Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate 7025861 Shewana3_3010 oxidoreductase FAD-binding subunit (RefSeq)
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__ANA3:7025861 Length = 380 Score = 141 bits (356), Expect = 2e-38 Identities = 109/359 (30%), Positives = 177/359 (49%), Gaps = 28/359 (7%) Query: 4 FHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC-TG 62 F L E ET D VS F + F + GQ + + +++GE+ RSY++ T Sbjct: 30 FSQLVCVERWNETADVVSFRFQAGEPM--KFDYKPGQFMTLVLEINGEQACRSYTLSSTP 87 Query: 63 VNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAAGS 122 L + IKRV GG S Y + L+ GQ + V+PP+G F++ A+ YL ++AG Sbjct: 88 SRPYSLMLTIKRVDGGLVSNYLIDHLQPGQTVRVLPPTGQFNLFDIPAK--KYLFLSAGC 145 Query: 123 GITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSREQ 182 GITP+ S+ + +++ ++ + ++ R+ A +F+ LE + R+ + L ++ Sbjct: 146 GITPMYSMSRYLTDSQMNADIAFVHSARTQADIIFKTSLETMATRH-RDFKLRYIVEDVT 204 Query: 183 QDVD------LYN-GRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMA 235 D L+N GR+ D L + + F+CGP+ + V+ L Sbjct: 205 ADTAWHPEAVLHNVGRLRPDNLRDLVPDFAE----RTVFLCGPEPYMQAVKTILAELNFD 260 Query: 236 AERIHFELFAAA-GSAQKR----EARESAAQDSSVSQITVISDG-RELSFELPRNSQSIL 289 +++ E FA A AQ R E + A + S S + I D R L+ E Q++L Sbjct: 261 MTQLYHESFATAVKEAQSRVKQAEMQTEAPESGSNSFMLSIGDKKRALTAE-----QTLL 315 Query: 290 DAGNAQGAELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISD 348 + A+G + +C++GVC CKC+V+EGE E S+ L E+ AGYVL+C T SD Sbjct: 316 EGIEAEGLPIIAACRSGVCGACKCQVLEGETESTSSMTLTPSEIEAGYVLACSTKLKSD 374 Lambda K H 0.319 0.133 0.377 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: 274 Number of extensions: 17 Number of successful extensions: 5 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: 357 Length of database: 380 Length adjustment: 30 Effective length of query: 327 Effective length of database: 350 Effective search space: 114450 Effective search space used: 114450 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 (21.8 bits) S2: 49 (23.5 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