Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_011840755.1 RSPH17029_RS05260 SDR family oxidoreductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000015985.1:WP_011840755.1 Length = 248 Score = 154 bits (389), Expect = 2e-42 Identities = 100/246 (40%), Positives = 137/246 (55%), Gaps = 4/246 (1%) Query: 7 KTVLVTGASTGIGRAAAIGAAQHGADVAIN--YAHSDGPAQSCVAEIEALGQRAIAVKGD 64 KT +VTGA+ GIGRA A+G A+ G DVA+ A ++G A++ A IEA G+RA D Sbjct: 3 KTAVVTGAARGIGRALAVGLAEAGYDVAVTDLAAQAEGLAETR-ALIEAAGRRAFVETVD 61 Query: 65 VADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQ 124 V+D +A+ E G +DV+V+NAGI D+ + VN+ G Q Sbjct: 62 VSDRAAVVAAMARIEEAAGGIDVLVNNAGILKPARLEDLSEADWDAHMDVNVKGVLSCCQ 121 Query: 125 AAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNS 184 A M R G IV ++SI+ G Q HY TKA V +L + A G GI N+ Sbjct: 122 AVLPGM-RARKAGRIVNIASIAGRQGVPTQGHYAATKAAVITLTRVLAQEAGMDGITVNA 180 Query: 185 VLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAALL 244 + PG ILTE+ K++L E + E L RLGAPED+ GP++F A + +A+VTG AL Sbjct: 181 ICPGIILTEMGKNNLGSDEAIRHWEEVAALKRLGAPEDIVGPVLFFAGEQSAFVTGQALN 240 Query: 245 VDGGMY 250 V GG+Y Sbjct: 241 VCGGIY 246 Lambda K H 0.318 0.133 0.379 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: 131 Number of extensions: 5 Number of successful extensions: 2 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: 254 Length of database: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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