Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_015929947.1 MNOD_RS15905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000022085.1:WP_015929947.1 Length = 261 Score = 148 bits (374), Expect = 1e-40 Identities = 93/250 (37%), Positives = 140/250 (56%), Gaps = 14/250 (5%) Query: 17 VTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGADIGMMST---- 72 +TLNRP LN+ N+ L L AAL + + DDA A+++TG+ + F AG D+G + Sbjct: 16 LTLNRPDRLNSFNEELSRALAAALDDAE-DDACRAVLLTGAGRGFCAGQDLGERVSADGP 74 Query: 73 ----YTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADTAKF 128 YT ++ + + R +R +RKP++ AV G A G G LA+ CDI+ AA +AKF Sbjct: 75 PDLGYT-IETFYNPLVRR----LRGLRKPVVCAVNGVAAGAGANLALACDIVLAARSAKF 129 Query: 129 GQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAASLVD 188 Q K+G++P +GGT LPR + +A+A + L A + A AE GL+ R + +L+ Sbjct: 130 IQAFAKIGLVPDSGGTFFLPRLIGEARARAVSLLAEPVSAETAESWGLIWRAVDDVALLP 189 Query: 189 EAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMAAFV 248 EA A AA +A P+ + + K ++N + TL + ER L T D +EG+ AF+ Sbjct: 190 EARALAAHLATQPTQGLALAKAALNASAGNTLDAQLDLERDLQREAGRTPDYREGVTAFM 249 Query: 249 EKRKPVFKHR 258 EKR F R Sbjct: 250 EKRPARFSGR 259 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: 142 Number of extensions: 8 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: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 Sep 24 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