Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_010935925.1 DET_RS00710 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000011905.1:WP_010935925.1 Length = 498 Score = 456 bits (1174), Expect = e-133 Identities = 252/504 (50%), Positives = 332/504 (65%), Gaps = 24/504 (4%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 M KIL+ANRGEIA R+++ R++GI+TVAVYSDAD+ AL V ADEA HIGP ++SY Sbjct: 1 MLNKILVANRGEIAIRIMRACRELGIKTVAVYSDADKGALFVKYADEAYHIGPSQLSESY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + I KI+ A K +G + VHPGYGFLSE FA ALE AG+ FIGP S IE MG+KI ++ Sbjct: 61 LNIKKIVSAAKKAGVDGVHPGYGFLSENPGFALALEKAGIKFIGPSSRVIELMGNKIAAR 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 + K+AGV +PG G ++ ++A + + IGYPV+IK S GGGG GMR+A E+K+ Sbjct: 121 REMKKAGVPVLPGTEGCVSGIEQATEAAAAIGYPVIIKPSGGGGGIGMRVANGPDELKDA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 ESS+ A N+FG ++IEK+++ PRHIEIQ++ D GN VYL ERECSIQRR QK+IE Sbjct: 181 IESSQKVAGNTFGLAEVYIEKYISNPRHIEIQIMGDSQGNVVYLGERECSIQRRYQKLIE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIV-DGQKNFYFLEMNTRLQVEHPV 299 EAPSP + RK MGE A K V Y AGT+EFI +GQ FYFLE NTR+QVEHPV Sbjct: 241 EAPSPVITPELRKKMGEVAIKAGKWVNYEGAGTIEFIFSNGQ--FYFLEANTRVQVEHPV 298 Query: 300 TELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYR 359 TE++TGID+V++ I VA+G++L F+Q D+++ GWA+E R+ AEDP F PS +L YR Sbjct: 299 TEMVTGIDIVKEQIMVASGDELSFKQEDVQMRGWAIECRINAEDPLNEFAPSAAKLKGYR 358 Query: 360 PPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEG 419 P VR D+GV+ I YDPMI+KL W TRE AI MR AL + + G Sbjct: 359 SP-----GGIGVRVDSGVHTRYNIPYLYDPMISKLIVWGRTREEAIARMRRALYEYIIVG 413 Query: 420 IGHNLPFVGAVMDHPRFVKGDITTAFIAEEYP--DGFQGAVLDEPTL-----------RR 466 + N+PF AV+ +P FV G++ T FI +E D + + +E L RR Sbjct: 414 VKTNIPFHKAVLVNPNFVAGNLHTHFIEKETTLLDEMKRIMSEEQPLEEKLSEIFDDTRR 473 Query: 467 VA--AAAAAMNRV-AEIRRTRISG 487 +A AA AA+ ++ AEI I+G Sbjct: 474 IAAIAAVAALTQLPAEIDEDEITG 497 Lambda K H 0.318 0.134 0.386 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: 811 Number of extensions: 44 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: 666 Length of database: 498 Length adjustment: 36 Effective length of query: 630 Effective length of database: 462 Effective search space: 291060 Effective search space used: 291060 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: 53 (25.0 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