Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_084055699.1 B9A12_RS01110 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_900176285.1:WP_084055699.1 Length = 259 Score = 123 bits (309), Expect = 3e-33 Identities = 88/258 (34%), Positives = 125/258 (48%), Gaps = 8/258 (3%) Query: 4 ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAA 63 E + + G+V V LNRPK LNALN +M EL AL AD ++ + +TG KAF A Sbjct: 3 ELVEIIDHGKVREVALNRPKNLNALNLQIMTELADALTAAAADASVRGVCLTGRGKAFCA 62 Query: 64 GADIGMMSTYTYMDVYKGDYIT------RNWETVRSIRKPIIAAVAGFALGGGCELAMMC 117 G D+ T + D + T R +R + KP++AAV G A G G LA+ C Sbjct: 63 GGDLKW--TLDFADDPGVSFHTLAGQLNRVAVELRHMPKPVVAAVQGAAAGAGFTLALAC 120 Query: 118 DIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLV 177 D +A F Q G+ GGT LPR V A+A+++ + A +A GL Sbjct: 121 DFRIMERSAFFLQAYTSNGLCMDGGGTFTLPRLVGLARALEIAAFDERIPAEKALEWGLA 180 Query: 178 SRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFAT 237 +R++ + DEA +AE + KE N+A++ ERR + Sbjct: 181 NRLVDDGTARDEAFTMLNHLAERSLHSFARCKELFNQAFQNDFETQAERERRALAACARH 240 Query: 238 EDQKEGMAAFVEKRKPVF 255 +D +EG+ AFVEKR P F Sbjct: 241 DDGREGLRAFVEKRPPKF 258 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: 158 Number of extensions: 10 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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