Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Phaeo:GFF1301 Length = 257 Score = 153 bits (386), Expect = 4e-42 Identities = 98/261 (37%), Positives = 142/261 (54%), Gaps = 16/261 (6%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K ++TGA+RGIG A A A +GARVVI + D RA A + A G AIA Sbjct: 4 LSGKRALITGAARGIGAAFAEAYANEGARVVI--ADIDTARAEATA-----AQIGAAAIA 56 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 V D D S ++ ++ VE FG +D+L+NNA + +++ RE Y +T N++G Sbjct: 57 VELDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTL 116 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 F +QAAA++M QG GG II ++S + G + + Y TKA ++SL QS + L +GI Sbjct: 117 FMMQAAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGI 176 Query: 183 RCNAVLPGTI---------ATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLA 233 NA+ PG + A E + +K+ + VP GR+G DL G VFLA Sbjct: 177 NVNAIAPGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLA 236 Query: 234 SDMARYVTGASLLVDGGLFVN 254 S+ A YV + VDGG +++ Sbjct: 237 SEDADYVVAQTYNVDGGQWMS 257 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: 163 Number of extensions: 6 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: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 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 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