Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein
Query= SwissProt::Q9JLZ3 (314 letters) >NCBI__GCF_900129305.1:WP_073037062.1 Length = 263 Score = 173 bits (438), Expect = 5e-48 Identities = 98/257 (38%), Positives = 141/257 (54%), Gaps = 4/257 (1%) Query: 57 LEEENRGIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 116 L E G+ ++ NR NAL+ L+ L++AV A + D VR +++ F AGA Sbjct: 7 LFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDKAFVAGA 66 Query: 117 DLKERAKMHSSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAAS 176 D+ E KM+ E F K + V + +LP P IA ++G ALGGG ELA++CD A+ Sbjct: 67 DITELQKMNPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCDFIYASD 126 Query: 177 SAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQN 236 AK G E L IIPG GGTQRL R +G + AKEL + ++D Q+AK +GL++ V Sbjct: 127 KAKFGQPEINLGIIPGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLVAKVFPH- 185 Query: 237 QEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTKDR 296 +A + L A + A+R K +++GM+ DL TG A+E + + +D Sbjct: 186 ---EALLEETLKAATAMAAKSCTALRAIKHVVDRGMDADLKTGCALEAEAFGVCFAGQDA 242 Query: 297 LEGLLAFKEKRPPRYKG 313 EG AF EKR P +KG Sbjct: 243 KEGTTAFLEKRKPVFKG 259 Lambda K H 0.318 0.135 0.377 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: 161 Number of extensions: 5 Number of successful extensions: 2 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: 314 Length of database: 263 Length adjustment: 26 Effective length of query: 288 Effective length of database: 237 Effective search space: 68256 Effective search space used: 68256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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