Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_104914316.1 C3B54_RS06590 glucose 1-dehydrogenase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_002950575.1:WP_104914316.1 Length = 239 Score = 102 bits (254), Expect = 8e-27 Identities = 79/257 (30%), Positives = 126/257 (49%), Gaps = 25/257 (9%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPTDISSASEV 66 L+ K+ VTG GIG AI + +GA V + H+ + +F +++ Sbjct: 4 LEGKVAIVTGAGRGIGRAIAEIFHQEGATV--VATSQSPNHEFAPGIDFIQQEVAEEKAW 61 Query: 67 HKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGVFLM 126 V +QR GR+D LVNNAG+ L D L A ++++V +NQ GVFL Sbjct: 62 ELVVATTMQRHGRVDVLVNNAGIIAYEPLGD---------LTLADWDRVVAVNQTGVFLG 112 Query: 127 SQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGIRVV 186 +AV M++Q++G I+N+SS G G Y ATK A+ + +++ + G+RV Sbjct: 113 MKAVLPHMLQQKTGSIINISSIWGNAAVAGAHAYHATKGAVRNMSKNAAITYATTGVRVN 172 Query: 187 GVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVCYLL 246 + PG + TP L ++ V + G + P+GR+G+ E+A +L Sbjct: 173 SLHPGF-----IATP-----LTDAQDPDVNKFVVGMT----PMGRAGQPEEIAWGAVFLA 218 Query: 247 SERASYMTGVTTNIAGG 263 S+ +S+MTG I GG Sbjct: 219 SDESSFMTGSELVIDGG 235 Lambda K H 0.315 0.132 0.378 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: 164 Number of extensions: 7 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: 267 Length of database: 239 Length adjustment: 24 Effective length of query: 243 Effective length of database: 215 Effective search space: 52245 Effective search space used: 52245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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