Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__PV4:5209977 Length = 706 Score = 140 bits (353), Expect = 7e-38 Identities = 85/197 (43%), Positives = 127/197 (64%), Gaps = 8/197 (4%) Query: 17 ITLNRP-DKLNALNAKLLEELDRAVSQAESDPEIR-VIIITGKGKAFCAGADITQFNQLT 74 +T++ P + +N L A+ E+ +++ ++D IR V+II+GK +F AGADI+ + Sbjct: 17 LTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADISMLDACA 76 Query: 75 PAE-AWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAE--EAQLGL 131 AE A + SK+G E+ +E+LS P +A ING LGGGLELALAC R+ + + LGL Sbjct: 77 TAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSNKTMLGL 136 Query: 132 PEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQET 191 PE+ LG+ PG GGTQRL R++G ++L+MM+TG ++ K A K GLV+ VVP + L Q Sbjct: 137 PEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVVPESILLQTA 196 Query: 192 RKLA---EKIAKKSPIS 205 ++A + AKK +S Sbjct: 197 IEMALAGARPAKKPKLS 213 Lambda K H 0.315 0.135 0.382 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: 373 Number of extensions: 24 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: 259 Length of database: 706 Length adjustment: 32 Effective length of query: 227 Effective length of database: 674 Effective search space: 152998 Effective search space used: 152998 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: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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