Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf1N1B4_4777 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4777 Length = 270 Score = 124 bits (312), Expect = 2e-33 Identities = 81/265 (30%), Positives = 133/265 (50%), Gaps = 12/265 (4%) Query: 3 YENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFA 62 Y VE + V +NRP+ +N++N A E+ + D D + +V++G+ K F+ Sbjct: 4 YTAFSVELADNIAHVQINRPEKINSMNAAFWSEIIEIFQWIDDTDEVRVVVLSGAGKHFS 63 Query: 63 AGADIGMMSTYTY---MDVYKGDYITR--------NWETVRSIRKPIIAAVAGFALGGGC 111 +G D+ MM+ DV + + R ++ V + RKP++AA+ G+ LGG Sbjct: 64 SGIDLMMMAGMLNELGKDVSRNARLLRRTILTLQASFNAVDNCRKPVLAAIQGYCLGGAI 123 Query: 112 ELAMMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEA 171 +L CD+ +AA+ A+F EI +G+ G QRLPR + +L T R A EA Sbjct: 124 DLISACDMRYAAEDAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRTFGADEA 183 Query: 172 ERAGLVSRVI-PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRL 230 GLV+RV AASL++ + A IA AV KE ++ + + +G+ + Sbjct: 184 RSIGLVNRVYSDAASLLEGVMGIAREIAGKSPIAVTGTKEMISYMRDHRIDDGLEYVATW 243 Query: 231 FHSLFATEDQKEGMAAFVEKRKPVF 255 ++ + D + MAA + K+KP F Sbjct: 244 NAAMLQSTDLRVAMAAHMSKQKPEF 268 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: 157 Number of extensions: 6 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: 270 Length adjustment: 25 Effective length of query: 233 Effective length of database: 245 Effective search space: 57085 Effective search space used: 57085 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