Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_052666539.1 NITAL_RS12625 short-chain dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000969705.1:WP_052666539.1 Length = 315 Score = 146 bits (368), Expect = 6e-40 Identities = 93/252 (36%), Positives = 138/252 (54%), Gaps = 24/252 (9%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGH-----SGSDEGRAGALSLAEEIAAFGGTA 60 K + +TG GIGRA A CA +GA+VV+ GSD A A ++ EEI GG A Sbjct: 8 KAIAITGGGGGIGRAVALACAAEGAKVVVADHGVSMDGSDPSSAVADAVVEEIRDTGGEA 67 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 +AV ++ GE++VA AV+AFGS+D +V AGI +M + + V +L G Sbjct: 68 VAVADTVTTMEGGERVVATAVDAFGSIDGVVCVAGILRERMLFNMTEDEWDPVVDVHLKG 127 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 + +AAA RM+ + R G+++ +S A G Q +Y+ K G++SL++S A+ L Y Sbjct: 128 HFTVFRAAAARMR-KARSGSLVGFTS-GAFQGSIAQANYSAAKGGVVSLVRSAAVGLAKY 185 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVP--LGRLGEPDDLAGPIVFLASDMAR 238 G+ NA+ P IA R RM+ VP L +G+P+D+A +V+L SD A+ Sbjct: 186 GVTANAIAP--IA-------------RTRMSDNVPGDLAEMGDPEDVAPMVVYLLSDHAK 230 Query: 239 YVTGASLLVDGG 250 +VTG GG Sbjct: 231 HVTGQVYTAVGG 242 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: 231 Number of extensions: 13 Number of successful extensions: 4 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: 315 Length adjustment: 26 Effective length of query: 230 Effective length of database: 289 Effective search space: 66470 Effective search space used: 66470 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 24 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