Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate WP_045586134.1 AL072_RS14870 acyl-CoA carboxylase subunit beta
Query= reanno::PS:Dsui_0517 (510 letters) >NCBI__GCF_001305595.1:WP_045586134.1 Length = 510 Score = 830 bits (2143), Expect = 0.0 Identities = 409/510 (80%), Positives = 455/510 (89%) Query: 1 MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60 M DI+ +LE KR AARLGGG+KRI QH KGKLTARER++L LD SFEE+DMF EHRC Sbjct: 1 MQDILAKLESKRAAARLGGGEKRIAGQHAKGKLTARERIDLFLDEGSFEEFDMFVEHRCI 60 Query: 61 DFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGA 120 DFGM K PGDGVVTG+GT+NGRLVFVFSQDFTVFGG+LSE HAEKICK+MD A+KVGA Sbjct: 61 DFGMEGQKIPGDGVVTGHGTVNGRLVFVFSQDFTVFGGALSEAHAEKICKIMDQALKVGA 120 Query: 121 PVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEGVASLGGYA+VFQRNV ASGVIPQISMIMGPCAGGAVYSPAMTDF Sbjct: 121 PVIGLNDSGGARIQEGVASLGGYAEVFQRNVDASGVIPQISMIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRR 240 IFMVKDSSYMFVTGP+VVKTVTHE VTAEELGGAVTH+T+SGVADLAFENDVEAL LRR Sbjct: 181 IFMVKDSSYMFVTGPDVVKTVTHEVVTAEELGGAVTHSTRSGVADLAFENDVEALLQLRR 240 Query: 241 LVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQ 300 V+FLP++NREK PV+ DP +R DFSLDTLVP+N NKPYDMKELI+K+VD+ DFFE+Q Sbjct: 241 FVDFLPSSNREKAPVRPCVDPLDREDFSLDTLVPENPNKPYDMKELILKIVDEGDFFELQ 300 Query: 301 PDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVD 360 PD+AKNI+ GFARM+G VGIVANQP+VLAGCLDI SS KAARFVRFCDAF IP++TLVD Sbjct: 301 PDFAKNILIGFARMNGSTVGIVANQPMVLAGCLDIDSSKKAARFVRFCDAFEIPILTLVD 360 Query: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNL 420 VPGFMPGTSQEYGGIIKHGAKLLYAYAE TVPKVT+ITRKAYGGAYDVMSSKHLRGDVN Sbjct: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAEATVPKVTIITRKAYGGAYDVMSSKHLRGDVNY 420 Query: 421 AWPSAEIAVMGPKGAVEIIFREEKNDPAKLAEREAEYKAKFANPFVAGARGFIDDVIMPN 480 AWPSAEIAVMG KGAVEIIFR + D AK+ R EY+ KFANPFVA +RG+IDDVIMP+ Sbjct: 421 AWPSAEIAVMGAKGAVEIIFRADIGDTAKIEARTEEYRQKFANPFVAASRGYIDDVIMPH 480 Query: 481 ETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510 TR+R+ ++L+ML++K+L PWRKH NIPL Sbjct: 481 GTRRRVTKALSMLKNKQLQTPWRKHDNIPL 510 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: 925 Number of extensions: 34 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 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