Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_073036815.1 BUB04_RS02735 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_900129305.1:WP_073036815.1 Length = 517 Score = 662 bits (1709), Expect = 0.0 Identities = 316/514 (61%), Positives = 401/514 (78%) Query: 2 TMEDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRN 61 T+ ++I ELRE+ + + GGE +A QH++GKMTARER++YF D GTFRE D F HR Sbjct: 3 TVAEKIKELREREAKIKQMGGEKAVAKQHERGKMTARERLEYFFDPGTFRELDIFVKHRG 62 Query: 62 HKFGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVG 121 FG+++ +P DGVITG+G V+GR VF F+ DFT G+LGE+ ++KICKVMD A++ G Sbjct: 63 TLFGLDKMDIPADGVITGYGLVNGRQVFAFSQDFTARAGTLGEMHSKKICKVMDLALKTG 122 Query: 122 APVIGLNDSAGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTD 181 P++G NDS GARIQEGV +L G+G+IF RN ASGV+PQISAIMGPCAGGAVYSPA+TD Sbjct: 123 KPLVGFNDSGGARIQEGVDALSGYGQIFYRNAIASGVIPQISAIMGPCAGGAVYSPAMTD 182 Query: 182 FTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIR 241 F FMV++TS+MFITGPDVIK+V GEEVT +ELGGA H+S SGVAHFA ++++ A+D+I+ Sbjct: 183 FVFMVKNTSYMFITGPDVIKSVLGEEVTQEELGGAMAHSSKSGVAHFACESDQHAIDEIK 242 Query: 242 HLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGV 301 LLS+LP NN+EDPP VE DDP R+ L+ I+PD P PYD+ DV+ ++D G FF V Sbjct: 243 RLLSFLPDNNMEDPPVVETGDDPNRMDPALDTILPDNPMGPYDMKDVIRAIVDNGDFFEV 302 Query: 302 QEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFV 361 E++A+NIVVG RL GHSVGI+ANQP+V AG LD+++S+K RFIRFCD+FNIP+L+ Sbjct: 303 HENYAQNIVVGLARLGGHSVGIIANQPKVLAGCLDVDSSDKATRFIRFCDAFNIPLLTLA 362 Query: 362 DVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVN 421 DVPG+LPG QE GIIRHGAKLL+ YSEATVP +T+I RK YGG+Y M SK LGAD+ Sbjct: 363 DVPGYLPGKQQEWGGIIRHGAKLLWCYSEATVPKITLIIRKDYGGSYLAMCSKDLGADIA 422 Query: 422 YAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDD 481 AWPTAEIAVMG +GA NI++R E++AA+DP A+R E IEEYR NPY AA RG++D Sbjct: 423 LAWPTAEIAVMGAEGAANIIFRKEIQAAEDPKAKRAEKIEEYRNLLYNPYIAASRGYIDG 482 Query: 482 VIEPGDTRNRLIADLRMLKSKRKSQPDKKHGNIP 515 VI P +TR RLI ML++KR++ P KKHGNIP Sbjct: 483 VIVPSETRPRLIEAYAMLRTKRQALPPKKHGNIP 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: 811 Number of extensions: 33 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: 517 Length adjustment: 35 Effective length of query: 481 Effective length of database: 482 Effective search space: 231842 Effective search space used: 231842 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