Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate SM_b20755 SM_b20755 propionyl-CoA carboxylase subunit beta
Query= SwissProt::Q3J4E3 (510 letters) >FitnessBrowser__Smeli:SM_b20755 Length = 510 Score = 844 bits (2180), Expect = 0.0 Identities = 416/510 (81%), Positives = 458/510 (89%) Query: 1 MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60 M+ +L+++E RRA ARAGGG+RR+ AQH +GKLTARERI++LLDEGSFEE+DM+V HR Sbjct: 1 MRAVLEQVEARRAEARAGGGERRIAAQHGKGKLTARERIDVLLDEGSFEEYDMYVTHRSV 60 Query: 61 DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120 DFGM + GDGVVTGWGTINGR VYVFSQDFTV GGSLSETHAQKICKIMDMA +NGA Sbjct: 61 DFGMAGQKIPGDGVVTGWGTINGRQVYVFSQDFTVLGGSLSETHAQKICKIMDMAARNGA 120 Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEGVASLAGYA+VF+RN SGVIPQISVIMGPCAGGAVYSPAMTDF Sbjct: 121 PVIGLNDSGGARIQEGVASLAGYAEVFRRNAEVSGVIPQISVIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240 IFMVRD+SYMFVTGPDVVKTVTNE+VTAEELGGA THT KSSVADGA+END+EAL +R Sbjct: 181 IFMVRDSSYMFVTGPDVVKTVTNEIVTAEELGGARTHTTKSSVADGAYENDIEALEHVRL 240 Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300 L DFLPL+NR PVRPF DD R+E LD+LIPD+ +PYDMKELIL IADEADF+E+Q Sbjct: 241 LFDFLPLNNREKPPVRPFHDDPGRLEMRLDSLIPDSAAKPYDMKELILAIADEADFFELQ 300 Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360 FA NIITGFIR+EGQTVGV+ANQPMVLAGCLDIDSSRKAARFVRFCDAF+IPILTLVD Sbjct: 301 ASFARNIITGFIRIEGQTVGVIANQPMVLAGCLDIDSSRKAARFVRFCDAFSIPILTLVD 360 Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420 VPGFLPGT QEYGGVIKHGAKLLFAY +ATVP VT+ITRKAYGGAYDVMASKH+ D NY Sbjct: 361 VPGFLPGTAQEYGGVIKHGAKLLFAYSQATVPMVTLITRKAYGGAYDVMASKHIGADVNY 420 Query: 421 AWPTAEIAVMGAKGATEILYRSELGDKEKIAARAKEYEDRFANPFVAAERGFIDEVIMPH 480 AWPTAEIAVMGAKGATEILYRSELGD KIAAR KEYE+RFANPFVAAERGFIDEVIMPH Sbjct: 421 AWPTAEIAVMGAKGATEILYRSELGDPAKIAARTKEYEERFANPFVAAERGFIDEVIMPH 480 Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510 S+RRR+++AFASLRNK++ W+KHD IPL Sbjct: 481 SSRRRIARAFASLRNKQVETRWRKHDTIPL 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: 906 Number of extensions: 25 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 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