Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_013257705.1 DEBA_RS04420 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000143965.1:WP_013257705.1 Length = 522 Score = 647 bits (1670), Expect = 0.0 Identities = 308/515 (59%), Positives = 396/515 (76%) Query: 2 TMEDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRN 61 T + +++EL + +EAL GGGE+RI +QH KGK+TARERID LD+GTF+EFD+F HR Sbjct: 8 TTKSKLEELERRNQEALLGGGEERIKAQHAKGKLTARERIDQLLDEGTFQEFDRFVVHRC 67 Query: 62 HKFGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVG 121 H F M++ K+PGDGV+TG G++DGR VF+F+ DFTVFGGSL F EK+CK+MD A++ G Sbjct: 68 HDFDMDKQKIPGDGVVTGFGKIDGRPVFLFSQDFTVFGGSLSGPFGEKVCKIMDLAVKAG 127 Query: 122 APVIGLNDSAGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTD 181 APVIGLNDS GARIQEGV SL +GEIFRRN +SGVVPQISAIMGPCAGGAVYSPA+TD Sbjct: 128 APVIGLNDSGGARIQEGVVSLASYGEIFRRNVLSSGVVPQISAIMGPCAGGAVYSPAITD 187 Query: 182 FTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIR 241 F FMV S+M ITGP VIKTVTGE+VT + +GGA H + SGVA F ++ L +R Sbjct: 188 FIFMVDQNSYMHITGPQVIKTVTGEDVTSETVGGAKVHNTKSGVAQFMAKDGKECLAQVR 247 Query: 242 HLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGV 301 LLSYLP N + PP + DDP R EL++I+PD P+ PY++ ++ V+D+G+FF Sbjct: 248 QLLSYLPSNWEQKPPYLATGDDPRRTCPELDQIIPDNPKSPYNMKQLIKTVVDQGTFFEA 307 Query: 302 QEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFV 361 + +AKN++ F R+ G++VGIVAN P AG LDI+AS K ARF+RFCD+FNIP+++FV Sbjct: 308 AKHWAKNMITAFARMGGNAVGIVANNPMHMAGCLDIDASRKCARFVRFCDAFNIPVVTFV 367 Query: 362 DVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVN 421 DVPGFLPG QE+ GII HG+K++YAY EATVPL+T+ITRKAYGGAYDVM SKH GADVN Sbjct: 368 DVPGFLPGVQQEYGGIITHGSKVIYAYCEATVPLITIITRKAYGGAYDVMGSKHHGADVN 427 Query: 422 YAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDD 481 +A+PTAEIAVMGP+GAVNI++R +L A D A EL+ +YR+ A+PY AA+ G++D+ Sbjct: 428 FAFPTAEIAVMGPEGAVNIVFRKQLNDATDKAAAYAELVADYRKNIASPYRAAELGYIDE 487 Query: 482 VIEPGDTRNRLIADLRMLKSKRKSQPDKKHGNIPL 516 +I P TR ++I L LK KR +P ++HGN+PL Sbjct: 488 IIMPHSTRAKVIQALEALKGKRTFRPVRRHGNVPL 522 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: 859 Number of extensions: 35 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: 522 Length adjustment: 35 Effective length of query: 481 Effective length of database: 487 Effective search space: 234247 Effective search space used: 234247 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