Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate WP_011386592.1 AMB_RS21450 acyl-CoA carboxylase subunit beta
Query= reanno::PS:Dsui_0517 (510 letters) >NCBI__GCF_000009985.1:WP_011386592.1 Length = 512 Score = 877 bits (2265), Expect = 0.0 Identities = 426/512 (83%), Positives = 468/512 (91%), Gaps = 2/512 (0%) Query: 1 MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60 MH+II +LE+KRE AR+GGG+KRI +QHK+GKLTARER+ELLLDPDSFEEWDMFKEHRCT Sbjct: 1 MHEIIQQLEEKREGARMGGGEKRIAAQHKRGKLTARERIELLLDPDSFEEWDMFKEHRCT 60 Query: 61 DFGMAETKN--PGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKV 118 DFGM N PGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSE HAEKICK+MD A++V Sbjct: 61 DFGMDSEDNMIPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSEAHAEKICKIMDKAVQV 120 Query: 119 GAPVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMT 178 GAPVIGLNDSGGARIQEGVASL GYA+VFQRNVMASGV+PQISMIMGPCAGGAVYSPAMT Sbjct: 121 GAPVIGLNDSGGARIQEGVASLAGYAEVFQRNVMASGVVPQISMIMGPCAGGAVYSPAMT 180 Query: 179 DFIFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYL 238 D+IFMVKDSSYMFVTGP+VVKTVTHE VTAEELGGAVTH+TKSGVADLAFENDVEAL L Sbjct: 181 DYIFMVKDSSYMFVTGPDVVKTVTHETVTAEELGGAVTHSTKSGVADLAFENDVEALLQL 240 Query: 239 RRLVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFE 298 RR ++FLP++NREKPPV+ T+D ER++ SLDTL+PDNANKPYDMKELI+K+VD+ DFFE Sbjct: 241 RRFMDFLPSSNREKPPVRPTSDGPERIETSLDTLIPDNANKPYDMKELILKVVDEGDFFE 300 Query: 299 IQPDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTL 358 +QP YA NII GFARM+G VGIVANQP+VLAGCLDI SSIK ARFVRFCDAFNIP+VT Sbjct: 301 VQPGYAGNIIVGFARMEGRTVGIVANQPMVLAGCLDISSSIKGARFVRFCDAFNIPIVTF 360 Query: 359 VDVPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDV 418 VDVPGF+PGTSQEYGGIIKHGAKLLYAYAECTVPK+T+ITRKAYGGAYDVMSSKHLRGDV Sbjct: 361 VDVPGFLPGTSQEYGGIIKHGAKLLYAYAECTVPKITVITRKAYGGAYDVMSSKHLRGDV 420 Query: 419 NLAWPSAEIAVMGPKGAVEIIFREEKNDPAKLAEREAEYKAKFANPFVAGARGFIDDVIM 478 N AWP+AEIAVMGPKGAVEIIFR + D K+A R EY+ KFANPF+AG RGFIDDVIM Sbjct: 421 NFAWPTAEIAVMGPKGAVEIIFRSDIGDAEKIAARTEEYRQKFANPFIAGHRGFIDDVIM 480 Query: 479 PNETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510 P TRKRICRSLAML+DK + NPWRKHGNIPL Sbjct: 481 PRNTRKRICRSLAMLKDKDVKNPWRKHGNIPL 512 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: 937 Number of extensions: 27 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: 512 Length adjustment: 35 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 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