Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_047007388.1 AAW01_RS11455 SDR family oxidoreductase
Query= metacyc::MONOMER-13092 (266 letters) >NCBI__GCF_001010925.1:WP_047007388.1 Length = 266 Score = 107 bits (268), Expect = 2e-28 Identities = 88/274 (32%), Positives = 132/274 (48%), Gaps = 35/274 (12%) Query: 9 GKTVIVTGASS------GIGKAIVDELLSLKVKVANFDLTDNGEKHE------NLLFQKV 56 GKT++VTG+ GI +A DE + V D +G E + + Sbjct: 6 GKTIVVTGSGKEKGLGQGILQAFADEGANCVVSDVRLDDEVDGVADELRQRGAKVATVQC 65 Query: 57 DVTSREQVEASVAAVVEHFGTVDAVVNNAGINI---PRLLVDPKDPHGQYELDDATFEKI 113 DV+ +A VA ++HFG+VD VNNAGI P L VD D ++++ Sbjct: 66 DVSDAASCQALVAQALDHFGSVDVFVNNAGIGFKMKPLLDVDTADE----------WDQV 115 Query: 114 TMINQKGLYLVSQAVGRLLV-AKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSW 172 +N G + +QA R +V A K G IIN+AS+A G AY +K + TR+ Sbjct: 116 LAVNLSGAFYCTQAAARAMVDAGKGGRIINIASQAAKTGFPHLPAYVSSKHGMVGLTRAS 175 Query: 173 AKELGKYGVRVVGIAPGIMEATGL---RTLAYEEALGYTRGKTVEEIRAGYASTTTTPLG 229 A ELG +G+ V I P + TGL + + + LG+ + VE+ A A+ P+G Sbjct: 176 AVELGAHGITVNAICPNHV-TTGLGAQQNEYFSKLLGFAK---VEDYLANMAA--KNPMG 229 Query: 230 RSGKLSEVADLVAYYISDRSSYITGITTNVAGGK 263 R G S+ A + SD + Y+TG N++GG+ Sbjct: 230 RPGLPSDTAAACLWLASDEAVYVTGEALNISGGE 263 Lambda K H 0.313 0.131 0.361 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: 192 Number of extensions: 15 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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