Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_053936590.1 WG78_RS04575 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_001294205.1:WP_053936590.1 Length = 246 Score = 159 bits (401), Expect = 7e-44 Identities = 98/251 (39%), Positives = 141/251 (56%), Gaps = 7/251 (2%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L +K I+TGA+ GIG A AR+ +GARVV+ D RAG ++ E+ A GG A Sbjct: 1 MKLKNKVAIITGAASGIGHATARKFVTEGARVVV----CDVNRAGVDAVVSELIAQGGQA 56 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 + D + +VA + FG +D+LVNNAGI M + + + + NL G Sbjct: 57 LGFEVDVTNKAQIAAMVAGTQQQFGRIDILVNNAGIVADAQLSKMTEDQFDRVIDINLKG 116 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 Y +A M EQ + G I+ SS+ L G QT+Y K G++ ++++ A LG Sbjct: 117 VYNCTRAVVDIMIEQ-QSGVILNASSVVGLYGNFGQTNYAAAKFGVIGMVKTWARELGKK 175 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240 GIR NAV PG +AT I K D+ D + + M RVPL R+ +P+++A FLASD A Y+ Sbjct: 176 GIRANAVCPGFVATPILK-DMPD-KVIQGMEERVPLRRMAQPEEIANVYAFLASDEASYI 233 Query: 241 TGASLLVDGGL 251 +GA++ V GGL Sbjct: 234 SGAAIEVTGGL 244 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: 148 Number of extensions: 5 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: 246 Length adjustment: 24 Effective length of query: 232 Effective length of database: 222 Effective search space: 51504 Effective search space used: 51504 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 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