Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate GFF42 HP15_42 short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Marino:GFF42 Length = 266 Score = 149 bits (377), Expect = 4e-41 Identities = 96/252 (38%), Positives = 138/252 (54%), Gaps = 7/252 (2%) Query: 2 LLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAI 61 LL +K ++TGA GIG AR +QGA V+I G A +A ++ A GG A+ Sbjct: 3 LLENKVALITGAGGGIGEGVARYFVKQGAAVIIAELSEQLGEA----VAADLRAQGGKAL 58 Query: 62 AVGADAADLDSGEKLVAAAVEAFGSVDVLVNNA-GICPFHSFLDMPRELYLKTVGTNLNG 120 D ++ S E VA AV+ FGS+DVLVNNA P + E+ +T+ T + Sbjct: 59 FCHTDVSNKSSIENAVATAVDHFGSIDVLVNNAFAPTPNVKLEEKTDEMLTQTLNTTVWA 118 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 A++ ++AA M E+G GG+I+ SI +G + Y K+ +L L +S A G + Sbjct: 119 AWWAMKAAFPHMCERG-GGSIVNFYSIDTEIGAWLHGDYNTAKSAILGLTRSAAAEWGRF 177 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIV-FLASDMARY 239 IR NA+ P + +K + ER + PLGR GEP+ GP+V FLAS+M+R+ Sbjct: 178 NIRANAIAPTAMGATFHKLAAENPGFEERSAAMRPLGRCGEPEADIGPVVAFLASEMSRF 237 Query: 240 VTGASLLVDGGL 251 VTG S+ VDGGL Sbjct: 238 VTGESIHVDGGL 249 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: 161 Number of extensions: 8 Number of successful extensions: 5 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: 266 Length adjustment: 25 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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 Apr 09 2024. 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