Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate CCNA_01794 CCNA_01794 enoyl-CoA hydratase/isomerase family
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Caulo:CCNA_01794 Length = 256 Score = 146 bits (369), Expect = 4e-40 Identities = 87/251 (34%), Positives = 137/251 (54%), Gaps = 5/251 (1%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAAG 64 +L+E RG + +VTLNRP+A+NAL+ AL L A+ + D D + +++TG+ ++AF AG Sbjct: 2 LLIERRGAIAIVTLNRPEAMNALSKALRLALHDAIVQLDQDPDVSVVILTGAGDRAFTAG 61 Query: 65 ADIGMMSTYTYMDVYKGDYITRN--WETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122 D+ + D R+ V + RKP+I A+ G A+ GG ELA+ CD++ A Sbjct: 62 LDLKELGGDPAAMGAANDQDARSNPVRAVETCRKPVIGAINGVAITGGFELALACDVLLA 121 Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182 ++ A+F ++GIMPG G +Q+L R + +A +L LT F+DA A GLV+RV Sbjct: 122 SENARFADTHARVGIMPGWGLSQKLSRLIGPYRAKELSLTGNFLDARTAADWGLVNRVTT 181 Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEG--VHFERRLFHSLFATEDQ 240 A+ L+ A+ A +A P A+ K ++ Y EG + ER H+ T ++ Sbjct: 182 ASELLPTALRMAQDMASIPVEALSFYKSLIDDGYAVAFGEGLALEHERSSAHNRTVTPER 241 Query: 241 KEGMAAFVEKR 251 E V +R Sbjct: 242 VEAQRRQVMER 252 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: 155 Number of extensions: 9 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: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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