Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate CCNA_02252 CCNA_02252 methylcrotonyl-CoA carboxylase carboxyl transferase subunit
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__Caulo:CCNA_02252 Length = 530 Score = 719 bits (1855), Expect = 0.0 Identities = 357/535 (66%), Positives = 419/535 (78%), Gaps = 5/535 (0%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M ++S I +S F N A++++L +LR ++AQ GG R RH RGKL R+R+ Sbjct: 1 MPKLNSVIDASSDAFAKNAAHNRALVDELRAKVAQAALGGPESARERHTARGKLLPRERV 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120 + L+DP S FLE+G LAA ++Y+ E P AG++CG+GRV+GR VMI+AND TVKGG YFP+ Sbjct: 61 ERLLDPGSPFLEVGQLAACDLYNGEAPGAGMICGVGRVSGREVMIVANDPTVKGGAYFPM 120 Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180 TVKKHLRAQEIA +NRLPC+YLVDSGGA LP Q+EVFPDRDHFGRIF+NQA+MSA IPQ Sbjct: 121 TVKKHLRAQEIAAQNRLPCLYLVDSGGANLPHQAEVFPDRDHFGRIFFNQARMSAASIPQ 180 Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240 IACVMGSCTAGGAYVPAMSDE VIV+ GTIFL GPPLVKAATGE ++AEELGGA+ H R Sbjct: 181 IACVMGSCTAGGAYVPAMSDETVIVRNQGTIFLAGPPLVKAATGEVISAEELGGAETHGR 240 Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300 SGV D+ A +D AL IVR IVA+L + L DPEPP YDP E+YGI+P D R Sbjct: 241 RSGVVDHVAENDEHALEIVRSIVANLNTTKPDQLVLADPEPPAYDPEELYGIVPTDVRAP 300 Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360 YDVREVIARIVDGS+ EFK YGTTLVCGFA I G PV ILANNG+LFSESALKGAHFI Sbjct: 301 YDVREVIARIVDGSQFDEFKALYGTTLVCGFARIWGQPVAILANNGVLFSESALKGAHFI 360 Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420 EL C R IPL+FLQNI+GFMVG +YE GGIAKDGAKLVTAV+ A VPKFTV+IGGSFGAG Sbjct: 361 ELACKRKIPLIFLQNISGFMVGGKYEAGGIAKDGAKLVTAVASAEVPKFTVLIGGSFGAG 420 Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480 NYGMCGRAY PR L+ WPN+RISVMGG QAA+VL T+ RD + +PEE E F AP Sbjct: 421 NYGMCGRAYSPRFLFTWPNSRISVMGGEQAASVLATVHRDAAK-----WSPEEAEAFKAP 475 Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 I +YE EG+PY+A+ARLWDDG+IDP +TR L L ++A+ AP+ T FGVFRM Sbjct: 476 IRQRYEDEGNPYHATARLWDDGIIDPAQTRDALGLAISASLNAPIPETTFGVFRM 530 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: 953 Number of extensions: 43 Number of successful extensions: 4 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: 530 Length adjustment: 35 Effective length of query: 500 Effective length of database: 495 Effective search space: 247500 Effective search space used: 247500 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 17 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