Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate HSERO_RS05340 HSERO_RS05340 short-chain dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__HerbieS:HSERO_RS05340 Length = 241 Score = 139 bits (349), Expect = 7e-38 Identities = 100/251 (39%), Positives = 132/251 (52%), Gaps = 15/251 (5%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVV-IGHSGSDEGRAGALSLAEEIAAFGGT 59 M KTVI+TGA RGIGRA A A++GA+V+ + + SD R L EEI G Sbjct: 1 MSFAGKTVIITGAGRGIGRACALLLAQRGAQVIALARTASDLAR-----LQEEI---GAR 52 Query: 60 AIAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLN 119 IAV D +D + + +A A G+ D L+N+AGI S L+M E Y +G NL Sbjct: 53 VIAV--DLSDPAAARRAMAEA----GTADFLINSAGINVLESVLEMSDEGYEAVLGVNLR 106 Query: 120 GAYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGP 179 A T QA AR QG GGA++ ++SI+ G Y +KAGL + A LGP Sbjct: 107 AALITCQAFARMRIAQGGGGAMVNITSIAGHRGFEQHLCYAASKAGLEGATRVLARELGP 166 Query: 180 YGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARY 239 +GIR NAV P T++ + SD K M +R P R P+D+A I L S A Sbjct: 167 HGIRVNAVAPTITLTELAEAAWSDPAKSGPMMARHPSARFASPEDVARSIAMLLSPDAAM 226 Query: 240 VTGASLLVDGG 250 + GA + VDGG Sbjct: 227 LNGAVVPVDGG 237 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: 157 Number of extensions: 9 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: 241 Length adjustment: 24 Effective length of query: 232 Effective length of database: 217 Effective search space: 50344 Effective search space used: 50344 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: 46 (22.3 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