Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate GFF2642 PGA1_c26820 probable enoyl-CoA hydratase PaaG
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__Phaeo:GFF2642 Length = 261 Score = 134 bits (336), Expect = 3e-36 Identities = 83/245 (33%), Positives = 128/245 (52%), Gaps = 2/245 (0%) Query: 19 LTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRAK 78 +TL+ P N+ +M+ A AL++ RD RAV++TGA FCAG +L + Sbjct: 16 ITLNRPDRLNSFTEEMHHALRAALEAA-RDGGARAVLLTGAGRGFCAGQDLGDRDPRKMD 74 Query: 79 DPSVQAQSI-DLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVMS 137 P ++ A ++ +R PVI AV+G AAGAG +LALACD+++AA+ AKF+ S Sbjct: 75 GPPDLGHTVRTFYAPLVNLIRALDFPVICAVNGVAAGAGANLALACDVVLAAESAKFIQS 134 Query: 138 YARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAAV 197 +++VGL PD GGSW L + L A + + +P+ A + + G++ K A Sbjct: 135 FSKVGLIPDTGGSWHLPRLLGEARAKGLALTAEPLPAKKAEDWGLIWKAVPDEELMAEAR 194 Query: 198 AWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEKR 257 A A++ + K + AA LS+ L E D + EG+++FLEKR Sbjct: 195 AMAEKFANGPTLGLGLTKQTIQAAAVTTLSDQLEIEADAMKTCGESADYAEGVASFLEKR 254 Query: 258 APVYK 262 P +K Sbjct: 255 VPAFK 259 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: 144 Number of extensions: 7 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: 262 Length of database: 261 Length adjustment: 25 Effective length of query: 237 Effective length of database: 236 Effective search space: 55932 Effective search space used: 55932 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: 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