Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate Ac3H11_2518 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2518 Length = 263 Score = 119 bits (297), Expect = 8e-32 Identities = 78/248 (31%), Positives = 126/248 (50%), Gaps = 6/248 (2%) Query: 12 KTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVS 71 KT +VTGG+RG+GL A+ AGA + + R A D E T ++ + G+ + D + Sbjct: 14 KTALVTGGSRGLGLQLAHALGEAGAKIMLSSRKASDLEEATAEL-QAAGIDARWIAADCA 72 Query: 72 NTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAV 131 N + + + LG + LI NAG + PA + + + V ++NV G F + + Sbjct: 73 NETDIRRLADETLECLGHVDILINNAGAAWGAPAEDHPVDAWDKVMNLNVRGYFILSQHI 132 Query: 132 AKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASAG 191 AK + ++ GSI+ +S++ N +N + YN+SK A N + LAAEW + Sbjct: 133 AKHSMIGRRSGSIINVASIAGLGGNPKGMN----TIAYNTSKGAVINFTRALAAEWGAYN 188 Query: 192 IRVNALSPGYVNTDQTAHMDKKIRDHQ-ASNIPLNRFAQPEEMTGQAILLLSDHATYMTG 250 IRVNA+ PG+ + T K + + A++ PL R E++ G L SD ++TG Sbjct: 189 IRVNAICPGFFPSKMTVGTLKAMGEEALAAHAPLGRLGDDEDLKGLCALYASDAGKHITG 248 Query: 251 GEYFIDGG 258 +DGG Sbjct: 249 QWLAVDGG 256 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: 181 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: 262 Length of database: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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