Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__PV4:5209125 Length = 248 Score = 123 bits (308), Expect = 4e-33 Identities = 78/245 (31%), Positives = 131/245 (53%), Gaps = 8/245 (3%) Query: 31 LKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYKCA 90 L GKVA +TG+S GIG AVAE +AGA V + S+ A + + G + Sbjct: 7 LTGKVALVTGASRGIGRAVAETLVEAGALVI---GTATSERGAAAIQEYLGDKGHGLVLN 63 Query: 91 VTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAYYC 150 VT+++ ++ +I++ G++DI + NAGI T ++ +EW ++D +L Y Sbjct: 64 VTDSESIDHLFASIKEKVGEVDILVNNAGI--TRDNLLMRMKEDEWTDIIDTNLTSLYRT 121 Query: 151 AKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAGFA-R 209 +K + K+ G I S+ G + N Q C AAK ++ ++SLA E A Sbjct: 122 SKQVLRAMMKKRSGRIINIGSVVGTMGNAGQTNYC--AAKAGLIGFTKSLAREVASRQIT 179 Query: 210 CNTVSPGYMATEISDFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDASTYTTGADI 269 N ++PG++ T+++D + + ++ +PM R G P E+A A ++LASD++ Y TG + Sbjct: 180 VNAIAPGFIQTDMTDELTEEQQKGIMSQVPMERLGQPQEIANAVLFLASDSAAYITGETL 239 Query: 270 LVDGG 274 V+GG Sbjct: 240 HVNGG 244 Lambda K H 0.317 0.132 0.409 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: 5 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: 278 Length of database: 248 Length adjustment: 25 Effective length of query: 253 Effective length of database: 223 Effective search space: 56419 Effective search space used: 56419 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