Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate WP_011907061.1 SARO_RS19990 CoA transferase subunit A
Query= reanno::psRCH2:GFF1045 (231 letters) >NCBI__GCF_000013325.1:WP_011907061.1 Length = 242 Score = 293 bits (751), Expect = 2e-84 Identities = 148/228 (64%), Positives = 174/228 (76%) Query: 3 KIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFGL 62 KI+PS AL+GL+ DGMTI GGFGL G PE LI +RDSG LT ISNNAG +GFGL Sbjct: 4 KIFPSPKAALDGLLFDGMTIMSGGFGLSGNPESLIPEIRDSGVTGLTVISNNAGAEGFGL 63 Query: 63 GLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTKT 122 +LL++RQ+ +M+SSYVG+NK FE QYL+GEL LE PQGTLAE++RAGGAGIPAFYT+T Sbjct: 64 WMLLQSRQVRRMISSYVGDNKLFEEQYLSGELELELNPQGTLAERIRAGGAGIPAFYTRT 123 Query: 123 GYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAAMA 182 G GT+VAEGK F GE YV E L ADLA++KAW+AD +GNL+FR+TARNFNP+ A A Sbjct: 124 GVGTVVAEGKPVEVFEGEEYVRETWLRADLAIIKAWRADTSGNLMFRRTARNFNPVMATA 183 Query: 183 GEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVR 230 V V EVEEIV G DPD IH PGIYV R+V + EKRIEK T R Sbjct: 184 ARVTVAEVEEIVPAGTFDPDCIHTPGIYVDRVVLSTINEKRIEKLTTR 231 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: 200 Number of extensions: 3 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: 242 Length adjustment: 23 Effective length of query: 208 Effective length of database: 219 Effective search space: 45552 Effective search space used: 45552 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 24 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