Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_043919846.1 jaqu_RS15175 SDR family oxidoreductase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000877395.1:WP_043919846.1 Length = 246 Score = 270 bits (689), Expect = 3e-77 Identities = 144/248 (58%), Positives = 173/248 (69%), Gaps = 6/248 (2%) Query: 6 GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVTD 65 GRL GK LITAA QGIGRA+ E F EGA V ATD+ L+ L ET LD D Sbjct: 3 GRLEGKRALITAAGQGIGRATAEAFVAEGAEVFATDLDLALLDGL----DCETFALDARD 58 Query: 66 DDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGML 125 D +++A V + DVLFNCAG+V G++L+ D + F F+LN +MF TIRA LPGML Sbjct: 59 DASVRAGVDRAQP-DVLFNCAGFVHHGSVLDATDDDFAFGFDLNVHSMFRTIRAALPGML 117 Query: 126 AKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTIE 185 + GSIVN++SA SSV G NRF YGA+KAAV+GLTKSVA DF+ QGIRCN ICPGT+E Sbjct: 118 ERGGGSIVNMSSACSSVIGAPNRFIYGATKAAVIGLTKSVAVDFIKQGIRCNCICPGTVE 177 Query: 186 SPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTGSI 245 SPS + R+ +E G S D+ AFVARQPMGR+ A E+AAL +YL SDES FTTG Sbjct: 178 SPSWHDRVKALGEEMG-SYDKAMEAFVARQPMGRVATAAEIAALVVYLGSDESAFTTGHP 236 Query: 246 HMIDGGWS 253 H+IDGGWS Sbjct: 237 HIIDGGWS 244 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: 202 Number of extensions: 13 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: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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 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