Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_101586893.1 BJEO58_RS00860 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_900169175.1:WP_101586893.1 Length = 536 Score = 688 bits (1775), Expect = 0.0 Identities = 344/540 (63%), Positives = 410/540 (75%), Gaps = 9/540 (1%) Query: 1 MSIIHSHIQPN-SPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDR 59 M I S + P SP QA H L +L +R A GG R+RH +RGKL RDR Sbjct: 1 MRSIGSPVDPQTSPHTQA----HAQLLDELGQRTAATALGGSESSRQRHLDRGKLLPRDR 56 Query: 60 IDTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFP 119 ++ L+DP S FLE ALAA +YD+ P AGI+ G+G ++GR +I+ANDATVKGGTY+P Sbjct: 57 VEGLLDPGSPFLEFSALAANGMYDDASPGAGIITGMGLISGRLCVIVANDATVKGGTYYP 116 Query: 120 LTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIP 179 +TVKKHLRAQEIA++N LPC+YLVDSGGA LP Q +VFPDRDHFGRIF+NQA +SA GIP Sbjct: 117 VTVKKHLRAQEIAQQNNLPCLYLVDSGGANLPNQDDVFPDRDHFGRIFFNQATLSAAGIP 176 Query: 180 QIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHT 239 Q+A VMGSCTAGGAYVPAM+DE VIV GTIFLGGPPLVKAATGE VTAEELGG +H+ Sbjct: 177 QLAAVMGSCTAGGAYVPAMADESVIVNEQGTIFLGGPPLVKAATGEVVTAEELGGGALHS 236 Query: 240 RISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQ 299 R SGV D+ A +D AL I+RDIVA GPR W+ +P+ P +DP EI ++P D + Sbjct: 237 RTSGVTDHLAANDEHALEILRDIVATFGPRHAPAWDRAEPQAPAHDPDEITAVVPVDSKV 296 Query: 300 SYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHF 359 YDVREVIAR+VD S HEFK YGTTLV GFA I+G PVGI+ANNGILF ESA+KGAHF Sbjct: 297 PYDVREVIARLVDASEFHEFKAEYGTTLVTGFARIDGHPVGIIANNGILFGESAMKGAHF 356 Query: 360 IELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGA 419 IELC R+ PLVFLQNI+GFMVG+ YE GIAK GAK+V AV+ A VPKFTV+IGGSFGA Sbjct: 357 IELCDQRSTPLVFLQNISGFMVGRDYEAAGIAKHGAKMVNAVATARVPKFTVVIGGSFGA 416 Query: 420 GNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMA 479 GNY MCGRAY PR LWMWPNARISVMGG QAA+VL T++RD + RG+D + E++E F Sbjct: 417 GNYSMCGRAYSPRFLWMWPNARISVMGGEQAASVLATVKRDQIAGRGEDWSTEDEESFKD 476 Query: 480 PILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAA----AEAPVQPTRFGVFRM 535 PI +YE +G+PYY++ARLWDDG+I P +TRRVLAL L AA E P+ + +GVFRM Sbjct: 477 PIRQQYEDQGNPYYSTARLWDDGIIAPADTRRVLALALEAARFSPLERPLAASGYGVFRM 536 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: 966 Number of extensions: 46 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: 536 Length adjustment: 35 Effective length of query: 500 Effective length of database: 501 Effective search space: 250500 Effective search space used: 250500 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