Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_2276 Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3)
Query= reanno::PS:Dsui_0517 (510 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2276 Length = 510 Score = 916 bits (2367), Expect = 0.0 Identities = 449/510 (88%), Positives = 478/510 (93%) Query: 1 MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60 M DI+ +LEKKR ARLGGGQKRID+QH KGKLTARER+ELLLD +FEEWDMF EHRCT Sbjct: 1 MQDILEQLEKKRALARLGGGQKRIDAQHAKGKLTARERIELLLDDGTFEEWDMFVEHRCT 60 Query: 61 DFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGA 120 DFGM + K PGDGVVTGYG INGRLVFVFSQDFTVFGG+LSETHAEKICKVMD AMKVGA Sbjct: 61 DFGMEDNKIPGDGVVTGYGMINGRLVFVFSQDFTVFGGALSETHAEKICKVMDQAMKVGA 120 Query: 121 PVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDF 180 PVIGLNDSGGARIQEGVASLGGYADVFQ+NV+ASGVIPQISMIMGP AGGAVYSPAMTDF Sbjct: 121 PVIGLNDSGGARIQEGVASLGGYADVFQKNVLASGVIPQISMIMGPSAGGAVYSPAMTDF 180 Query: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRR 240 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVAD+AFENDVEAL LRR Sbjct: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADMAFENDVEALMMLRR 240 Query: 241 LVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQ 300 L N+LP NNREK PV+K+NDPA+R+D SLDTLVP+N NKPYDMKELI+K VDD DFFE+Q Sbjct: 241 LYNYLPLNNREKAPVRKSNDPADRMDLSLDTLVPENPNKPYDMKELILKTVDDGDFFELQ 300 Query: 301 PDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVD 360 P+YAKNI+ GFARM+G VGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVT VD Sbjct: 301 PEYAKNILIGFARMEGQTVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTFVD 360 Query: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNL 420 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPK+T+ITRKAYGGAYDVMSSKHLRGDVNL Sbjct: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKITVITRKAYGGAYDVMSSKHLRGDVNL 420 Query: 421 AWPSAEIAVMGPKGAVEIIFREEKNDPAKLAEREAEYKAKFANPFVAGARGFIDDVIMPN 480 AWP+AEIAVMG KGAVEIIFRE+KNDP KLA REAEYK +FANPFVAGARGFIDDVI+P+ Sbjct: 421 AWPNAEIAVMGAKGAVEIIFREDKNDPVKLAAREAEYKQRFANPFVAGARGFIDDVILPH 480 Query: 481 ETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510 ETRKRICRSL MLRDKKL+NPWRKHGNIPL Sbjct: 481 ETRKRICRSLVMLRDKKLENPWRKHGNIPL 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: 971 Number of extensions: 27 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 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