Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate Pf1N1B4_3809 Oxidoreductase, short chain dehydrogenase/reductase family
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3809 Length = 248 Score = 100 bits (249), Expect = 3e-26 Identities = 76/261 (29%), Positives = 127/261 (48%), Gaps = 32/261 (12%) Query: 3 QVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSD-KAANVAQEINAEYGESMAYGFGAD 61 +VA++ GG + +GA + LAAEG VA + S KA + I + G ++A AD Sbjct: 9 KVALIQGGSRGIGAAIVKRLAAEGATVAFTYVSSTAKAEELQNSITSAGGNALA--IKAD 66 Query: 62 ATSEQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLCAR 121 + ++ + E FGR+D+LV +AG+ A + DF+L DFD++L +N+ F+ + Sbjct: 67 SADAVAIRNAVKVTVEAFGRLDILVNNAGVLAVASLEDFKLEDFDQTLAINVRSVFIATQ 126 Query: 122 EFSRLMIRDGIQGRIIQINSKSGKVGSKHNSG-YSAAKFGGVGLTQSLALDLAEYGITVH 180 E ++ M GRI+ I S + + G Y+ +K VGLT+ LA DL GIT++ Sbjct: 127 EAAKHMTEG---GRIVNIGSTNAERMPFAGGGPYAMSKSALVGLTKGLARDLGPRGITIN 183 Query: 181 SLMLG------NLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNML 234 ++ G N +SL+P A + R +++ + + Sbjct: 184 NVQPGPVDTDMNPASGDFAESLIPLMA-------------------VGRYGRVEEIASFV 224 Query: 235 LFYASPKASYCTGQSINVTGG 255 + P+A Y TG S+ + GG Sbjct: 225 AYLVGPEAGYITGASLTIDGG 245 Lambda K H 0.320 0.137 0.391 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: 150 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: 259 Length of database: 248 Length adjustment: 24 Effective length of query: 235 Effective length of database: 224 Effective search space: 52640 Effective search space used: 52640 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