Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_041939569.1 FRAAL_RS20780 acetyl-CoA acetyltransferase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_000058485.1:WP_041939569.1 Length = 792 Score = 127 bits (319), Expect = 7e-34 Identities = 86/248 (34%), Positives = 129/248 (52%), Gaps = 8/248 (3%) Query: 17 LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGA-DNFFCAGGNLNRLLEN 75 L +T++ P RNALHP E D+ DP + +ITGA D F AG +L Sbjct: 549 LEVTINRPQVRNALHPPANTELAEVFDAYFADPDLWVAIITGAGDTAFSAGNDLTWTASG 608 Query: 76 RAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFV 135 + + + +++ R +KPVIAAV+G A G G +ALAC L+VA A+F Sbjct: 609 KRGSVPLTGFA------GLTSRRDLTKPVIAAVNGHALGGGCEIALACHLVVADTTARFA 662 Query: 136 MSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDA 195 ++ RVGL GG L +ALP +LATE+++ G+ + A H G+VN++ GTA D Sbjct: 663 LTEVRVGLAAGAGGLVRLPRALPPKLATEMILTGRRLDATEAHAHGLVNRIVPAGTALDG 722 Query: 196 AVAWADELGKISPNSV-ARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFL 254 A A A ++ SP SV ++ + AG + + + L + LEG++AF Sbjct: 723 ARALAADILAGSPTSVRVSLQIMNETAGITDPHDAVTHDSPALDDLLLSEDMLEGLTAFA 782 Query: 255 EKRAPVYK 262 EKR P ++ Sbjct: 783 EKRTPHWR 790 Lambda K H 0.317 0.132 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: 494 Number of extensions: 32 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: 262 Length of database: 792 Length adjustment: 33 Effective length of query: 229 Effective length of database: 759 Effective search space: 173811 Effective search space used: 173811 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: 51 (24.3 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