Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AZOBR_RS31390 AZOBR_RS31390 3-ketoacyl-ACP reductase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__azobra:AZOBR_RS31390 Length = 252 Score = 154 bits (390), Expect = 1e-42 Identities = 101/248 (40%), Positives = 135/248 (54%), Gaps = 12/248 (4%) Query: 14 FRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTD 73 F L G+ ALVTGG GIG IA LA+AGA + +A P A E G D Sbjct: 5 FDLTGKTALVTGGNGGIGQAIAVALARAGADIAVAGRTPPDETRALVEGLGRRFAAIPAD 64 Query: 74 ADAVADLARRLPD-------VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCR 126 ++A + + + +D+LVNNAG++R D + DW AVL VNL VF+ C+ Sbjct: 65 LSSIAPIPALMEETVGTLGGLDILVNNAGLIRRDDPLDFTEADWDAVLDVNLKSVFFLCQ 124 Query: 127 EFGRTMLARGR-GAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 FGR L GR G I++ ASM P +Y ASK+ + +TR LA EWA +G+ V Sbjct: 125 AFGRYALGNGRKGKIINIASMLSFQGGIRVP--SYAASKSGIAGITRLLANEWAGKGINV 182 Query: 186 NAVAPGYTATPLTRRGLETPEWRET-WLKETPLGRLAEPREIAPAVLYLASDAASFVTGH 244 NA+APGY AT +T L E R L P GR +EP ++ ++LASDA+ +V G Sbjct: 183 NAIAPGYVATSVT-TALRADERRNAEILARIPAGRWSEPADMGGPAVFLASDASDYVHGT 241 Query: 245 TLVVDGGY 252 L VDGG+ Sbjct: 242 ILPVDGGW 249 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: 198 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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: 47 (22.7 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