Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AZOBR_RS08390 AZOBR_RS08390 3-oxoacyl-ACP synthase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__azobra:AZOBR_RS08390 Length = 245 Score = 160 bits (406), Expect = 2e-44 Identities = 106/248 (42%), Positives = 139/248 (56%), Gaps = 16/248 (6%) Query: 13 LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERL--- 69 +F L G+ ALVTG + GIG +IAR L GA V ++ E A EL ER Sbjct: 1 MFDLTGKKALVTGASGGIGAQIARALHAQGATVALSGTRVAPLEALAAELG---ERALVV 57 Query: 70 --NVTDADAVADLAR----RLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFW 123 N+ DA LA+ L +D+LVNNAG+ R+ A DDDW++VL VNL F Sbjct: 58 PGNLADAAGTEQLAKDAEAALGQIDILVNNAGLTRDQLAMRMKDDDWQSVLDVNLTAAFR 117 Query: 124 CCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGV 183 R R M+ R G I+ S+ G+ N QA Y ASKA +I +++SLA E ASRG+ Sbjct: 118 LSRAVLRGMMKRRWGRIIGITSIVGVTGN--PGQANYAASKAGMIGMSKSLAAEVASRGI 175 Query: 184 RVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTG 243 VN VAPG+ T +T E ++ L P GR+ EP EIA V+YLASD A++VTG Sbjct: 176 TVNCVAPGFITTAMT--DALNSEQKDKLLTAIPSGRMGEPGEIAAGVVYLASDEAAYVTG 233 Query: 244 HTLVVDGG 251 TL ++GG Sbjct: 234 QTLHINGG 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: 158 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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