Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate H281DRAFT_04160 H281DRAFT_04160 D-sorbitol dehydrogenase (acceptor)
Query= curated2:P37079 (267 letters) >FitnessBrowser__Burk376:H281DRAFT_04160 Length = 260 Score = 139 bits (351), Expect = 5e-38 Identities = 91/266 (34%), Positives = 144/266 (54%), Gaps = 23/266 (8%) Query: 7 LKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGD------RHHNGDNYHFWSTDI 60 L+D V I+TG ASGIG A+ L +GA ++D+ D R G+ S D+ Sbjct: 5 LQDKVAILTGAASGIGEAVARRYLDEGAQCVLVDVKPADSFGDTLRAAYGERVLTVSADV 64 Query: 61 SSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQ 120 + ++++ + + ++R+ +D L NNA + R ++DE F+++ +N Sbjct: 65 TRREDIERIVASTLERFGHVDILFNNAALFDMRPILDESWDV---------FDRLFAVNV 115 Query: 121 KGVFFMSQAVARQMVKQ-RAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELG 179 KG+FF+ QAVARQMV+Q R G I+N+SS++G G S Y ATKAA+ S+T+S + L Sbjct: 116 KGMFFLMQAVARQMVEQGRGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALA 175 Query: 180 KYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQL--REGYTKNAIPIGRAGKLSE 237 + I V G+APG+++ TP ++E A L ++ A+P+GR G + Sbjct: 176 PHKINVNGIAPGVVD-----TPMWKEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDD 230 Query: 238 VADFVCYLLSARASYITGVTTNIAGG 263 + +L SA A YIT T N+ GG Sbjct: 231 LTGAALFLASADADYITAQTLNVDGG 256 Lambda K H 0.316 0.133 0.386 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: 14 Number of successful extensions: 5 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: 267 Length of database: 260 Length adjustment: 25 Effective length of query: 242 Effective length of database: 235 Effective search space: 56870 Effective search space used: 56870 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 (21.6 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