Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate AZOBR_RS31390 AZOBR_RS31390 3-ketoacyl-ACP reductase
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__azobra:AZOBR_RS31390 Length = 252 Score = 130 bits (326), Expect = 4e-35 Identities = 86/252 (34%), Positives = 131/252 (51%), Gaps = 14/252 (5%) Query: 12 KTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVE-VTEKVGKEFGVKTKAYQCDV 70 KT +VTGGN GIG A A+A AGA++AV R+ D + E +G+ F A D+ Sbjct: 10 KTALVTGGNGGIGQAIAVALARAGADIAVAGRTPPDETRALVEGLGRRFA----AIPADL 65 Query: 71 SNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRA 130 S+ + +++ LG + L+ NAG+ + T D+ V DVN+ VF C+A Sbjct: 66 SSIAPIPALMEETVGTLGGLDILVNNAGLIRRDDPLDFTEADWDAVLDVNLKSVFFLCQA 125 Query: 131 VAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASA 190 + L +KG I+ +SM S G + Y +SK+ + + + LA EWA Sbjct: 126 FGRYALGNGRKGKIINIASMLS-------FQGGIRVPSYAASKSGIAGITRLLANEWAGK 178 Query: 191 GIRVNALSPGYVNTDQTAHM--DKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYM 248 GI VNA++PGYV T T + D++ + IP R+++P +M G A+ L SD + Y+ Sbjct: 179 GINVNAIAPGYVATSVTTALRADERRNAEILARIPAGRWSEPADMGGPAVFLASDASDYV 238 Query: 249 TGGEYFIDGGQL 260 G +DGG L Sbjct: 239 HGTILPVDGGWL 250 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: 135 Number of extensions: 9 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: 262 Length of database: 252 Length adjustment: 24 Effective length of query: 238 Effective length of database: 228 Effective search space: 54264 Effective search space used: 54264 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: 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