Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate Pf1N1B4_4777 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= reanno::psRCH2:GFF2389 (257 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4777 Length = 270 Score = 134 bits (337), Expect = 2e-36 Identities = 84/266 (31%), Positives = 138/266 (51%), Gaps = 25/266 (9%) Query: 8 VDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGADI 67 V++ + +A + +NRP+ +N++N SE+ + ++ ++ +VL+G+ K F++G D+ Sbjct: 9 VELADNIAHVQINRPEKINSMNAAFWSEIIEIFQWIDDTDEVRVVVLSGAGKHFSSGIDL 68 Query: 68 KEMAELTYPQIYLDDFFADADRIATR------------------RKPLIAAVAGYALGGG 109 MA + L++ D R A RKP++AA+ GY LGG Sbjct: 69 MMMAGM------LNELGKDVSRNARLLRRTILTLQASFNAVDNCRKPVLAAIQGYCLGGA 122 Query: 110 CELALLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAE 169 +L CDM +AA++A+F E+++G+ +G QRL R +G ++ TGR A E Sbjct: 123 IDLISACDMRYAAEDAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRTFGADE 182 Query: 170 AERAGLVARVF-PAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERR 228 A GLV RV+ A SLLE + AR IA KS A KE ++ + + +G+ + Sbjct: 183 ARSIGLVNRVYSDAASLLEGVMGIAREIAGKSPIAVTGTKEMISYMRDHRIDDGLEYVAT 242 Query: 229 VFHAVFATADQKEGMAAFSEKRKPEF 254 A+ + D + MAA K+KPEF Sbjct: 243 WNAAMLQSTDLRVAMAAHMSKQKPEF 268 Lambda K H 0.321 0.135 0.375 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: 130 Number of extensions: 5 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: 257 Length of database: 270 Length adjustment: 25 Effective length of query: 232 Effective length of database: 245 Effective search space: 56840 Effective search space used: 56840 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