Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_097030693.1 CRO07_RS10730 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_900207575.1:WP_097030693.1 Length = 534 Score = 686 bits (1770), Expect = 0.0 Identities = 333/530 (62%), Positives = 403/530 (76%) Query: 6 SHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLID 65 S + P+S F+ N H +L AD+ GGG + RH RGKL R+R+ L+D Sbjct: 5 SRVLPSSESFRRNREAHLALIADIARAADLAAAGGGPAAQARHAARGKLPPRERVAGLLD 64 Query: 66 PDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKH 125 P S FLEIGA AA+ +YD PAAG++ GIGRV G VM++ NDATVKGGTY+P+TVKKH Sbjct: 65 PGSPFLEIGAFAAHGMYDGAAPAAGVIAGIGRVHGAEVMVVCNDATVKGGTYYPMTVKKH 124 Query: 126 LRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVM 185 LRAQEIA E RLPC+YLVDSGGA LP Q EVFPDRDHFGRIF+NQA+MSA GIPQIA VM Sbjct: 125 LRAQEIAAECRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFFNQARMSAAGIPQIAVVM 184 Query: 186 GSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVA 245 GSCTAGGAYVPAMSD +IV+ GTIFL GPPLV+AATGE V+AE+LGG DVHTR+SGVA Sbjct: 185 GSCTAGGAYVPAMSDVTIIVRDQGTIFLAGPPLVRAATGEVVSAEDLGGGDVHTRLSGVA 244 Query: 246 DYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVRE 305 DY A DD AL + R + +L + A + + PE P +DP +I G++P D R +D+RE Sbjct: 245 DYLAEDDAHALILARRALGNLNRTRPATVQWQSPEDPAHDPEDILGLVPADLRTPWDIRE 304 Query: 306 VIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCA 365 +IARI DGSR EFK R+G TLV GFAH+ G PVGI+ANNG+LFSE+A+KGAHFIELC Sbjct: 305 LIARITDGSRFDEFKPRFGETLVTGFAHLMGCPVGIVANNGVLFSEAAIKGAHFIELCSQ 364 Query: 366 RNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMC 425 R IPL+FLQNITGFMVG++YEN GIA+ GAK+VTAV+ VPK T+++GGSFGAGNYGM Sbjct: 365 RAIPLIFLQNITGFMVGRKYENEGIARHGAKMVTAVATTAVPKITMLVGGSFGAGNYGMA 424 Query: 426 GRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKY 485 GRAY PR LW WPN+RISVMGG QAA VL T+R D L G TPE++ F P + + Sbjct: 425 GRAYSPRFLWTWPNSRISVMGGEQAAGVLATVRGDALARAGTPWTPEDEAAFKRPTIEMF 484 Query: 486 EQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 +++ HP YASARLWDDG++DP +TR LAL L+AA AP++PTRFG+FRM Sbjct: 485 DRQSHPLYASARLWDDGIVDPRKTRETLALSLSAALNAPIEPTRFGLFRM 534 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: 924 Number of extensions: 34 Number of successful extensions: 3 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: 534 Length adjustment: 35 Effective length of query: 500 Effective length of database: 499 Effective search space: 249500 Effective search space used: 249500 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