Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_011841235.1 RSPH17029_RS09045 enoyl-CoA hydratase/isomerase family protein
Query= reanno::Phaeo:GFF1711 (348 letters) >NCBI__GCF_000015985.1:WP_011841235.1 Length = 343 Score = 376 bits (966), Expect = e-109 Identities = 198/348 (56%), Positives = 250/348 (71%), Gaps = 7/348 (2%) Query: 1 MSDIDIRITGRAGRITLTRSKALNALSYDMCMAVDAALKAWADDDAVDLVVMDAEGEKAF 60 MSD+ IR RAGRITL R ALNAL+ M +DAAL+ W D V+LVV+DAEG +AF Sbjct: 1 MSDVLIRKVRRAGRITLNRPAALNALTCAMVQEIDAALRGWIGDPEVELVVIDAEGPRAF 60 Query: 61 CAGGDIAELYQTGTSGDYDYGRRFWRDEYRMNARIFEYPKPVLSFLQGFVMGGGVGLGCH 120 CAGGDIAEL+ G +GD+ +G+ FWR EYRMN RI +PKP++S +QGF MGGGVGLGCH Sbjct: 61 CAGGDIAELHGRGVAGDHAFGQDFWRVEYRMNDRIAAFPKPIVSLMQGFTMGGGVGLGCH 120 Query: 121 GTHRIVGDSTKIAMPEVGIGLIPDVGGTLMLALAPGRLGEYLGLTGARMTAADAIYAGFA 180 HRIVG++++I+MPE IGL+PDVGGT +LA APGR+G +LGLTGARM DAI+AGFA Sbjct: 121 ARHRIVGETSQISMPECAIGLVPDVGGTHLLARAPGRIGVWLGLTGARMGPGDAIFAGFA 180 Query: 181 DHYVPETRWPNLISELEQTGRADLLAESAETAPAGTLAPMYDDIGRNFGGETLTDILTAL 240 D +VPE WP+LI+ LE LA AP G L + D+I R F G TL +IL L Sbjct: 181 DRFVPEADWPDLIAALE----GGDLALPDHAAPEGRLPVLQDEIDRLFAG-TLAEILARL 235 Query: 241 DHDDSSFADATLKTLRRNAPLSMAATVELLHRLRLGNMGIRKALELEYRFTHRAMEKGDF 300 + D+ A LK LRR++PL++AAT+E+L RL + GIR+AL+LEYRFT+RA + DF Sbjct: 236 EATDTPLAAEALKALRRSSPLALAATLEILQRLG-PSAGIREALDLEYRFTYRAQGQADF 294 Query: 301 LEGIRAQIIDKDRQPKWQYADRD-VPATAVSQMLMPLATQTLQFEEEN 347 LEGIRA IIDKDR P+W++ D + V V+ +L PL Q L FEEE+ Sbjct: 295 LEGIRAAIIDKDRSPRWRHGDPEAVRPEEVATLLAPLGPQALTFEEES 342 Lambda K H 0.320 0.137 0.406 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: 346 Number of extensions: 11 Number of successful extensions: 5 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: 348 Length of database: 343 Length adjustment: 29 Effective length of query: 319 Effective length of database: 314 Effective search space: 100166 Effective search space used: 100166 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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