Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Miya:8502394 Length = 247 Score = 154 bits (388), Expect = 2e-42 Identities = 99/241 (41%), Positives = 142/241 (58%), Gaps = 14/241 (5%) Query: 21 ALVTGGAQGIGFEIARGLAQAGARVTIADLN-PDVGEGAARELDGTFE-----RLNVTDA 74 ALVTGG++GIG +A LA+ G +V + ++ P+ E A ++ RL+V+DA Sbjct: 8 ALVTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSDA 67 Query: 75 DAVA----DLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGR 130 AVA + R +DVLVNNAGI ++ DDD+ VL VNL G F C RE + Sbjct: 68 AAVAAFFQEEIREKVTLDVLVNNAGITKDGLILRMKDDDFDRVLDVNLSGAFTCLREAAK 127 Query: 131 TMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAP 190 M + +G IV+ S+ G + N Q Y+A+KA +I +T+S A E A R V VNAVAP Sbjct: 128 LMTRQRKGRIVNITSVVGQMGN--AGQVNYSAAKAGLIGMTKSAAKELAGRNVTVNAVAP 185 Query: 191 GYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVDG 250 G+ T +T + T E R +++ PL RL +P++IA AV +LASD A ++TG + V+G Sbjct: 186 GFIETDMTAK--LTDEVRAAYIEAIPLRRLGQPQDIADAVAFLASDKAGYITGQVIAVNG 243 Query: 251 G 251 G Sbjct: 244 G 244 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: 163 Number of extensions: 7 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: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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 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