Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_004266003.1 C665_RS01140 beta-ketoacyl-ACP reductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000310185.1:WP_004266003.1 Length = 246 Score = 120 bits (301), Expect = 3e-32 Identities = 83/242 (34%), Positives = 129/242 (53%), Gaps = 16/242 (6%) Query: 21 ALVTGGAQGIGFEIARGLAQAGARVTIADLNP-----DVGEGAARELDGTFERL--NVTD 73 ALVTG G+G I + LA+ G +V +A+ P D A R+L F +V++ Sbjct: 6 ALVTGAMGGLGTAICQSLAKDGFKV-VANCLPNFELKDAWLSAQRDLGFDFAAAEGDVSN 64 Query: 74 ADAVADLARRLP----DVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFG 129 ++ A + ++ +DVLVNNAGI R+ W AV++ NL+ +F Sbjct: 65 YESCAAMVAKIEADVGPIDVLVNNAGITRDKFFPKMEKGQWDAVINTNLNSLFNVTHHVS 124 Query: 130 RTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVA 189 M RG G I++ +S++G+ Q Y+ +KA V+ T++LA E A++GV VNA+A Sbjct: 125 AKMAERGWGRIINISSVNGV--KGQAGQTNYSTAKAGVLGFTKALAAELATKGVTVNAIA 182 Query: 190 PGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVD 249 PGY T + E + R+ + P+ RL P EI YLASD A+++TG T+ ++ Sbjct: 183 PGYIGTDMVMAIRE--DIRQGIIDTVPMKRLGRPDEIGDLCAYLASDKAAYITGATININ 240 Query: 250 GG 251 GG Sbjct: 241 GG 242 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: 132 Number of extensions: 8 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: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 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 24 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