Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_025763370.1 X939_RS0111250 glucose 1-dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000566685.1:WP_025763370.1 Length = 257 Score = 153 bits (386), Expect = 4e-42 Identities = 89/256 (34%), Positives = 147/256 (57%), Gaps = 20/256 (7%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIA---GVETHLL-- 61 RL K LIT + GIGR + LFAREGA+++ +D+++ ++ A + G E + + Sbjct: 2 RLKNKVALITGGSGGIGRETALLFAREGAQIVVSDVNQEMGQQTADMIVEQGGEAYFIYS 61 Query: 62 DVTDDDAIKALVA----KVGTVDVLFNCAGYVAAG--NILECDDKAWDFSFNLNAKAMFH 115 DV+ D KA+VA K G +++LFN AG + + N + ++ WD + N+NAK +F Sbjct: 62 DVSKDADCKAMVAFTEEKFGKLNILFNNAGIMHSDDDNAMTTEESVWDLTMNINAKGVFL 121 Query: 116 TIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIR 175 + +P + GS++N AS + + + AY ASK AV+ LT+ +A + IR Sbjct: 122 GCKYGIPALQRAGGGSVINTASFVAILGAATPQIAYTASKGAVLALTRELAVIHARENIR 181 Query: 176 CNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLAS 235 NA+CPG + + L + ++T+ K+ + + PMGR G+A+E+A+ L+LAS Sbjct: 182 VNALCPGPLRTELLMKFLNTEEKKQRR---------LVHVPMGRFGEAKEMASAVLFLAS 232 Query: 236 DESNFTTGSIHMIDGG 251 DES + TG+ ++DGG Sbjct: 233 DESTYVTGTDFLVDGG 248 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: 152 Number of extensions: 7 Number of successful extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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: 47 (22.7 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