Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30295 Length = 703 Score = 134 bits (337), Expect = 5e-36 Identities = 91/225 (40%), Positives = 126/225 (56%), Gaps = 34/225 (15%) Query: 9 EKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAGADI 68 E E +AV+ +N P +NAL + I DAVT N DPAV +++ G G ++F+AGADI Sbjct: 10 EVEGVVAVITVNNPP-VNALTPEMRGSIIDAVTHANADPAVAAIVLMGGG-QNFIAGADI 67 Query: 69 AFMQNLSAMEAREFGALGQKVFRL----IEAMEKPVIAAVNGFALGGGCELAMCCDFRIA 124 R+FG + ++A KP +AA++G+ALGGG E A+ C +RIA Sbjct: 68 -----------RQFGKARTITTSMSAAALDASAKPTVAAIHGYALGGGLEHALACHYRIA 116 Query: 125 ASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVV- 183 AK G PEV LG+ PG GGTQRLPRLVG +A LL ++ I+A EA +IGL++++V Sbjct: 117 LPTAKLGLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVP 176 Query: 184 --QPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAM 226 Q +EL AVR +KA A+ Q D A+ Sbjct: 177 GTQNQEL--------------RDAAVRYAKAVAHAQPQRVRDLAL 207 Lambda K H 0.319 0.136 0.378 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: 383 Number of extensions: 12 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: 260 Length of database: 703 Length adjustment: 32 Effective length of query: 228 Effective length of database: 671 Effective search space: 152988 Effective search space used: 152988 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 (21.8 bits) S2: 50 (23.9 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