Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AZOBR_RS04810 AZOBR_RS04810 shikimate 5-dehydrogenase
Query= reanno::Phaeo:GFF1301 (257 letters) >FitnessBrowser__azobra:AZOBR_RS04810 Length = 261 Score = 177 bits (450), Expect = 1e-49 Identities = 108/258 (41%), Positives = 145/258 (56%), Gaps = 6/258 (2%) Query: 1 MKRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQI---GAAAIAV 57 M L K ++TGA RGIGA A A A +GAR++IAD A+ A I G A+AV Sbjct: 1 MSNLKDKSIIVTGAGRGIGATMARALAADGARLIIADRTEEDAKTVAESIRAKGGDAVAV 60 Query: 58 ELDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLF 117 +DV D+A++ R + V FG LD+L NNA V P +++T E ++ D+N G L Sbjct: 61 TVDVRDRAAVRRMIDTAVTSFGRLDVLFNNAGVAQTKPFLDITEEDWRFVTDVNALGVLI 120 Query: 118 MMQAAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGIN 177 MQ A + QG GGKIIN AS AG++G ++ Y A+K AV++LTQ+A I Sbjct: 121 GMQEAIKTFRAQGGGGKIINTASIAGKQGYEPLAHYSASKFAVVALTQAAARAFGKEKIT 180 Query: 178 VNAIAPGVVDGEHWDGVDAFFAKYEGKAPGQKKA--EVAQSVPYGRMGTAADLTGMAVFL 235 NAI PGVV E W +D F + G + +A A GR TA DL G+A FL Sbjct: 181 ANAICPGVVATEMWKIIDKGF-RDTGLTTAEDEAFNHFAAGAVLGRPSTAEDLVGVARFL 239 Query: 236 ASEDADYVVAQTYNVDGG 253 AS D+D++ Q+ VDGG Sbjct: 240 ASSDSDFMTGQSLLVDGG 257 Lambda K H 0.317 0.130 0.365 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: 129 Number of extensions: 4 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: 257 Length of database: 261 Length adjustment: 24 Effective length of query: 233 Effective length of database: 237 Effective search space: 55221 Effective search space used: 55221 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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