Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF2748 HP15_2692 phenylacetate degradation probable enoyl-CoA hydratase paaB
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Marino:GFF2748 Length = 263 Score = 151 bits (381), Expect = 1e-41 Identities = 90/258 (34%), Positives = 137/258 (53%), Gaps = 6/258 (2%) Query: 4 LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63 +++ Q V LLTLNRP N+ N + ++ + D S+ V VITG+ R F AG Sbjct: 6 ILLEIDQGVALLTLNRPDNLNSFNVEMHERMREAISTVRKDESVRVLVITGSGRGFCAGQ 65 Query: 64 DLNEMAEK------DLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVV 117 DL++ + DL A+L + L L+ P++ AVNG A GAG +AL CD+ Sbjct: 66 DLSDRSVSPDQEMPDLGASLENYYNPLMRSLRDLPMPVLCAVNGVAAGAGANIALACDIT 125 Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177 +A +A F LG++P +GGT L R G + A M L G+ I+A+QA+ G++ Sbjct: 126 LAARSANFVQAFCKLGLVPDSGGTWTLPRVAGMARAKGMALLGDKISAEQAENWGMIWRC 185 Query: 178 FPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDR 237 ++ +E ++LA A L K+AL S + + ER L + TED Sbjct: 186 VDNEQLMEETMKLARHFATQPTKGLALIKRALHASASNTFEEQINLERDLQRMAGQTEDY 245 Query: 238 HEGISAFLQKRTPDFKGR 255 EG++AF++KRTP+FKG+ Sbjct: 246 REGVAAFMEKRTPNFKGK 263 Lambda K H 0.318 0.130 0.356 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: 122 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: 255 Length of database: 263 Length adjustment: 24 Effective length of query: 231 Effective length of database: 239 Effective search space: 55209 Effective search space used: 55209 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 (21.8 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