Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_043526531.1 JH15_RS02125 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000759345.1:WP_043526531.1 Length = 535 Score = 735 bits (1897), Expect = 0.0 Identities = 366/535 (68%), Positives = 425/535 (79%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M+ I +HI P S FQAN ++ LRE A I QGGG + R RHE RGKLFVRDRI Sbjct: 1 MATITTHINPRSEAFQANADAMRAEVGKLRELTAAIAQGGGEKARARHESRGKLFVRDRI 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120 D L+D S FLE+ ALAA+ VYD VPAAGIV GIGRV+G +I+ANDATVKGGTY PL Sbjct: 61 DHLLDEGSPFLELSALAAHEVYDGPVPAAGIVTGIGRVSGVECVIVANDATVKGGTYHPL 120 Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180 TVKKHLRAQEIAR++RLPCIYLVDSGGA+LP Q EVFPDRDHFGRIFYNQA +SAEGIPQ Sbjct: 121 TVKKHLRAQEIARKHRLPCIYLVDSGGAHLPHQDEVFPDRDHFGRIFYNQATLSAEGIPQ 180 Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240 IA VMGSCTAGGAYVPAM+DE +IV+ GTIFLGGPPLVKAATGE ++AE LGGADVH R Sbjct: 181 IAVVMGSCTAGGAYVPAMADESIIVREQGTIFLGGPPLVKAATGESISAEALGGADVHAR 240 Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300 ISGVAD++A++D AL + R VA+L ++R L++ PP+ DP EIYGI+ D ++ Sbjct: 241 ISGVADHYADNDAHALQLARRCVANLNWQKRGQLALKESRPPQLDPSEIYGIVGTDLKKP 300 Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360 YDVREVI R+VDGS EFK YG TLV GFAH+ G PVGI+ANNG+LFSESA+KGAHFI Sbjct: 301 YDVREVIGRLVDGSEFDEFKRYYGDTLVTGFAHLHGHPVGIVANNGVLFSESAVKGAHFI 360 Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420 ELC R IPL+FLQNITGFMVG +YE+ GIAK GAKLVTAV+CA VPKFTV+IGGSFGAG Sbjct: 361 ELCAQRKIPLLFLQNITGFMVGSKYEHEGIAKHGAKLVTAVACAKVPKFTVLIGGSFGAG 420 Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480 NYGMCGRAY P L+MWPNARISVMGG QAANVL ++R+ GQ + E+++ F P Sbjct: 421 NYGMCGRAYDPNLLFMWPNARISVMGGEQAANVLAQVKREQYERDGQAWSAEDEDAFKKP 480 Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 +YE +GHPYYASARLWDDGVIDP++TR VL L L+AA A ++ TRFGVFRM Sbjct: 481 TRDQYEHQGHPYYASARLWDDGVIDPLQTRDVLGLALSAAMNAEIEETRFGVFRM 535 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: 998 Number of extensions: 44 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: 535 Length adjustment: 35 Effective length of query: 500 Effective length of database: 500 Effective search space: 250000 Effective search space used: 250000 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