Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 90.9 bits (224), Expect = 4e-23 Identities = 76/241 (31%), Positives = 120/241 (49%), Gaps = 15/241 (6%) Query: 31 IGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAGGDI--RAL 88 IG++TLNRP Q NALS M+ ++ + +I +++ GAG K FCAG D+ R L Sbjct: 14 IGIMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLKERRL 73 Query: 89 YDSFHAGTALH--RQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQAAHLRVLTE 146 A A+ +Q F D + P PV+A+++G +GGG+ LA A LR+ Sbjct: 74 MTEQEAKEAVLTIQQTFTD-------IESLPVPVIAVINGHALGGGLELALACDLRIARA 126 Query: 147 RSRVAMPETGIGLVPDVGASHFLSKL-PLALALYVGLTGVTLGAADTLLCKLADIAVPAA 205 + + +PETG+ ++P G + L +L A + TG +L A + + L + A Sbjct: 127 GAALGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTAD 186 Query: 206 SLEHFEQTLA-AINRTGDV-LADLRAALQATPDAGEQAAPLQSVLPAVLRHFRADASVAG 263 SL + TLA I + G + L + + A+Q++ D Q L A LR + + G Sbjct: 187 SLMNDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTG-LTKEYEAYLRLIHTEDRLEG 245 Query: 264 L 264 L Sbjct: 246 L 246 Lambda K H 0.322 0.137 0.405 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: 207 Number of extensions: 9 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: 384 Length of database: 260 Length adjustment: 27 Effective length of query: 357 Effective length of database: 233 Effective search space: 83181 Effective search space used: 83181 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 (21.9 bits) S2: 48 (23.1 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