V+ L+ RN L +DDV+ GCVTQ Sbjct: 1 MKDVVIVDAVRTPVGRFR--GSLAGVRADHLGALVLNELLYRNGLAAESIDDVVFGCVTQ 58 Query: 61 AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120 GEQSA R + L AG+P VP TIDRKCGS + AVH A I AG+ +IV+A G E+ Sbjct: 59 IGEQSANIARTSLLGAGWPTSVPGLTIDRKCGSGEAAVHCAFGAIAAGSAEIVVAGGAEN 118 Query: 121 MSRVPMGSAR-IGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHEL 179 MSRVPMGS R + +G + RY + SQG AAE VA K+ L R +D+++ SH Sbjct: 119 MSRVPMGSNRDLHGEAFGHLVSDRYE--MTSQGEAAERVAEKWNLDREQLDAFALESHRR 176 Query: 180 AATARESGAFRREIL----------GISTPNGLVEQDETIRPGTSVEKLGTLQASFRNDE 229 AA A +SG F+ EI+ G G DETIR TS+EKL TL+ SFR + Sbjct: 177 AAVAADSGYFKSEIVPVPVADYRENGAEKVEGKFAADETIRRDTSLEKLATLKTSFRKEN 236 Query: 230 LSARFPQIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMML 289 +TAGN+SQISDG SA+LLMS +A+ LGLKP+AR A G DP +ML Sbjct: 237 ---------GRITAGNSSQISDGCSALLLMSSDVARNLGLKPKARIRAVTTVGADPTLML 287 Query: 290 TAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHP 349 T PI A+++ + K+GL+LD+ID +EINEAFA VPLAW + +GADP RLN GGAIALGHP Sbjct: 288 TGPIGATRKVLAKAGLELDEIDLFEINEAFASVPLAWMKEVGADPERLNVNGGAIALGHP 347 Query: 350 LGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 LGASG R+MT+ML+ LE RY LQ++C AGGM ATIIER+ Sbjct: 348 LGASGARIMTSMLNELERRRGRYALQAICCAGGMGTATIIERI 390 Lambda K H 0.318 0.132 0.384 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: 408 Number of extensions: 16 Number of successful extensions: 5 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: 392 Length of database: 391 Length adjustment: 31 Effective length of query: 361 Effective length of database: 360 Effective search space: 129960 Effective search space used: 129960 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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