Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase
Query= CharProtDB::CH_091826 (259 letters) >NCBI__GCF_002117405.1:WP_085770280.1 Length = 246 Score = 114 bits (285), Expect = 2e-30 Identities = 81/256 (31%), Positives = 129/256 (50%), Gaps = 18/256 (7%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDA 62 + A+V G LG + L QAG V ++ LA + R A+ + Sbjct: 7 KTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKER-----AHILPCNL 61 Query: 63 TDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSRE 122 +D A + L A + G D+LV +AG+ + + + D+D L VNL F SR Sbjct: 62 SDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLSRA 121 Query: 123 FSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSL 182 + M+R GRII I S +G VG+ + YSAAK G G+T+SLA ++A G+TV+ + Sbjct: 122 VLRGMMRKR-HGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCV 180 Query: 183 MLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDKA 242 G +++SPM Q L E+L + +P++R ++ +L+ ASD+A Sbjct: 181 APG-VIESPMTQVLNEAQRERL-----------LKLIPMERFGSADEIGAAVLYLASDEA 228 Query: 243 AYCTGQSINVTGGQVM 258 A+ TGQ++++ GG M Sbjct: 229 AFITGQTLHINGGMAM 244 Lambda K H 0.319 0.136 0.387 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: 161 Number of extensions: 14 Number of successful extensions: 3 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: 259 Length of database: 246 Length adjustment: 24 Effective length of query: 235 Effective length of database: 222 Effective search space: 52170 Effective search space used: 52170 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 (21.7 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