Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate 6938114 Sama_2235 NAD dependent epimerase/dehydratase family protein (RefSeq)
Query= BRENDA::Q888H1 (275 letters) >FitnessBrowser__SB2B:6938114 Length = 334 Score = 64.3 bits (155), Expect = 3e-15 Identities = 53/178 (29%), Positives = 82/178 (46%), Gaps = 20/178 (11%) Query: 13 RLLLTGAAGGLGKVLRETLRPYSH----ILRLSDIAEM--------APAVGDHEEVQVCD 60 ++L+TGAAG +G + L H I L+D ++ A A H + Q + Sbjct: 2 KILVTGAAGFIGAAACKRLLSQGHQVHGIDNLNDYYDVSLKQARLAALASHPHFQFQRME 61 Query: 61 LADKDAVHRLVEGV--DAILHFGG-----VSVERPFEEILGANICGVFHIYEAARRHGVK 113 LAD+ A+ L + D +LH G S++ P AN+ G +I E R+ GVK Sbjct: 62 LADRGAIATLFSTIKPDWVLHLGAQAGVRYSIDNP-HAYADANLVGHLNILEGCRQTGVK 120 Query: 114 RVIFASSNHVIGFYKQNETIDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIR 171 +++ASS+ V G K+ + S P S Y +K E M+ Y YG+ +R Sbjct: 121 HLVYASSSSVYGLNKKLPFATSDSVDHPVSLYAATKKANELMSHSYAHLYGVPCTGLR 178 Lambda K H 0.320 0.137 0.413 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: 193 Number of extensions: 6 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: 275 Length of database: 334 Length adjustment: 27 Effective length of query: 248 Effective length of database: 307 Effective search space: 76136 Effective search space used: 76136 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: 48 (23.1 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