Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate RR42_RS19805 RR42_RS19805 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS19805 Length = 258 Score = 153 bits (387), Expect = 3e-42 Identities = 95/257 (36%), Positives = 141/257 (54%), Gaps = 7/257 (2%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 +L V +TLNRP LNALN AL+ EL AA+ D+A+ A+V++ + + F AGA Sbjct: 5 VLYHAAEGVATITLNRPDVLNALNSALLLELRAAVERAAQDEAVRAVVLSANGRGFCAGA 64 Query: 66 DIGMMSTYTYMDVYKGDYITRNWETV----RSIRKPIIAAVAGFALGGGCELAMMCDIIF 121 D+ T G + + + R++ KP+I +V G A G G LA+ D++ Sbjct: 65 DLAGRGTGLQDS---GTLLRERYHPIILALRNMPKPVITSVNGVAAGAGMSLALAGDVVL 121 Query: 122 AADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVI 181 A +A F Q K+G++P AG T LPR + +A L + A +DA EA R GLV +V Sbjct: 122 AGRSASFLQAFSKIGLVPDAGSTYFLPRYAGEMRARALAILAEKIDAEEAHRIGLVWKVH 181 Query: 182 PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQK 241 +L E AA +A+ P+ A ++KE++N + ++ L + E L +ED K Sbjct: 182 EDEALPAETARLAAHLAQMPTFAYGLIKEALNASLQSDLPAQLEREATLQSRASKSEDVK 241 Query: 242 EGMAAFVEKRKPVFKHR 258 EG+AAF+EKRKP FK R Sbjct: 242 EGVAAFLEKRKPAFKGR 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: 144 Number of extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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