Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate CCNA_02488 CCNA_02488 acetate/3-ketoacid CoA transferase, subunit A
Query= reanno::psRCH2:GFF1045 (231 letters) >FitnessBrowser__Caulo:CCNA_02488 Length = 245 Score = 300 bits (769), Expect = 1e-86 Identities = 157/229 (68%), Positives = 177/229 (77%) Query: 2 NKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFG 61 +KIY SAA ALEG+V DGMT+ GGFGL G PE LI AL+D+G K LT ISNN G DGFG Sbjct: 7 SKIYESAAAALEGVVFDGMTLMSGGFGLSGNPETLIPALKDTGVKALTVISNNCGADGFG 66 Query: 62 LGLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTK 121 L +LL QI KMVSSYVGENK FE+ YL+GEL LE PQGTLAE++RAGGAGIPAFYTK Sbjct: 67 LWMLLNNGQIRKMVSSYVGENKLFEQLYLSGELELELNPQGTLAERIRAGGAGIPAFYTK 126 Query: 122 TGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAAM 181 TG GT+VAEGK F GE Y+ E L ADL++VKAWKAD GNL+FR TARNFNP+ A Sbjct: 127 TGVGTVVAEGKPVETFEGEPYLRETWLRADLSIVKAWKADPEGNLVFRMTARNFNPVMAT 186 Query: 182 AGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVR 230 AG+V +VEVEEIVE GELD + IH PGIYV RIV + EKRIEK T R Sbjct: 187 AGKVTIVEVEEIVEAGELDANAIHTPGIYVDRIVKSTINEKRIEKLTTR 235 Lambda K H 0.316 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: 217 Number of extensions: 6 Number of successful extensions: 1 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: 231 Length of database: 245 Length adjustment: 23 Effective length of query: 208 Effective length of database: 222 Effective search space: 46176 Effective search space used: 46176 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 (21.6 bits) S2: 46 (22.3 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