Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate WP_066918785.1 ACG33_RS03660 acyl-CoA carboxylase subunit beta
Query= reanno::PS:Dsui_0517 (510 letters) >NCBI__GCF_001579945.1:WP_066918785.1 Length = 510 Score = 882 bits (2278), Expect = 0.0 Identities = 429/510 (84%), Positives = 469/510 (91%) Query: 1 MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60 M+DII +LE+KR AARLGGG KRID+QH KGKLTARERLELLLDP +FEEWDMF EHRC Sbjct: 1 MYDIIEQLEEKRAAARLGGGTKRIDAQHAKGKLTARERLELLLDPGTFEEWDMFVEHRCA 60 Query: 61 DFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGA 120 +FGMA+ K PGDGVVTGYG INGRL FVFSQDFTVFGG+LSE HAEKICKVMD AMKVGA Sbjct: 61 EFGMADNKIPGDGVVTGYGMINGRLAFVFSQDFTVFGGALSEAHAEKICKVMDQAMKVGA 120 Query: 121 PVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEGVASLGGYA+VFQRN +ASGVIPQIS+IMGPCAGGAVYSPAMTDF Sbjct: 121 PVIGLNDSGGARIQEGVASLGGYAEVFQRNALASGVIPQISLIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRR 240 IFMVKDSSYMFVTGPEVVKTVTHEEVT+EELGGA TH+T+SGVADLAFENDVEA+ LRR Sbjct: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTSEELGGAGTHSTRSGVADLAFENDVEAILMLRR 240 Query: 241 LVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQ 300 N+LP NNR+KP V+ +D +R+D SLDTL+PDN NKPYDMKELI+K+VDD DFFE+Q Sbjct: 241 FFNYLPLNNRDKPSVRPGSDQRDRVDMSLDTLMPDNPNKPYDMKELILKVVDDGDFFELQ 300 Query: 301 PDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVD 360 P +A NI+ GFARM+G VG+VAN P+VLAGCLDIKSSIKAARFVRFCDAFNIPV+T VD Sbjct: 301 PTFAANIVIGFARMEGATVGVVANNPMVLAGCLDIKSSIKAARFVRFCDAFNIPVITFVD 360 Query: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNL 420 VPGF+PGT+QEYGGIIKHGAKLLYAYAECTVPKVT+ITRKAYGGAYDVMSSKHLRGDVN Sbjct: 361 VPGFLPGTAQEYGGIIKHGAKLLYAYAECTVPKVTVITRKAYGGAYDVMSSKHLRGDVNF 420 Query: 421 AWPSAEIAVMGPKGAVEIIFREEKNDPAKLAEREAEYKAKFANPFVAGARGFIDDVIMPN 480 AWPSAEIAVMG KGAVEIIFR+ K DPAKLA REAEYKA+FANPFVAGARG+IDDVI P+ Sbjct: 421 AWPSAEIAVMGAKGAVEIIFRDYKGDPAKLAAREAEYKARFANPFVAGARGYIDDVIQPH 480 Query: 481 ETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510 ETRKRICRSLAML+DKKL+NPWRKHGNIPL Sbjct: 481 ETRKRICRSLAMLKDKKLENPWRKHGNIPL 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: 948 Number of extensions: 29 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