Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate GFF1651 Psest_1688 3-oxoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__psRCH2:GFF1651 Length = 247 Score = 141 bits (355), Expect = 1e-38 Identities = 93/254 (36%), Positives = 141/254 (55%), Gaps = 7/254 (2%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L K +VTGASRGIG+A A E RQGA V+ G+ +GA +AE + G Sbjct: 1 MNLQGKVALVTGASRGIGQAIALELGRQGAIVI----GTATTSSGAERIAETLKENGIEG 56 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 + D + +S + + G +LVNNAGI + L M + + + TNL+ Sbjct: 57 AGLVLDVGNDESVSSTLEHIQQHLGQPAILVNNAGITRDNLMLRMKDDEWHDVINTNLSS 116 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 Y +A R M + R G II + S+ +G A Q +Y KAGL ++ A +G Sbjct: 117 LYRLSKAVLRGMTK-ARWGRIINIGSVVGAMGNAGQVNYAAAKAGLEGFSRALAREVGSR 175 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240 GI N+V PG I TD+ +E L + + R+ + ++PLGRLG+ +++A + FLASD A YV Sbjct: 176 GITVNSVAPGFIDTDMTRE-LPEAQ-RDALLGQIPLGRLGQAEEIAKVVAFLASDGAAYV 233 Query: 241 TGASLLVDGGLFVN 254 TGA++ V+GG++++ Sbjct: 234 TGATVPVNGGMYMS 247 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: 167 Number of extensions: 11 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: 247 Length adjustment: 24 Effective length of query: 232 Effective length of database: 223 Effective search space: 51736 Effective search space used: 51736 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