Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_085771999.1 B1812_RS13135 glucose 1-dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_002117405.1:WP_085771999.1 Length = 249 Score = 129 bits (323), Expect = 7e-35 Identities = 81/252 (32%), Positives = 136/252 (53%), Gaps = 14/252 (5%) Query: 6 GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELAS-----IAGVETHL 60 G+L+GK ++T GIG ++ +LFA EGA ++ T K L+ + GV+ + Sbjct: 2 GKLSGKVAVVTGGNSGIGLSTAQLFAAEGAHLVVTGRRKAELDTAVAEIGHGAVGVQGDV 61 Query: 61 LDVTDDDAIKALV-AKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRA 119 + D DA+ A V +K G +D+LF AG ++ ++ +D F++N K + T++ Sbjct: 62 SKLADLDALYAEVKSKFGRIDILFANAGVCELAPLVGVSEEHFDKVFDINVKGLLFTVQK 121 Query: 120 VLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAI 179 LP L GSI+ + S+ ++ G+ Y A+KAAV ++ ++ + IR N I Sbjct: 122 ALP--LFADGGSII-LNSSVANTTGIPAFGVYSATKAAVRSFARTWTSELKDRNIRVNVI 178 Query: 180 CPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESN 239 PG IE+P ++ A++ E A A+ P+GR GK EE+A AL+LASD+++ Sbjct: 179 SPGPIETPIFG-KVGLSAEQL----QEFDAQISAKVPLGRFGKPEEIAKAALFLASDDAS 233 Query: 240 FTTGSIHMIDGG 251 + G+ +DGG Sbjct: 234 YVAGADLYVDGG 245 Lambda K H 0.316 0.129 0.359 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: 160 Number of extensions: 12 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: 254 Length of database: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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