Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate BPHYT_RS24115 BPHYT_RS24115 epimerase
Query= BRENDA::Q7CRQ0 (265 letters) >FitnessBrowser__BFirm:BPHYT_RS24115 Length = 278 Score = 219 bits (559), Expect = 4e-62 Identities = 120/259 (46%), Positives = 153/259 (59%), Gaps = 5/259 (1%) Query: 1 MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSP-LDPAGPNEECVQCDLADANAVNAM 59 MK++ ++GA GQLG V+R L LR A S L P E+ + DL D V+ + Sbjct: 1 MKKIALSGAGGQLGSVVRAALIARGTPLRSAAGSKALVPLVDGEDVMHGDLRDPAVVDRL 60 Query: 60 VAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQT 119 + G D ++H G SVE+P +I++ N+ GL +YE AR G RIVFASSNH IG YP T Sbjct: 61 LEGVDVLIHFAGTSVERPLPEIIENNLRGLVEVYEGARRQGVKRIVFASSNHAIGMYPVT 120 Query: 120 ERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFS 179 E L D RPDG YG+SK +GE LARMY+DK G E+ VRIGSC P R LSTWF Sbjct: 121 EHLSLDCELRPDGFYGLSKVWGEALARMYWDKHGIESVCVRIGSCLERPTEPRHLSTWFG 180 Query: 180 HDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETT 239 H D + ++ A +G +WG SAN WWDNS LG++P +AE + I Sbjct: 181 HRDLLHFLDRCVEAENVGFLTIWGVSANTRSWWDNSGAERLGYQPTQDAEVYAEEILAR- 239 Query: 240 PPPDPNDAL-VRFQGGTFV 257 P+P DAL RFQGG+FV Sbjct: 240 --PNPLDALGQRFQGGSFV 256 Lambda K H 0.321 0.139 0.443 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: 256 Number of extensions: 15 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: 265 Length of database: 278 Length adjustment: 25 Effective length of query: 240 Effective length of database: 253 Effective search space: 60720 Effective search space used: 60720 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: 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