Align acyl CoA carboxylase carboxyltransferase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate WP_046008372.1 OLEAN_RS05310 acetyl-CoA carboxylase
Query= metacyc::MONOMER-13598 (524 letters) >NCBI__GCF_000967895.1:WP_046008372.1 Length = 555 Score = 309 bits (792), Expect = 2e-88 Identities = 185/497 (37%), Positives = 276/497 (55%), Gaps = 32/497 (6%) Query: 26 QGGGEDKIKAQHDKGKLTARERLALLFDEGSFNEIMPLATTRATEFGLDKNKFYGDGVVT 85 + G + I QH K ++T ER+++L DE P + LD G +VT Sbjct: 55 KAAGINAITRQHAKKRMTIWERISVLTDES------PTVLFQNWGKNLD-----GASLVT 103 Query: 86 GWGKIEGRTVFAFSQDFTELGGTLGETHANKIGKVYELALKVGAPVIGINDSGGARIQEG 145 KI GR V + DFT G++ T+ K+ +++ELA K P++G+NDS GA + G Sbjct: 104 AIVKINGRDVALYGHDFTVRAGSMDATNGKKLARLFELAGKRKIPLVGLNDSAGAYVPAG 163 Query: 146 AIALEGYATVFKMNTLASGVIPQITIMAGPAAGGAVYSPALTDFIIMIKGDAYYMFVTGP 205 L+GYA F SGV+P I M G AGG Y P F MI+ + + +TGP Sbjct: 164 VGGLDGYAEAFTALRKISGVVPSIMCMFGFNAGGGSYLPRQGSF--MIQPNNTFFGLTGP 221 Query: 206 EITKVVLGEEVTFQDLGGAVVHATKSGVVHFLAENEQDAISIAKRLLSYLPSNNMEDPPY 265 + K VLGE+VT +LGG VH+ +SGV F+ ++E A+ KRLL+Y+P+NN E PY Sbjct: 222 GVVKSVLGEDVTPDELGGPSVHS-QSGVTDFVVKDEVSALKKVKRLLNYIPNNNSEFAPY 280 Query: 266 MDTGDPSDRETKDVESIV------PTDSAKPFDMREVIYRIVDNGEFMEVHRHWAQNIVV 319 +T DP DR T D++ ++ P+ P D+ +I ++ D+G+FME+ A+N + Sbjct: 281 QETSDPVDRRTWDIDVLLKKAFNSPSGFNTPMDVTIMIQQLCDHGDFMEIQPDRARNTIT 340 Query: 320 GFARVAGNVIGIVANNSNTLGAAIDIDAADKAARFIRFCDAFNIPLLSLVDTPGYIPGTE 379 R+ GNVIG VANNS IDI AA K ARFIRFC+ +NIP++ + DT G++PG + Sbjct: 341 ALGRMGGNVIGFVANNSAVSSGQIDIAAAYKNARFIRFCNLYNIPVIFMEDTTGFLPGKD 400 Query: 380 QEYKGIIRHGAKMLYAFSEATVPKISVIIRKSYGGAHIAMSIKNLGADLVYAWPTAEIAV 439 QE +GI++ G ML A + P+ +IIR ++GGA+ + + GAD V A P+ AV Sbjct: 401 QEAQGIVQAGRAMLDAIIDLRTPRFLLIIRNAFGGAYASYNNYPTGADFVIALPSTRAAV 460 Query: 440 TGPEGAVRILYKRD-------IQNSQNPDEFLKQKIA----EYKKLFANPYWAAEKGLID 488 GP G V +YK + ++N Q ++ K++ A Y++ NP A G I Sbjct: 461 MGPAG-VEFVYKNELRAIRSAVKNKQQTAQWAKEQEALLAKRYEEELMNPNEALSLGSIS 519 Query: 489 DVIEPKDTRRIIVNALS 505 ++ P D R+++ +S Sbjct: 520 QIVMPSDLRKVLSENMS 536 Lambda K H 0.318 0.137 0.394 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: 715 Number of extensions: 34 Number of successful extensions: 6 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: 524 Length of database: 555 Length adjustment: 35 Effective length of query: 489 Effective length of database: 520 Effective search space: 254280 Effective search space used: 254280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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