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 Echvi_0275 Echvi_0275 Acetyl/propionyl-CoA carboxylase, alpha subunit
Query= metacyc::MONOMER-13596 (167 letters) >FitnessBrowser__Cola:Echvi_0275 Length = 164 Score = 63.5 bits (153), Expect = 2e-15 Identities = 42/131 (32%), Positives = 64/131 (48%), Gaps = 16/131 (12%) Query: 34 FEIEYLGKGTRENEYLFKVNGKVHRAFIDNGYILLDNASVFRLERLTELPSKEGESIEEM 93 + +E + + E K+N K I + + LL LE+L + Sbjct: 48 YVVELVKLDAAKKELTLKINNKSAEVKIQDKFDLL-------LEKL---------GMNGQ 91 Query: 94 IKGKEGEVISPLQGRIVTIRVNEGDAVNKGQPLLSVEAMKSETIISAPIAGIVEKIIVKP 153 K + +P+ G I+ I V EGD V K QP++ +EAMK E II +P GIV+KI+V Sbjct: 92 ANAKLTSITAPMPGLILEINVQEGDTVEKDQPMVILEAMKMENIIKSPGDGIVKKILVTT 151 Query: 154 GQGVKKGDTLL 164 G+ V+K L+ Sbjct: 152 GESVEKKQILI 162 Score = 28.1 bits (61), Expect = 8e-05 Identities = 21/89 (23%), Positives = 46/89 (51%), Gaps = 13/89 (14%) Query: 92 EMIKGKEGEVISPLQ----GRIVTIRVNEGDAVNKGQPLLSV---------EAMKSETII 138 ++IKG++ V+ ++ + +T+++N A K Q + +A T I Sbjct: 40 QIIKGQKSYVVELVKLDAAKKELTLKINNKSAEVKIQDKFDLLLEKLGMNGQANAKLTSI 99 Query: 139 SAPIAGIVEKIIVKPGQGVKKGDTLLIIK 167 +AP+ G++ +I V+ G V+K ++I++ Sbjct: 100 TAPMPGLILEINVQEGDTVEKDQPMVILE 128 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: 100 Number of extensions: 6 Number of successful extensions: 2 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: 164 Length adjustment: 18 Effective length of query: 149 Effective length of database: 146 Effective search space: 21754 Effective search space used: 21754 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: 43 (21.2 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