Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate AZOBR_RS04810 AZOBR_RS04810 shikimate 5-dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__azobra:AZOBR_RS04810 Length = 261 Score = 150 bits (379), Expect = 3e-41 Identities = 96/259 (37%), Positives = 136/259 (52%), Gaps = 14/259 (5%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L DK++IVTGA RGIG AR A GAR++I +D A ++AE I A GG A+A Sbjct: 4 LKDKSIIVTGAGRGIGATMARALAADGARLII----ADRTEEDAKTVAESIRAKGGDAVA 59 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 V D D + +++ AV +FG +DVL NNAG+ FLD+ E + N G Sbjct: 60 VTVDVRDRAAVRRMIDTAVTSFGRLDVLFNNAGVAQTKPFLDITEEDWRFVTDVNALGVL 119 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 +Q A + + QG GG II +SI+ G HY+ +K +++L Q+ A A G I Sbjct: 120 IGMQEAIKTFRAQGGGGKIINTASIAGKQGYEPLAHYSASKFAVVALTQAAARAFGKEKI 179 Query: 183 RCNAVLPGTIATDINK----------EDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFL 232 NA+ PG +AT++ K ++ E + LGR +DL G FL Sbjct: 180 TANAICPGVVATEMWKIIDKGFRDTGLTTAEDEAFNHFAAGAVLGRPSTAEDLVGVARFL 239 Query: 233 ASDMARYVTGASLLVDGGL 251 AS + ++TG SLLVDGG+ Sbjct: 240 ASSDSDFMTGQSLLVDGGM 258 Lambda K H 0.319 0.136 0.383 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: 160 Number of extensions: 4 Number of successful extensions: 3 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: 256 Length of database: 261 Length adjustment: 24 Effective length of query: 232 Effective length of database: 237 Effective search space: 54984 Effective search space used: 54984 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