Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_012116695.1 XAUT_RS23945 acyl-CoA carboxylase subunit beta
Query= SwissProt::Q3J4E3 (510 letters) >NCBI__GCF_000017645.1:WP_012116695.1 Length = 510 Score = 792 bits (2045), Expect = 0.0 Identities = 380/510 (74%), Positives = 446/510 (87%) Query: 1 MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60 MKDIL+ELE+RR++AR GGG RR+EAQH RGKLTARERIELLLD G+FEE+D FV+HRC Sbjct: 1 MKDILEELESRRSVARLGGGARRIEAQHARGKLTARERIELLLDRGTFEEYDTFVQHRCV 60 Query: 61 DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120 DFGM D + GDGVVTGWGT+NGR V+VF++DFTVFGGSLSE HA+KI KI DMA++ A Sbjct: 61 DFGMADQKVPGDGVVTGWGTVNGRKVFVFAKDFTVFGGSLSEEHARKITKIQDMALKTRA 120 Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180 P+IGL D+GGARIQEGVA+L GY +VF+RN++ASGVIPQIS+IMGPCAGG VYSPAMTDF Sbjct: 121 PIIGLFDAGGARIQEGVAALGGYGEVFKRNVVASGVIPQISLIMGPCAGGDVYSPAMTDF 180 Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240 IFMVRDTSYMFVTGP+VVKTVTNE VT+EELGGA HT KSSVADG++ENDVE L E RR Sbjct: 181 IFMVRDTSYMFVTGPEVVKTVTNETVTSEELGGAKVHTSKSSVADGSYENDVEMLLETRR 240 Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300 L+DFLP +N+ AP P FDD R ++SLDTL+PDNPN+PYD+KELILK+ DE DF+EIQ Sbjct: 241 LIDFLPSNNQEGAPEWPSFDDPGRYDESLDTLVPDNPNKPYDIKELILKVVDEGDFFEIQ 300 Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360 +A N++TGF R+EG+TVG VANQPMVLAG LD D+SRKAARFVRFCDAF IPI+T VD Sbjct: 301 AAYARNMVTGFGRIEGRTVGFVANQPMVLAGVLDSDASRKAARFVRFCDAFEIPIVTFVD 360 Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420 VPGFLPGT QEYGG+IKHGAKLLFAY +ATVP VTVITRKA+GGAYDVMASKH+ D NY Sbjct: 361 VPGFLPGTAQEYGGLIKHGAKLLFAYSQATVPLVTVITRKAFGGAYDVMASKHVGADVNY 420 Query: 421 AWPTAEIAVMGAKGATEILYRSELGDKEKIAARAKEYEDRFANPFVAAERGFIDEVIMPH 480 AWPTA+IAVMGAKGA EI++R+++GD +KIAA+ K YE+RF +PFVAAERG++DEVIMPH Sbjct: 421 AWPTAQIAVMGAKGAVEIIFRADMGDPDKIAAQTKNYEERFLSPFVAAERGYVDEVIMPH 480 Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510 STRRR+++A A LR KKL P +KHDN+PL Sbjct: 481 STRRRLARALAMLRTKKLEQPSRKHDNMPL 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: 888 Number of extensions: 36 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: 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