Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG
Query= SwissProt::O93868 (262 letters) >NCBI__GCF_000527155.1:WP_025272362.1 Length = 236 Score = 127 bits (320), Expect = 2e-34 Identities = 81/248 (32%), Positives = 127/248 (51%), Gaps = 17/248 (6%) Query: 14 IIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVSNT 73 +++TGG RGIG A + + G VAV RS DA E + YQ DVS+ Sbjct: 6 VLITGGTRGIGRAAAQRLKDDGFTVAVASRSIPDA---------ENRLDVHHYQVDVSDG 56 Query: 74 DIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAVAK 133 + I ++ ++G I LI +AG+ P +T +D+ V N+ G +N CR++A Sbjct: 57 NACKDLITTVEDEVGDIDVLINSAGIVRDSPLLTMTGDDWNDVIRTNLDGTYNMCRSMA- 115 Query: 134 LWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASAGIR 193 + K++ GSI+ SS++ + G+ TQ Y++SKA K L+ E IR Sbjct: 116 FSMMKRKNGSIINLSSVAG-------IQGNPTQSNYSASKAGIIGFSKALSKELGRFNIR 168 Query: 194 VNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYMTGGEY 253 VN ++PG++ TD TA + + ++ NIPL R +++ L S ATYMTG Sbjct: 169 VNVVAPGFIETDMTADLAESVKKKAVENIPLGRMGSVDDVAHLVGFLASPRATYMTGAVV 228 Query: 254 FIDGGQLI 261 +DGG ++ Sbjct: 229 PVDGGIIL 236 Lambda K H 0.317 0.130 0.372 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: 134 Number of extensions: 6 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: 262 Length of database: 236 Length adjustment: 24 Effective length of query: 238 Effective length of database: 212 Effective search space: 50456 Effective search space used: 50456 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: 46 (22.3 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