Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate CCNA_03495 CCNA_03495 D-beta-hydroxybutyrate dehydrogenase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__Caulo:CCNA_03495 Length = 265 Score = 117 bits (292), Expect = 3e-31 Identities = 81/257 (31%), Positives = 129/257 (50%), Gaps = 5/257 (1%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNA-NRLADTINSRYGAGRAYGFKVD 61 QVA+V G +G + + LA G ++ + L E NA R + +G Y D Sbjct: 10 QVAIVTGSTSGIGHAMADALAAQGCNIVMNGLGEMNAIERARAEMAETHGVEVLY-HGAD 68 Query: 62 ATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121 T + + RA FG D+LV +AGV AP+ F +DL + VNL F ++ Sbjct: 69 MTRPIEIADMVRAAKAEFGELDILVNNAGVQHVAPVEDFPEDKWDLIIAVNLSSAFHATK 128 Query: 122 EFSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHS 181 +M G +GRI+ I S G V S S Y AAK G +GLT+++AL++A++GIT ++ Sbjct: 129 AAVPIMKEQG-RGRIVNIASAHGLVASPFKSAYVAAKHGIMGLTKTVALEVAQHGITCNA 187 Query: 182 LMLGNLLKSPMFQSLLPQYAEKLGITPEEV-EPYYVDKVPLKRGCDYQDVLNVLLFYASD 240 + G +K+P+ ++ + A+ GI+ E V + P K+ + + +LL+ SD Sbjct: 188 ICPG-FVKTPLVEAQIADQAKARGISEEAVMRDVILASQPTKQFVTFDQLNGMLLYLVSD 246 Query: 241 KAAYCTGQSINVTGGQV 257 A G + + GG V Sbjct: 247 LGASANGAAYQIDGGWV 263 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: 153 Number of extensions: 6 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: 265 Length adjustment: 25 Effective length of query: 234 Effective length of database: 240 Effective search space: 56160 Effective search space used: 56160 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: 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