Align acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 5208717 Shew_1220 pyruvate carboxylase subunit B (RefSeq)
Query= metacyc::MONOMER-13596 (167 letters) >FitnessBrowser__PV4:5208717 Length = 601 Score = 54.7 bits (130), Expect = 3e-12 Identities = 30/73 (41%), Positives = 41/73 (56%) Query: 94 IKGKEGEVISPLQGRIVTIRVNEGDAVNKGQPLLSVEAMKSETIISAPIAGIVEKIIVKP 153 + G+ + +PL G I + V GDAV G ++ +EAMK ET I A G+V K+ VK Sbjct: 528 VVGEGSPMNAPLSGNIFKVNVQPGDAVKAGDVVIILEAMKMETEIRAESDGVVAKVWVKE 587 Query: 154 GQGVKKGDTLLII 166 G V G+ LL I Sbjct: 588 GDSVAVGNQLLAI 600 Score = 33.9 bits (76), Expect = 5e-06 Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 11/83 (13%) Query: 95 KGKEGEVISPLQGRIVTIRVNEGDAVNKGQPLLSVEAMKSETIIS----------APIAG 144 +GKE ++ +QG+ + V+ G +++ P +V + ++ AP++G Sbjct: 483 QGKETYTVN-VQGQSFVVEVSPGGDISQIVPSENVVPFAAPEPVAPVVGEGSPMNAPLSG 541 Query: 145 IVEKIIVKPGQGVKKGDTLLIIK 167 + K+ V+PG VK GD ++I++ Sbjct: 542 NIFKVNVQPGDAVKAGDVVIILE 564 Lambda K H 0.313 0.136 0.368 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: 223 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 167 Length of database: 601 Length adjustment: 27 Effective length of query: 140 Effective length of database: 574 Effective search space: 80360 Effective search space used: 80360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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