Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate WP_011764422.1 AZO_RS03450 acyl-CoA carboxylase subunit beta
Query= reanno::PS:Dsui_0517 (510 letters) >NCBI__GCF_000061505.1:WP_011764422.1 Length = 511 Score = 949 bits (2453), Expect = 0.0 Identities = 465/511 (90%), Positives = 489/511 (95%), Gaps = 1/511 (0%) Query: 1 MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60 MHDII +L++KR AARLGGGQKRIDSQH KGKLTARER+ELLLDPDSFEEWDMFKEHRC Sbjct: 1 MHDIIRQLDEKRAAARLGGGQKRIDSQHAKGKLTARERIELLLDPDSFEEWDMFKEHRCV 60 Query: 61 DFGMAET-KNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVG 119 DFGM + K PGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVG Sbjct: 61 DFGMDKAEKTPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVG 120 Query: 120 APVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTD 179 APVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSP+MTD Sbjct: 121 APVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPSMTD 180 Query: 180 FIFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLR 239 FIFMVKDSSYMFVTGPEVVKTVTHE+VTAEELGGAVTHT+KSGVADLAFENDVEAL LR Sbjct: 181 FIFMVKDSSYMFVTGPEVVKTVTHEDVTAEELGGAVTHTSKSGVADLAFENDVEALTMLR 240 Query: 240 RLVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEI 299 R +N+LP++NREKPPVQ TNDPA+R DFSLDTLVPDN NKPYDMKELIIK+VDDCDFFE+ Sbjct: 241 RFMNYLPSSNREKPPVQPTNDPADRQDFSLDTLVPDNPNKPYDMKELIIKVVDDCDFFEL 300 Query: 300 QPDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLV 359 QPDYAKNII G ARMDG PVGIVANQPLVLAGCLDIKS+IKAARFVRFCDAFNIPVVT V Sbjct: 301 QPDYAKNIIIGMARMDGQPVGIVANQPLVLAGCLDIKSAIKAARFVRFCDAFNIPVVTFV 360 Query: 360 DVPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVN 419 DVPGFMPGT+QEYGGIIKHGAKLLYAYAECTVPKVT+ITRKAYGGAYDVM+SKHLRGDVN Sbjct: 361 DVPGFMPGTAQEYGGIIKHGAKLLYAYAECTVPKVTVITRKAYGGAYDVMASKHLRGDVN 420 Query: 420 LAWPSAEIAVMGPKGAVEIIFREEKNDPAKLAEREAEYKAKFANPFVAGARGFIDDVIMP 479 LAWPSAEIAVMGPKGAVEIIFREEKN+P KLAEREAEYKAKFANPFVA +RGFIDDV+MP Sbjct: 421 LAWPSAEIAVMGPKGAVEIIFREEKNNPEKLAEREAEYKAKFANPFVAASRGFIDDVVMP 480 Query: 480 NETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510 + TRKRICRSLAML DK+LDNPWRKHGNIPL Sbjct: 481 HNTRKRICRSLAMLADKQLDNPWRKHGNIPL 511 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: 991 Number of extensions: 30 Number of successful extensions: 2 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: 511 Length adjustment: 35 Effective length of query: 475 Effective length of database: 476 Effective search space: 226100 Effective search space used: 226100 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