Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein
Query= SwissProt::Q0AVM1 (260 letters) >NCBI__GCF_900129305.1:WP_073037062.1 Length = 263 Score = 268 bits (685), Expect = 9e-77 Identities = 139/257 (54%), Positives = 177/257 (68%) Query: 1 MAYENIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDK 60 M ++NI+ E + +A++ NRPKA+NALN TL E+ AV A DD AV ++++TG+GDK Sbjct: 1 MDFQNILFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDK 60 Query: 61 SFVAGADIAFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCD 120 +FVAGADI +Q ++ +EAR F GQ VF +E + KPVIA VNGFALGGGCELAM CD Sbjct: 61 AFVAGADITELQKMNPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCD 120 Query: 121 FRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVN 180 F A+ AKFGQPE+ LGI PGFGGTQRL RLVG AK+L T ++I+A +A +GLV Sbjct: 121 FIYASDKAKFGQPEINLGIIPGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLVA 180 Query: 181 KVVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFATQ 240 KV E LL E K A + +K A+R K + GM D+ ++EA+AFG+CFA Q Sbjct: 181 KVFPHEALLEETLKAATAMAAKSCTALRAIKHVVDRGMDADLKTGCALEAEAFGVCFAGQ 240 Query: 241 DQKEGMTAFLEKRKANF 257 D KEG TAFLEKRK F Sbjct: 241 DAKEGTTAFLEKRKPVF 257 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: 232 Number of extensions: 7 Number of successful extensions: 1 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: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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 Apr 09 2024. 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