Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_049776088.1 XAUT_RS04520 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000017645.1:WP_049776088.1 Length = 258 Score = 150 bits (380), Expect = 2e-41 Identities = 92/249 (36%), Positives = 140/249 (56%), Gaps = 12/249 (4%) Query: 17 VTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGADIG-------M 69 +TLNRP LNA + L L AAL + ADDA A+++TG+ + F AG D+G Sbjct: 13 LTLNRPDRLNAFTEELHRSLAAAL-DAAADDACRAVLLTGAGRGFCAGQDLGDRAKAEGP 71 Query: 70 MSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADTAKFG 129 + ++ + I R +R++RKP++ AV G A G G +A CDI+ AA +AKF Sbjct: 72 LDLGATIEAFYNPLIRR----IRALRKPVVCAVNGVAAGAGANIAFACDIVLAARSAKFI 127 Query: 130 QPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAASLVDE 189 Q K+G++P +GGT LPR + A+A L L A + A +AE GL+ + + A+L+DE Sbjct: 128 QAFAKIGLVPDSGGTFFLPRLIGDARARALMLLAEPVSAEKAESWGLIWKAVDDAALMDE 187 Query: 190 AIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMAAFVE 249 A A A+ +A P+ + + K+++N + L + ER L T D +EG++AF+E Sbjct: 188 ARALASHLASQPTQGLALTKQALNASAGNALDAQLDLERDLQREAGRTPDYREGVSAFME 247 Query: 250 KRKPVFKHR 258 KR F R Sbjct: 248 KRPARFSGR 256 Lambda K H 0.321 0.134 0.380 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: 154 Number of extensions: 11 Number of successful extensions: 3 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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