Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Ac3H11_4006 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4006 Length = 259 Score = 197 bits (502), Expect = 1e-55 Identities = 111/257 (43%), Positives = 158/257 (61%), Gaps = 2/257 (0%) Query: 1 MEFETIETKKEGNLFW-ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGK 59 M +ETIE + E + ITLNRP +LNALN +L+ EL A+ ++D I +I+TG K Sbjct: 1 MAYETIEVRVEADKVGVITLNRPKQLNALNDQLMNELGAALKAFDADENIGCMIVTGSEK 60 Query: 60 AFCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACD 119 AF AGADI + + A+ +K R + I ++ KP IA ++G+ALGGG ELA+ CD Sbjct: 61 AFAAGADIGAMAKYSFADTYKGDYITRN-WETIRSIRKPVIAAVSGFALGGGCELAMMCD 119 Query: 120 IRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVN 179 IAA+ A+ G PEI LG+ PG GGTQRL R +GK +A++M +TG + +AE+ GLV+ Sbjct: 120 FIIAADNARFGQPEIKLGVIPGAGGTQRLPRAVGKSKAMDMALTGRMMDAAEAERAGLVS 179 Query: 180 RVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239 RVVP L E A +A S +++ KE VNR + L G+ E + +F+T+ Sbjct: 180 RVVPYDKLMDEALGAAIIVAGFSQLAVMAAKESVNRAFEGTLSDGVMFERRLFHALFATQ 239 Query: 240 DKKEGVSAFLEKREPTF 256 D+KEG+ AF+ KR F Sbjct: 240 DQKEGMDAFMNKRPANF 256 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: 158 Number of extensions: 6 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: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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: 47 (22.7 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