Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_061531854.1 CAter10_RS00460 crotonase/enoyl-CoA hydratase family protein
Query= SwissProt::Q0AVM1 (260 letters) >NCBI__GCF_001584165.1:WP_061531854.1 Length = 270 Score = 142 bits (358), Expect = 7e-39 Identities = 93/269 (34%), Positives = 137/269 (50%), Gaps = 13/269 (4%) Query: 1 MAYENIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDK 60 M YE + + + +A++ +NRP NA+N EI+ A V+ P + ++ G G K Sbjct: 1 MTYETLSVSLAQNIAIVRLNRPDKANAMNMQMWQEIRTAFEWVDATPEARVAVLEGEG-K 59 Query: 61 SFVAGADIAFMQNLSAM-----EAREFGALGQKVFRLIEAME------KPVIAAVNGFAL 109 +F AG D+ M L A E R+ AL + L +A+ KP++AAV+G + Sbjct: 60 TFTAGIDLQMMMGLGAQIQNPCEGRKREALRSIILNLQDALSSLERCRKPILAAVHGACV 119 Query: 110 GGGCELAMCCDFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVIN 169 GGG +L C D R +S+A F E+ +G+T G QRLP+L+G GMA++L YTA ++ Sbjct: 120 GGGIDLITCADMRYCSSDAYFSIKEIDIGMTADVGTLQRLPKLIGEGMARELAYTARKVD 179 Query: 170 ADEAFRIGLVNKVVQPEELLPE-VKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSI 228 A EA I LVN+V E L E V +IA I +K LA+R K + + Sbjct: 180 AAEARDIHLVNRVFASREALREGVMEIAASIAAKSPLAIRGVKEMITYARDHSVADGLKY 239 Query: 229 EADAFGLCFATQDQKEGMTAFLEKRKANF 257 A + D +E M A + KR A F Sbjct: 240 IATWNAAMLMSNDLQEAMMANVGKRPAEF 268 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: 148 Number of extensions: 6 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: 270 Length adjustment: 25 Effective length of query: 235 Effective length of database: 245 Effective search space: 57575 Effective search space used: 57575 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: 47 (22.7 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