Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_035253526.1 H567_RS0106055 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000422285.1:WP_035253526.1 Length = 516 Score = 667 bits (1722), Expect = 0.0 Identities = 323/516 (62%), Positives = 403/516 (78%) Query: 1 MTMEDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHR 60 M + D+I EL + EA GGG RI QH +GKMTARERI Y LD G+F+E D+F HR Sbjct: 1 MEIADKIKELERRNSEAELGGGLKRIEEQHARGKMTARERIAYLLDAGSFQELDKFVVHR 60 Query: 61 NHKFGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEV 120 H FGM++ K+PGDGV+TG G + GR VFVF+ DFTVFGGSL F EK+CK+MD A++ Sbjct: 61 CHDFGMDKKKIPGDGVVTGFGRIGGRLVFVFSQDFTVFGGSLSGPFGEKVCKIMDLALKN 120 Query: 121 GAPVIGLNDSAGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALT 180 GAPVIGLNDS GARIQEGV SLG +GEIF+RN ASGV+PQIS IMGPCAGGAVYSPALT Sbjct: 121 GAPVIGLNDSGGARIQEGVVSLGSYGEIFKRNVWASGVIPQISVIMGPCAGGAVYSPALT 180 Query: 181 DFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDI 240 DF MV+ TS+MFITGP VIK VT EEVT +ELGGA TH + SGVAHFA D+++ ALD + Sbjct: 181 DFVVMVKKTSNMFITGPQVIKAVTSEEVTPEELGGAMTHNTRSGVAHFAEDSDQAALDRV 240 Query: 241 RHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFG 300 + LLSYLPQN E PP V DDP+R L +VP PR PYD++ ++ VLD+ F Sbjct: 241 KALLSYLPQNCRERPPAVLCHDDPQRSDKTLNTVVPTNPRVPYDMNKIIVNVLDDHEFME 300 Query: 301 VQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSF 360 VQ+ +A+N+VVGFGRL+G VG+VANQP AG LDI+AS K ARF+R CD+FNIP+L+F Sbjct: 301 VQQHYARNMVVGFGRLNGEVVGVVANQPMFLAGCLDIDASMKCARFVRTCDAFNIPLLTF 360 Query: 361 VDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADV 420 VDVPGFLPGT QE+ GII+HGAK++YAY EATVP +TV+TRKAYGGAYDVM+SKH G D+ Sbjct: 361 VDVPGFLPGTAQEYGGIIKHGAKIIYAYCEATVPKITVVTRKAYGGAYDVMSSKHHGGDM 420 Query: 421 NYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVD 480 N+A+PTAEIAVMGP+GAVNI++R E+ +DDP++ R L++ YR FA+P+ AA+ G++D Sbjct: 421 NFAYPTAEIAVMGPEGAVNIIFRKEIAESDDPESTRARLVDAYRNNFASPFKAAELGYID 480 Query: 481 DVIEPGDTRNRLIADLRMLKSKRKSQPDKKHGNIPL 516 +I P +TR RLI L ML++KR+ P+++HGN+PL Sbjct: 481 QIIFPENTRPRLIQALEMLRTKREQHPERRHGNVPL 516 Lambda K H 0.318 0.138 0.407 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: 840 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: 516 Length of database: 516 Length adjustment: 35 Effective length of query: 481 Effective length of database: 481 Effective search space: 231361 Effective search space used: 231361 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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