Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_097029019.1 CRO07_RS00205 acyl-CoA carboxylase subunit beta
Query= SwissProt::Q3J4E3 (510 letters) >NCBI__GCF_900207575.1:WP_097029019.1 Length = 510 Score = 997 bits (2578), Expect = 0.0 Identities = 496/510 (97%), Positives = 506/510 (99%) Query: 1 MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60 MKDILQELE+RRAIARAGGGQRRVEAQHKRGKLTARERI+LLLDEGSFEEFDMFVRHRCT Sbjct: 1 MKDILQELEDRRAIARAGGGQRRVEAQHKRGKLTARERIDLLLDEGSFEEFDMFVRHRCT 60 Query: 61 DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120 DFGM+DDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA Sbjct: 61 DFGMEDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120 Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF Sbjct: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEAL EIRR Sbjct: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALAEIRR 240 Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300 LVDFLPLSNRTPAPVRPFFDDVAR+EDSLDTLIPDNPNQPYDMKELILKIADE DFYEIQ Sbjct: 241 LVDFLPLSNRTPAPVRPFFDDVARVEDSLDTLIPDNPNQPYDMKELILKIADEGDFYEIQ 300 Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360 KD+AANIITGFIRLEGQ+VGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD Sbjct: 301 KDYAANIITGFIRLEGQSVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360 Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVM+SKHLRGDFNY Sbjct: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMSSKHLRGDFNY 420 Query: 421 AWPTAEIAVMGAKGATEILYRSELGDKEKIAARAKEYEDRFANPFVAAERGFIDEVIMPH 480 AWPTAEIAVMGAKGATEILYR+EL DKEKIAAR KEYEDRFANPFVAAERGFIDEVIMPH Sbjct: 421 AWPTAEIAVMGAKGATEILYRAELADKEKIAARTKEYEDRFANPFVAAERGFIDEVIMPH 480 Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510 STRRRVS+AFASLRNKKL+NPWKKHDNIPL Sbjct: 481 STRRRVSRAFASLRNKKLSNPWKKHDNIPL 510 Lambda K H 0.321 0.138 0.404 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: 983 Number of extensions: 29 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: 510 Length of database: 510 Length adjustment: 34 Effective length of query: 476 Effective length of database: 476 Effective search space: 226576 Effective search space used: 226576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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