Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012044115.1 BBTA_RS18955 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000015165.1:WP_012044115.1 Length = 535 Score = 746 bits (1927), Expect = 0.0 Identities = 359/533 (67%), Positives = 434/533 (81%), Gaps = 1/533 (0%) Query: 4 IHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63 +HS I P+S DF N + L DL+ +L Q+ GGG R+RH RGK+ R R+D L Sbjct: 3 LHSTIDPSSADFARNAEAMRVLVEDLKAKLGQVAAGGGEASRKRHLARGKMLARQRVDLL 62 Query: 64 IDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVK 123 +DP ++FLE+ LAA+ +Y +V +A IV GIGR+AGR +++ANDAT+KGGTY+P+TVK Sbjct: 63 LDPGTAFLELSPLAAHGLYGGDVHSASIVTGIGRIAGRECVVVANDATIKGGTYYPMTVK 122 Query: 124 KHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIAC 183 KHLRAQ+IAR+N LPC+Y+VDSGGA+LPLQ E+FPD HFGRIF+NQAQMSA+GIPQIA Sbjct: 123 KHLRAQDIARQNNLPCVYMVDSGGAFLPLQDEIFPDERHFGRIFFNQAQMSAQGIPQIAI 182 Query: 184 VMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISG 243 VMGSCTAGGAYVPAMSDE +IV+ GTIFLGGPPLVKAATGE V+AEELGGADVH+R SG Sbjct: 183 VMGSCTAGGAYVPAMSDESIIVRNQGTIFLGGPPLVKAATGEVVSAEELGGADVHSRQSG 242 Query: 244 VADYFANDDREALAIVRDIVAHLGPR-QRANWELRDPEPPRYDPREIYGILPRDFRQSYD 302 V D++A +D A+ I R IV L P RA +R+ PRY EIYG++P D R+ +D Sbjct: 243 VTDHYAQNDAHAIGIARRIVGTLKPPGARAVLNMREVRAPRYPAEEIYGVVPADGRKPFD 302 Query: 303 VREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIEL 362 VR++IAR+VDGS EFK YG TLVCGFAHI G+PVGI+ANNGILFSES+LKGAHFIEL Sbjct: 303 VRDIIARVVDGSEFDEFKKLYGQTLVCGFAHIFGYPVGIIANNGILFSESSLKGAHFIEL 362 Query: 363 CCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNY 422 CC RNIPLVFLQNITGFMVGK+YE GGIA+DGAKLVTAV+ A+VPKFTV+IGGS+GAGNY Sbjct: 363 CCQRNIPLVFLQNITGFMVGKKYEAGGIARDGAKLVTAVATASVPKFTVVIGGSYGAGNY 422 Query: 423 GMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPIL 482 GMCGRAY PR LWMWPNARISVMGG QAA VL +RRD + A+G+ + EE+E+F +PI Sbjct: 423 GMCGRAYAPRFLWMWPNARISVMGGEQAAMVLSQVRRDGIEAKGESWSTEEEEKFRSPIR 482 Query: 483 AKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 A+YE +G+PYYA+ARLWDDGVIDP +TR VL LGL+AAA APV+PT+FG+FRM Sbjct: 483 AQYEAQGNPYYATARLWDDGVIDPADTRLVLGLGLSAAANAPVEPTKFGLFRM 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: 997 Number of extensions: 46 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