Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate H281DRAFT_02528 H281DRAFT_02528 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Burk376:H281DRAFT_02528 Length = 278 Score = 343 bits (880), Expect = 2e-99 Identities = 165/277 (59%), Positives = 201/277 (72%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGN 60 MKL R+G G EKPG++ +G RDLS ++D+ + LANLD+ TLP V Sbjct: 1 MKLFRFGPVGAEKPGVVDRNGTHRDLSAVIADIDPATIAAGLESRLANLDLTTLPEVPKG 60 Query: 61 PRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEK 120 R GPC+A G F+ IGLNY +HA ET A +P EPI+F KA S IVGP+DD+VLPRGSEK Sbjct: 61 TRFGPCIAQPGNFLAIGLNYVEHAKETNAPLPEEPILFNKAPSCIVGPDDDIVLPRGSEK 120 Query: 121 TDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGP 180 TDWEVEL VIGK A YVSEA+AL YV GYC +DVSERAFQ ER GQW KGK +FGP Sbjct: 121 TDWEVELAFVIGKRAHYVSEADALSYVFGYCVCNDVSERAFQLERGGQWVKGKCAPSFGP 180 Query: 181 TGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIS 240 GP+LVT +E+ DPQ L +WL+VNGE +Q+ T M++ +VSY+SQF+ L PGD+I+ Sbjct: 181 IGPYLVTAEEIPDPQKLPLWLEVNGERVQNSDTSDMIFSIRTIVSYVSQFVVLMPGDLIT 240 Query: 241 TGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRV 277 TGTPPGVG+GMKP RYLK GD V L +EGLG+Q QRV Sbjct: 241 TGTPPGVGLGMKPERYLKRGDTVRLSVEGLGTQTQRV 277 Lambda K H 0.315 0.136 0.408 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: 339 Number of extensions: 9 Number of successful extensions: 1 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: 281 Length of database: 278 Length adjustment: 26 Effective length of query: 255 Effective length of database: 252 Effective search space: 64260 Effective search space used: 64260 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: 42 (22.0 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