Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_002117405.1:WP_085770280.1 Length = 246 Score = 156 bits (394), Expect = 4e-43 Identities = 103/246 (41%), Positives = 139/246 (56%), Gaps = 12/246 (4%) Query: 13 LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVT 72 +F L G+ ALVTG + G+G IAR L QAGA V ++ + E A EL L Sbjct: 1 MFDLTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERAHILPCN 60 Query: 73 DADAVADLARRLP-------DVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125 +D A+ + +P VD+LVNNAGI R+ D+DW AVL+VNL F Sbjct: 61 LSDR-AETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLS 119 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 R R M+ + G I++ S++G + N QA Y+A+KA + +T+SLA E ASRGV V Sbjct: 120 RAVLRGMMRKRHGRIINITSVAGAVGN--PGQANYSAAKAGLTGMTKSLANEVASRGVTV 177 Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245 N VAPG +P+T+ + RE LK P+ R EI AVLYLASD A+F+TG T Sbjct: 178 NCVAPGVIESPMTQ--VLNEAQRERLLKLIPMERFGSADEIGAAVLYLASDEAAFITGQT 235 Query: 246 LVVDGG 251 L ++GG Sbjct: 236 LHINGG 241 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: 160 Number of extensions: 9 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 Apr 09 2024. 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