Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_034270164.1 AMYHA_RS09575 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000504245.1:WP_034270164.1 Length = 537 Score = 743 bits (1919), Expect = 0.0 Identities = 364/532 (68%), Positives = 418/532 (78%) Query: 4 IHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63 + S P S DFQ A H L ADL R+ Q GG + R RH ERGKL RDR+D L Sbjct: 6 LRSDADPASEDFQRYAAEHGQLVADLNGRVKQAMHGGPEKSRVRHVERGKLLPRDRVDAL 65 Query: 64 IDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVK 123 +DP S FLE+ LAA +YD+E PAAGI+ G+GRV+GR +I+ANDATVKGGTY+P+TVK Sbjct: 66 LDPGSPFLELSPLAANGMYDDEAPAAGIITGVGRVSGRECVIVANDATVKGGTYYPITVK 125 Query: 124 KHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIAC 183 KHLRAQE+A N LPC+YLVDSGGA+LP Q VFPDR+HFGRIFYNQA MSA GIPQIA Sbjct: 126 KHLRAQEVALHNNLPCVYLVDSGGAFLPEQDGVFPDREHFGRIFYNQATMSARGIPQIAA 185 Query: 184 VMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISG 243 V+GSCTAGGAYVPAMSDE VIV+ GTIFLGGPPLVKAATGEEVT EELGG DVH R SG Sbjct: 186 VLGSCTAGGAYVPAMSDEAVIVRNQGTIFLGGPPLVKAATGEEVTDEELGGGDVHARQSG 245 Query: 244 VADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDV 303 V D+ ANDD +AL IVR IV+ LGPR W++ E P DP E+YG++P D R YDV Sbjct: 246 VTDHLANDDTDALRIVRSIVSTLGPRVPRPWDVAPVEEPAVDPTELYGVVPTDSRTPYDV 305 Query: 304 REVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELC 363 REVIAR+VDGSR EFK YGTTLV GFA I G PVGI+ANNG+LF+ESA+KGAHFIELC Sbjct: 306 REVIARVVDGSRFAEFKAEYGTTLVTGFARIHGHPVGIIANNGVLFAESAMKGAHFIELC 365 Query: 364 CARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYG 423 R+IPL+FLQNITGFMVGK YE GGIAK GAK+VTAV+CA VPK TVIIGGSFGAGNY Sbjct: 366 DKRSIPLLFLQNITGFMVGKDYEAGGIAKHGAKMVTAVACARVPKLTVIIGGSFGAGNYS 425 Query: 424 MCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILA 483 MCGRAY PR LWMWPNARISVMGG QAA+VL T+RRD + RG+ + E++E F PI Sbjct: 426 MCGRAYSPRFLWMWPNARISVMGGEQAASVLSTVRRDAIERRGETWSAEDEEAFKDPIRE 485 Query: 484 KYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 +YE +GHPYY++ARLWDDGVIDPV+TR V+ L L+AAA AP+ +GVFRM Sbjct: 486 QYEHQGHPYYSTARLWDDGVIDPVDTRTVVGLALSAAANAPLDDISYGVFRM 537 Lambda K H 0.322 0.139 0.423 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: 985 Number of extensions: 42 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: 535 Length of database: 537 Length adjustment: 35 Effective length of query: 500 Effective length of database: 502 Effective search space: 251000 Effective search space used: 251000 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 (21.9 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