Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_015798850.1 AFER_RS07460 KR domain-containing protein
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000023265.1:WP_015798850.1 Length = 309 Score = 124 bits (312), Expect = 2e-33 Identities = 90/256 (35%), Positives = 132/256 (51%), Gaps = 21/256 (8%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGH-------SGSDEGRAGALSLAEEIAAFGG 58 + VIVTGA RGIGRA A A QGARVV+ SGS G AG + + I + GG Sbjct: 8 RVVIVTGAGRGIGRAHALAFAEQGARVVVNDLGAEVDGSGSSTGPAG--EVVDHIRSQGG 65 Query: 59 TAIAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNL 118 AIA G D A + ++L+ AA+E+FG +DV+VNNAGI ++M + + +L Sbjct: 66 AAIANGDDVASWEGAQRLINAAIESFGRLDVVVNNAGILRDRMLVNMTESEWDDVIRVHL 125 Query: 119 NGAYFTVQAAARRMKEQGRGGA-----IIAVSSISALVGGAMQTHYTPTKAGLLSLMQSC 173 G + + AA +EQ + G II +S S + G Q +Y KAG+ SL Sbjct: 126 KGTFAMTRWAAAYFREQAKAGVAQDARIINTTSASGIYGNVGQANYGAAKAGIASLTIIA 185 Query: 174 AIALGPYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLA 233 A+ L YG+ NA+ P +A E+L + +R ++ L P+++A +V+L Sbjct: 186 AMELARYGVTVNAIAP--VALTRMTENLGIVAPDDR-AAQAELA----PENIAPLVVWLG 238 Query: 234 SDMARYVTGASLLVDG 249 S + +TG V G Sbjct: 239 STHSAGITGRVFDVAG 254 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: 195 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 256 Length of database: 309 Length adjustment: 26 Effective length of query: 230 Effective length of database: 283 Effective search space: 65090 Effective search space used: 65090 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