Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_053937509.1 WG78_RS09155 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_001294205.1:WP_053937509.1 Length = 247 Score = 135 bits (339), Expect = 1e-36 Identities = 96/245 (39%), Positives = 136/245 (55%), Gaps = 13/245 (5%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGA-----ARELDGTFERLN 70 L+G+ ALVTG ++GIG IA L + GA V + + + A L G RL Sbjct: 3 LEGKVALVTGASRGIGQAIALELGRLGATVVGTATSQEGADAITAYLQAAGLKGHGLRLQ 62 Query: 71 VTDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCR 126 VT+ A L ++ + VLVNNAGI R+ DD+W A+++ NL V+ + Sbjct: 63 VTEDGACEALVSQIEKDSGAIAVLVNNAGITRDNLLMRMKDDEWDAIMATNLKPVYQLSK 122 Query: 127 EFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVN 186 R M+ G IV+ AS+ G N Q Y+A+KAA+ T+SLA E SRG+ VN Sbjct: 123 AVIRGMMKARWGRIVNIASVVGATGNPGQTN--YSAAKAALFGFTKSLAREIGSRGITVN 180 Query: 187 AVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTL 246 AVAPG+ T +T RGL E + ++ LGRL ++IA AV +L+SD A ++TG+TL Sbjct: 181 AVAPGFIDTDMT-RGL-PDEQKAKLVESIALGRLGAAQDIADAVAFLSSDKAGYITGNTL 238 Query: 247 VVDGG 251 V+GG Sbjct: 239 HVNGG 243 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: 176 Number of extensions: 10 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 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