Align D-galacturonate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate PP_0501 PP_0501 NAD-dependent epimerase/dehydratase family protein
Query= reanno::HerbieS:HSERO_RS23040 (284 letters) >FitnessBrowser__Putida:PP_0501 Length = 310 Score = 84.7 bits (208), Expect = 2e-21 Identities = 60/172 (34%), Positives = 84/172 (48%), Gaps = 6/172 (3%) Query: 18 LLLTGAAGGVGKQLRARLASFAEVVRVADLASAMAAVDPAAAHE--EALGCDLADRAAVD 75 +L+TG AG +G L L VR+ D S + H E + D+AD V Sbjct: 6 ILITGGAGFIGSHLCDALLDKGYAVRILDDFSTGRRSNLQVDHPRLELIEGDVADAGLVT 65 Query: 76 AMVAGCEAIIHLGGV-SVERPFEEIL---EANIKGVFHIYEAARRHGVKRVIFASSNHVT 131 AGC A++HL V SV+ E+ + ++N G ++ EA R HGV+RV+FASS V Sbjct: 66 QAAAGCRAVVHLAAVASVQASVEDPVRTHQSNFIGTLNVCEAMRVHGVRRVLFASSAAVY 125 Query: 132 GFYGQDERIDARDMKRPDGYYGLSKSYGEDMAQFYFDRYGVETVSIRIGSIF 183 G G+ E I K P Y + K E FY ++G+E V R +IF Sbjct: 126 GNNGEGESISEDTPKAPLTPYAVDKLASEQYLDFYRRQHGLEPVVFRFFNIF 177 Lambda K H 0.321 0.135 0.404 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: 169 Number of extensions: 4 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: 284 Length of database: 310 Length adjustment: 26 Effective length of query: 258 Effective length of database: 284 Effective search space: 73272 Effective search space used: 73272 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 (21.9 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