Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate BWI76_RS03850 BWI76_RS03850 2-oxo-hepta-3-ene-1,7-dioic acid hydratase
Query= metacyc::MONOMER-14738 (279 letters) >FitnessBrowser__Koxy:BWI76_RS03850 Length = 267 Score = 173 bits (439), Expect = 3e-48 Identities = 97/254 (38%), Positives = 140/254 (55%), Gaps = 6/254 (2%) Query: 31 LYQSLLDRQPVAPLTDREADITIEDAYQIQLRMIQRRLDAGERVVGKKIGVTSKVVMDML 90 L Q+ R+ + ++ ITIEDAY +Q + ++ G + G KIG+TSK + Sbjct: 14 LNQAEKQREQIRAISLDHPTITIEDAYAVQREWVNMKIAEGRVLKGHKIGLTSKAMQASS 73 Query: 91 KVNQPDFGHLLSGMVYNEGQPIPVSSMIAPKAEAEVAFILARDLEGPGVTAADVLRATDC 150 ++++PD+G LL M +++G IP I P+ E E+AF+LA+ L GP T DV ATD Sbjct: 74 QISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGPNCTLFDVYNATDY 133 Query: 151 VMPCFEIVDSRIKD------WKIKIQDTVADNASCGVLTLGGLRKSPRDLDLALAGMVLE 204 V+P E++D+R + K+ DT++DNA+ + LGG P +LDL +L Sbjct: 134 VIPALELIDARCHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKPDELDLRWISALLY 193 Query: 205 KNGEIISTSCGASVQGSPVNAVAWLANTLGRLGIGLKAGDIILSGSQSPLVPVVAGDSLY 264 +NG I T A V P N VAWLAN L + L+AG IIL GS + VP GD+ + Sbjct: 194 RNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSFTRPVPARKGDTFH 253 Query: 265 CSVGGLGGTSVRFV 278 G +G S RFV Sbjct: 254 VDYGNMGAISCRFV 267 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: 158 Number of extensions: 5 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: 267 Length adjustment: 25 Effective length of query: 254 Effective length of database: 242 Effective search space: 61468 Effective search space used: 61468 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