Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate 7023065 Shewana3_0303 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__ANA3:7023065 Length = 253 Score = 125 bits (314), Expect = 9e-34 Identities = 88/257 (34%), Positives = 137/257 (53%), Gaps = 19/257 (7%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATY---GDRVLTV 60 RL +K A++TGAA GIG+A+ R+ L EGAR V D+ D+L+ D+++T Sbjct: 2 RLLNKTAVVTGAAGGIGQAIIRKLLAEGARVVAADLS-----ADALKVFNDFPADKLVTF 56 Query: 61 SADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILE-ESWDVFDRLFAVNVKGMF 119 S DVT ++ +V ++FGQ+DIL NNA + +P+L+ + + F+ + VN KG++ Sbjct: 57 SVDVTDYKQVEAMVKHAADQFGQLDILINNAGIGLAKPLLQHDPINDFEPVTNVNQKGVY 116 Query: 120 FLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKI 179 + A ++ QG G I+N SS + + Y +KAAV T+ AAL LAP + Sbjct: 117 HGILAGGRQFQAQGSRGVILNTSSVYAQIASEMTFTYNVSKAAVDMMTKCAALELAPLGV 176 Query: 180 NVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLA 239 V +APG VDTPM + +AL R K+++ E P+++ FL Sbjct: 177 RVCAVAPGRVDTPMLRQYEALGLWEHIR----KEQMRQEFTQ------PNEIADVVAFLV 226 Query: 240 SADADYITAQTLNVDGG 256 S +A+ I T+N G Sbjct: 227 SDEANCINGCTVNASDG 243 Lambda K H 0.321 0.135 0.393 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: 154 Number of extensions: 9 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: 260 Length of database: 253 Length adjustment: 24 Effective length of query: 236 Effective length of database: 229 Effective search space: 54044 Effective search space used: 54044 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 (21.9 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