Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Pedo557:CA265_RS20005 Length = 259 Score = 177 bits (449), Expect = 2e-49 Identities = 107/261 (40%), Positives = 150/261 (57%), Gaps = 11/261 (4%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59 MAY+N++ E + + VT+NR KALNALN + EL + D + +++TG+ EK Sbjct: 1 MAYQNLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEK 60 Query: 60 AFAAGADIGMMSTYTYMDVYKGDYITRN-----WETVRSIRKPIIAAVAGFALGGGCELA 114 AF AGADI S Y+ +G+ + + + + + KP IAA+ GFALGGG ELA Sbjct: 61 AFVAGADIKEFSDYSGK---QGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELA 117 Query: 115 MMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERA 174 M C I A+D AK G PE+ LG++PG GGTQRL + V K KA+++ TA + A +AE+ Sbjct: 118 MACHIRIASDNAKLGLPEVTLGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKI 177 Query: 175 GLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSL 234 GLV+ V+P A L+ +A I + A+ +SV + T G E F Sbjct: 178 GLVNVVVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIASINNT--NGYATEIEEFGKC 235 Query: 235 FATEDQKEGMAAFVEKRKPVF 255 F T D KEG+ AFVEKRK +F Sbjct: 236 FETADFKEGVTAFVEKRKAIF 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: 176 Number of extensions: 9 Number of successful extensions: 4 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 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