Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate BPHYT_RS17350 BPHYT_RS17350 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__BFirm:BPHYT_RS17350 Length = 263 Score = 132 bits (333), Expect = 6e-36 Identities = 92/266 (34%), Positives = 135/266 (50%), Gaps = 9/266 (3%) Query: 1 MSAELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGAD 60 MS E + S +TL+ P N+ M+ ALD VE + RA+V+TGA Sbjct: 1 MSYEAIRLDIDASSHVATITLNRPDKLNSFTRAMHQELSAALDQVETSGA-RALVLTGAG 59 Query: 61 NFFCAGGNLNRLLENRAKDPSVQAQSIDLLAEWISAL--RLSSKP--VIAAVDGAAAGAG 116 FCAG +L L P +L+ + + L RL + P VIAAV+G AAGAG Sbjct: 60 RGFCAGQDLADL----DFTPGAMTDLGELIEQHFNPLIRRLQALPLPVIAAVNGTAAGAG 115 Query: 117 FSLALACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAAR 176 +LALACDL++AA A F+ ++ ++GL PD GG+WFL Q + A + I G + A + Sbjct: 116 ANLALACDLVLAARSASFIQAFVKIGLVPDSGGTWFLPQRVGMARALGLAITGDKLSAEK 175 Query: 177 LHELGVVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDN 236 G++ + + A A +L + ++A IK + A TQ L + L ERD Sbjct: 176 AESWGLIWQAVDDAELAETAAKLAAQLAQQPTRAIAAIKRAMRAGATQTLDQQLDLERDL 235 Query: 237 FVASLHHREGLEGISAFLEKRAPVYK 262 + EG+ AF+EKRAP ++ Sbjct: 236 QRELGASHDYAEGVQAFVEKRAPRFE 261 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: 149 Number of extensions: 6 Number of successful extensions: 4 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: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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