Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate Ac3H11_1483 2-oxo-hepta-3-ene-1,7-dioic acid hydratase (EC 4.2.-.-)
Query= metacyc::MONOMER-14738 (279 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1483 Length = 249 Score = 183 bits (465), Expect = 3e-51 Identities = 99/235 (42%), Positives = 138/235 (58%), Gaps = 6/235 (2%) Query: 50 DITIEDAYQIQLRMIQRRLDAGERVVGKKIGVTSKVVMDMLKVNQPDFGHLLSGMVYNEG 109 ++TIED Y IQ ++ L G + G+KIG+TS+ + ++ +PD+ L+ M ++ G Sbjct: 15 EMTIEDGYAIQREWVRLELAEGRTIKGRKIGLTSRAMQIASQITEPDYAPLMDDMFFDAG 74 Query: 110 QPIPVSSMIAPKAEAEVAFILARDLEGPGVTAADVLRATDCVMPCFEIVDSRIKDW---- 165 IP IAP+ E E+AFIL + L+GPGVT DVL ATD V+P EI+DSRI+ + Sbjct: 75 GDIPFERFIAPRVEVELAFILGKPLKGPGVTLFDVLSATDYVVPAIEIIDSRIEQFDRET 134 Query: 166 --KIKIQDTVADNASCGVLTLGGLRKSPRDLDLALAGMVLEKNGEIISTSCGASVQGSPV 223 K+ DT++D A+ + LGG P D+DL G +L KNG I + A+V P Sbjct: 135 RVMRKVFDTISDFAANAGIVLGGRPVKPLDVDLRWVGALLHKNGVIEESGLAAAVLNHPA 194 Query: 224 NAVAWLANTLGRLGIGLKAGDIILSGSQSPLVPVVAGDSLYCSVGGLGGTSVRFV 278 N VAWLAN + G L AGD++L+GS + VAGDS + G LG S RFV Sbjct: 195 NGVAWLANKIAPYGEQLNAGDVVLAGSFTRPTAAVAGDSFHADYGPLGSVSFRFV 249 Lambda K H 0.318 0.136 0.390 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: 174 Number of extensions: 10 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: 279 Length of database: 249 Length adjustment: 25 Effective length of query: 254 Effective length of database: 224 Effective search space: 56896 Effective search space used: 56896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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