Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate YP_002823367.1 NGR_b11610 methylcrotonyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000018545.1:YP_002823367.1 Length = 535 Score = 717 bits (1852), Expect = 0.0 Identities = 350/535 (65%), Positives = 415/535 (77%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M+I+ SHI P+S F+AN A + + E + GGG R RH RGKL RDR+ Sbjct: 1 MTILRSHISPSSDVFKANRAAMAEAISTIEEAVRLAAGGGGETARERHVSRGKLLPRDRV 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120 L+DP + FLEI A AA+ +Y+ + P AG++ GIGR++GR M++ ND TVKGGTY+P+ Sbjct: 61 AGLVDPGTPFLEIAATAAHGMYNGDAPGAGLIAGIGRISGRECMVVCNDPTVKGGTYYPI 120 Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180 TVKKHLRAQEIA ENRLPC+YLVDSGGA LP Q EVFPDRDHFGRIFYNQA MSA GIPQ Sbjct: 121 TVKKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQ 180 Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240 IA VMGSCTAGGAYVPAMSDE +IV+G GTIFL GPPLV+AATGE V+AE+LGGADVHTR Sbjct: 181 IAVVMGSCTAGGAYVPAMSDETIIVEGQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTR 240 Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300 +SGVAD+ A DD ALA+ R VA L + ELR+ EPP YDP EI GI+ D + Sbjct: 241 LSGVADHLARDDAHALALARRAVAALNREKPRTLELRESEPPLYDPDEIAGIVSGDLKTP 300 Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360 +++REVIARIVDGSR EFK R+GTTLVCGFAH+ G PVGI+ANNG+LFSESALKGAHF+ Sbjct: 301 FEIREVIARIVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESALKGAHFV 360 Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420 ELC R IPLVFLQNITGFMVG++YE GIAK GAKLVTAV+ VPK T+++GGSFGAG Sbjct: 361 ELCAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAG 420 Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480 NYGMCGRA+ PR LW WPN+RISVMGG QAA VL T+R + LR G EE+ RF P Sbjct: 421 NYGMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSTVRGEALRRAGTPWNEEEEARFRQP 480 Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 +L +E++ HP YA+ARLWDDGV+DP ++R VLAL L+AA APV+ TRFG+FRM Sbjct: 481 VLDLFERQSHPLYAAARLWDDGVVDPRKSREVLALSLSAALNAPVEDTRFGLFRM 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: 957 Number of extensions: 39 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: 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