Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate BPHYT_RS35475 BPHYT_RS35475 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__BFirm:BPHYT_RS35475 Length = 257 Score = 116 bits (290), Expect = 5e-31 Identities = 83/260 (31%), Positives = 131/260 (50%), Gaps = 17/260 (6%) Query: 3 QVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYG----F 58 Q AVV GGG +GA + L G RV ++ A+ ++ + + A G Sbjct: 11 QHAVVTGGGSGIGAAVAEALLRAGARVTLM-------GRNAERLDVQRAKCRALGDVACI 63 Query: 59 GADATSEQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFL 118 D T E SV + G +D+LV +AG A+AA + + + R L VNL G FL Sbjct: 64 SVDVTQEDSVASAFAEA----GAIDILVNNAGQAQAAPFTHTDMALWQRMLDVNLTGVFL 119 Query: 119 CAREFSRLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGIT 178 R M+ G GRI+ + S +G++G + + Y AAK G +GLT+SLAL++A G+T Sbjct: 120 GTRAALPGMLERG-HGRIVNVASTAGQIGYAYVAAYCAAKHGVIGLTRSLALEVATKGVT 178 Query: 179 VHSLMLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYA 238 V+++ G ++ + + L Q +K Q + + P R + V N +L+ Sbjct: 179 VNAVCPG-YTETELLHASLEQITSKTSRTEQQARETLLRSNPQHRFVSPEQVANAVLWLC 237 Query: 239 SPKASYCTGQSINVTGGQVM 258 P + TGQSI+++GG+VM Sbjct: 238 QPGSDAVTGQSISISGGEVM 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: 149 Number of extensions: 10 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