Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_051242527.1 H537_RS0112990 enoyl-CoA hydratase/isomerase family protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000430725.1:WP_051242527.1 Length = 275 Score = 171 bits (434), Expect = 1e-47 Identities = 109/258 (42%), Positives = 142/258 (55%), Gaps = 4/258 (1%) Query: 2 AYEN-ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59 A EN + V+ VG + LNRP +NA+ND + + AAL E +AD AI IV+ G + Sbjct: 15 AVENAVRVQREAGVGWIVLNRPGQINAINDDIRRGVPAALAEIEADPAIRVIVIRGEGPR 74 Query: 60 AFAAGADIG-MMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCD 118 F AGADI + V + R E + + KP+IAA+ GF +GGG ELA+ CD Sbjct: 75 GFCAGADIKEQRQAENSLQVRRRMEKARWIEALDRVEKPVIAAIHGFCMGGGLELALACD 134 Query: 119 IIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVS 178 I FAA A PE LG++PG GGTQRLPR V +A+D+ LT M A EA GLV+ Sbjct: 135 IRFAAPDAVLALPETGLGLIPGGGGTQRLPRVVGPGRALDILLTGARMSAQEASAIGLVT 194 Query: 179 RVIPA-ASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFAT 237 RV + +L+ E A A +IA P A VK++ A + L G+ E LF L Sbjct: 195 RVASSKEALLAEVTALAQSIAAKPPMATAYVKQAARAAQQLDLKSGLDLELDLFAMLAPM 254 Query: 238 EDQKEGMAAFVEKRKPVF 255 +D KE AF EKR P F Sbjct: 255 QDVKEAALAFREKRAPQF 272 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: 159 Number of extensions: 4 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: 275 Length adjustment: 25 Effective length of query: 233 Effective length of database: 250 Effective search space: 58250 Effective search space used: 58250 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