Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate Ga0059261_3982 Ga0059261_3982 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= SwissProt::Q3J4E3 (510 letters) >FitnessBrowser__Korea:Ga0059261_3982 Length = 508 Score = 794 bits (2050), Expect = 0.0 Identities = 392/510 (76%), Positives = 435/510 (85%), Gaps = 2/510 (0%) Query: 1 MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60 M ++ELE RRA AR GGGQ+R++AQH +GKLTARER+E+LLDEGSFEE DM+V H C Sbjct: 1 MSSTIEELERRRAAARLGGGQKRIDAQHAKGKLTARERVEVLLDEGSFEELDMYVEHNCV 60 Query: 61 DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120 DFGM D GDGVVTG GTINGR+V+VFSQDFTVFGGSLSE HAQKICKIMDMAM+ GA Sbjct: 61 DFGMPDQVVPGDGVVTGSGTINGRLVFVFSQDFTVFGGSLSERHAQKICKIMDMAMKVGA 120 Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEGVASLAGYA+VFQRN++ASGV+PQ+S+IMGPCAGGAVYSPAMTDF Sbjct: 121 PVIGLNDSGGARIQEGVASLAGYAEVFQRNVLASGVVPQLSLIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240 IFMV+D+SYMFVTGPDVVKTVTNE+VT E+LGGA THT KS VAD AFEND+EAL R Sbjct: 181 IFMVKDSSYMFVTGPDVVKTVTNEIVTQEDLGGAVTHTTKSGVADVAFENDIEALLAARD 240 Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300 VDFLP SNR P P RP D RIEDSLDTLIP + NQPYDM ELI K DE DF+E+Q Sbjct: 241 FVDFLPASNREPVPERPCEDPWDRIEDSLDTLIPPSANQPYDMHELIRKTVDEGDFFEVQ 300 Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360 AANII GF R+EG+TVG+VANQPMVLAG LDI+SS+KAARFVRFCDAF IPI+T VD Sbjct: 301 PTHAANIIIGFGRIEGRTVGIVANQPMVLAGVLDINSSKKAARFVRFCDAFEIPIVTFVD 360 Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420 VPGFLPG GQE+ G+IKHGAKLLFAY EATVPK+TVITRKAYGGAYDVMASKHLRGD NY Sbjct: 361 VPGFLPGVGQEHSGIIKHGAKLLFAYAEATVPKITVITRKAYGGAYDVMASKHLRGDLNY 420 Query: 421 AWPTAEIAVMGAKGATEILYRSELGDKEKIAARAKEYEDRFANPFVAAERGFIDEVIMPH 480 AWPTAEIAVMGAKGA EI++R + E+IA R EYE RFANPFVAA +GF+DEVIMPH Sbjct: 421 AWPTAEIAVMGAKGAVEIIFRGK--TPEEIAERTAEYEARFANPFVAASKGFVDEVIMPH 478 Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510 STRRR++ LRNK L NPWKKHDNIPL Sbjct: 479 STRRRIALGLRKLRNKSLENPWKKHDNIPL 508 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: 863 Number of extensions: 28 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: 510 Length of database: 508 Length adjustment: 34 Effective length of query: 476 Effective length of database: 474 Effective search space: 225624 Effective search space used: 225624 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