Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_010960235.1 MCA_RS04555 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000008325.1:WP_010960235.1 Length = 239 Score = 116 bits (291), Expect = 4e-31 Identities = 90/248 (36%), Positives = 126/248 (50%), Gaps = 27/248 (10%) Query: 19 RHALVTGGAQGIGFEIARGLAQAGARVTI--------ADLNPD---VGEGAARELDGTFE 67 R ALV+GG+ GIG I R LA G V + A+ D VG G+A + Sbjct: 2 RQALVSGGSGGIGAAICRRLALDGLHVWVHYHGHRQSAEQVVDAIRVGGGSAEAIG---- 57 Query: 68 RLNVTDADA----VADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFW 123 +V DA A +A + P + VLVNNAGI +A D W V+ V+L+G F Sbjct: 58 -FDVCDAAAAAAAIATMCAERP-IQVLVNNAGIHDDAVFPAMRSDQWHRVIDVSLNGFFN 115 Query: 124 CCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGV 183 + M+ G IV+ +S++ L N + Q Y+A+K A+ TRSLA E ASRGV Sbjct: 116 LTQPLVMPMIRERWGRIVNISSVAALTGN--RGQVNYSAAKGALHSATRSLALELASRGV 173 Query: 184 RVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTG 243 VNAVAPG T + + R + P+ R P E+A V +LASD A+++TG Sbjct: 174 TVNAVAPGIIETGMAESAFD----RAAIERLVPMKRAGRPEEVADLVAFLASDRAAYITG 229 Query: 244 HTLVVDGG 251 + ++GG Sbjct: 230 QVISINGG 237 Lambda K H 0.319 0.134 0.408 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: 164 Number of extensions: 12 Number of successful extensions: 4 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: 255 Length of database: 239 Length adjustment: 24 Effective length of query: 231 Effective length of database: 215 Effective search space: 49665 Effective search space used: 49665 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: 46 (22.3 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