Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate WP_072907702.1 BUB13_RS07135 acyl-CoA carboxylase subunit beta
Query= reanno::PS:Dsui_0517 (510 letters) >NCBI__GCF_900142125.1:WP_072907702.1 Length = 515 Score = 667 bits (1722), Expect = 0.0 Identities = 337/515 (65%), Positives = 400/515 (77%), Gaps = 5/515 (0%) Query: 1 MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60 M + I++L R+ A GGG ++I +H KG LTARER+ELL+D SFEE+DMFK HRC Sbjct: 1 MEEKINQLLDMRQHALEGGGAEKIKKRHAKGLLTARERIELLVDEGSFEEFDMFKTHRCH 60 Query: 61 DFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGA 120 FGMA+ + GDGVVTGYGTI+GRLV++FS DFTV GGSLSET AEKICKVMD A+K GA Sbjct: 61 HFGMAKHQALGDGVVTGYGTIDGRLVYLFSMDFTVLGGSLSETFAEKICKVMDMAVKNGA 120 Query: 121 PVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEG+ SL GY D+F RNV +SGV+PQ+S I GPCAGG+VYSPA+TDF Sbjct: 121 PVIGLNDSGGARIQEGIESLAGYTDIFLRNVTSSGVVPQLSGIFGPCAGGSVYSPALTDF 180 Query: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRR 240 MV+++SYMF+TGP+VVK VTHE+V E LGGA HTTKSGVA LA +++ +A+ YLR Sbjct: 181 TVMVRNNSYMFLTGPKVVKAVTHEDVDVETLGGASVHTTKSGVAHLAADSEEQAIAYLRE 240 Query: 241 LVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQ 300 L +++P NN E P +T+DP R D L L+PDN N PYD+K +I VDD FFEIQ Sbjct: 241 LFSYIPQNNMEPAPQVETSDPVSREDEGLCRLIPDNPNHPYDIKAVISSTVDDNRFFEIQ 300 Query: 301 PDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVD 360 PD+A N++ GF R G VGIVANQP LAG LD +SIK ARFVRFCDAFNIPVVT VD Sbjct: 301 PDFAPNLVIGFGRYGGQSVGIVANQPQHLAGVLDNDASIKGARFVRFCDAFNIPVVTFVD 360 Query: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNL 420 VPGF+PGT+QEYGGII++GAKLLYAYAE TVPKVT+ RK+YGGAY VMSSKHLRGDVN Sbjct: 361 VPGFLPGTTQEYGGIIRNGAKLLYAYAEATVPKVTVTVRKSYGGAYCVMSSKHLRGDVNY 420 Query: 421 AWPSAEIAVMGPKGAVEIIF-REEKNDPAK----LAEREAEYKAKFANPFVAGARGFIDD 475 AWP+AEIAVMG KGA EI+F +E K DP L ER EY+ KFANP+ A RG++D Sbjct: 421 AWPTAEIAVMGAKGAAEILFAKEVKKDPENAATILQERSDEYQEKFANPYEAARRGYVDA 480 Query: 476 VIMPNETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510 VI+P TR RIC +LAML K+ NP +KHGNIPL Sbjct: 481 VILPQRTRFRICNALAMLEGKQDSNPRKKHGNIPL 515 Lambda K H 0.320 0.137 0.409 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: 836 Number of extensions: 29 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: 515 Length adjustment: 35 Effective length of query: 475 Effective length of database: 480 Effective search space: 228000 Effective search space used: 228000 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