Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate H281DRAFT_03703 H281DRAFT_03703 NADP-dependent 3-hydroxy acid dehydrogenase YdfG
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__Burk376:H281DRAFT_03703 Length = 257 Score = 117 bits (294), Expect = 2e-31 Identities = 83/256 (32%), Positives = 138/256 (53%), Gaps = 9/256 (3%) Query: 3 QVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGFGADA 62 Q AVV GGG +GA + L G RV ++ S++ A ++ A +G+ D Sbjct: 11 QHAVVTGGGSGIGAAIAEALLHAGARVTLMGRNSERLAAQREKCRA-WGDVAC--ITVDV 67 Query: 63 TSEQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLCARE 122 T E+SV ++ +E G VD+L+ +AG A+AA + + + R L VNL G FL R Sbjct: 68 TQEESV---AKAFNEA-GAVDILINNAGQAQAAPFTHTDMTLWQRMLDVNLTGVFLGTRA 123 Query: 123 FSRLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSL 182 M+ + GRI+ + S +G++G + + Y AAK G +GLT+SLAL++A G+TV+++ Sbjct: 124 VLPGML-ERRHGRIVNVASTAGQIGYAYVAAYCAAKHGVIGLTRSLALEVATKGVTVNAV 182 Query: 183 MLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYASPKA 242 G ++ + + L Q +K +Q + + P R + V N +L+ P + Sbjct: 183 CPG-YTETELLHASLQQITSKTSRTEEQARESLLRSNPQHRFVSPEQVANAVLWLCQPGS 241 Query: 243 SYCTGQSINVTGGQVM 258 TGQS++++GG+VM Sbjct: 242 DAITGQSVSISGGEVM 257 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: 152 Number of extensions: 13 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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