Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_011841205.1 RSPH17029_RS08755 L-iditol 2-dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000015985.1:WP_011841205.1 Length = 256 Score = 154 bits (389), Expect = 2e-42 Identities = 96/259 (37%), Positives = 139/259 (53%), Gaps = 16/259 (6%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L KT ++TG++RGIGRA A R+GARV I + RA A A G A Sbjct: 1 MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATA-------ADIGPAA 53 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 A+G D D S ++ VA ++ +G +D+LVNNA + +++ RE Y + N++G Sbjct: 54 CAIGLDVTDQASIDRCVAELLDRWGRIDILVNNAALFDLAPIVEITRESYDRLFTINVSG 113 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 F +QA AR M GRGG II ++S + G A+ Y TKA ++SL QS + L + Sbjct: 114 TLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRH 173 Query: 181 GIRCNAVLPGTI---------ATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVF 231 GI NA+ PG + A E+L EK+ ++ + VP GR+G +DL G +F Sbjct: 174 GINVNAIAPGVVDGEHWDGVDAKFAEYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIF 233 Query: 232 LASDMARYVTGASLLVDGG 250 LA+ A Y+ + VDGG Sbjct: 234 LATPEADYIVAQTYNVDGG 252 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: 162 Number of extensions: 8 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: 256 Length adjustment: 24 Effective length of query: 232 Effective length of database: 232 Effective search space: 53824 Effective search space used: 53824 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 10 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