Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit B (characterized)
to candidate WP_012386182.1 BIND_RS16615 succinyl-CoA--3-ketoacid-CoA transferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2112 (221 letters) >NCBI__GCF_000019845.1:WP_012386182.1 Length = 218 Score = 196 bits (498), Expect = 3e-55 Identities = 105/211 (49%), Positives = 139/211 (65%), Gaps = 2/211 (0%) Query: 10 QRVAREMQDGYYVNLGIGIPTLVANYIPEGMEVMLQSENGLLGMGAFPTEAEVDADMINA 69 +R A E++ VNLGIG+PT VA Y+ ++ QSENGL+GMGA + + +A Sbjct: 9 ERTALELRPHTLVNLGIGLPTGVAYYVKPDSGILFQSENGLIGMGARAHAGTENPYLTDA 68 Query: 70 GKQTVTARIGASIFSSAESFAMIRGGHIDLTVLGAFEVDVEGNIASWMIPGKLVKGMGGA 129 G +TA GA F SA SF +IR H+D VLG EVD G +A+WM+PGKLV GMGGA Sbjct: 69 GGFCITAVPGAMSFDSALSFGLIRR-HVDTCVLGGLEVDETGRLANWMVPGKLVPGMGGA 127 Query: 130 MDLVAGAENIIVTMTHASKDGESKLLPRCSLPLTGAGCIKRVLTDLAYLEIQDGAFILKE 189 MDLVA A II+ M H +K GE K++P+C+LPLT + ++TDLA +E + +L+E Sbjct: 128 MDLVANANRIIIAMQHTAK-GEPKIVPKCTLPLTADRRVDLIVTDLAVIEPTEAGLVLRE 186 Query: 190 RAPGVSVEEIVAKTAGKLIVPDHVPEMQFAA 220 RAPGVSVE+I+A T+ KLIV +PEM A Sbjct: 187 RAPGVSVEDIIANTSAKLIVEGDIPEMPITA 217 Lambda K H 0.318 0.135 0.381 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: 197 Number of extensions: 10 Number of successful extensions: 3 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: 221 Length of database: 218 Length adjustment: 22 Effective length of query: 199 Effective length of database: 196 Effective search space: 39004 Effective search space used: 39004 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: 45 (21.9 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