Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_025272126.1 HALAL_RS0100575 SDR family NAD(P)-dependent oxidoreductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_000527155.1:WP_025272126.1 Length = 290 Score = 112 bits (280), Expect = 8e-30 Identities = 79/255 (30%), Positives = 126/255 (49%), Gaps = 30/255 (11%) Query: 5 LAGKTALITAAG--QGIGLATAELFAREGARV--IATDIRIDGLAGK-PVEARKLDVRDD 59 L GKTAL+T AG GIG+A A GAR+ ++T RI A + D+ D+ Sbjct: 46 LIGKTALVTGAGADDGIGMAIATRLRLAGARLALVSTTKRIHERANELDAVGFVADLTDE 105 Query: 60 AAIKALAAEI----GAVDVLFNCAGFVH------AGNILECSEEDWDFAFDLNVKAMYRM 109 A + L + G VD++ N AG + + +DW+ N+ + + + Sbjct: 106 AEVAGLGDAVTEGLGEVDIVVNNAGMTSKTAPAVTKPVAQLGFDDWEAEITRNLHSTFLV 165 Query: 110 IRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRC 169 R F+ +M + G G I+N+S+ A +P AY+++KA V GLT+++A + + GV Sbjct: 166 SRYFVQSMAESGWGRIVNVSATAGVSSVMPAEAAYASAKAGVAGLTRALATEVVADGVTV 225 Query: 170 NAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSD 229 NA+ PG + + S +T+ +Q P+GR G PEE+AA + S Sbjct: 226 NAVAPGLIHTGS-------------STVPELQRG--VDSPLGRPGTPEEVAAAVAFFCSP 270 Query: 230 ESSFTTGHAHVIDGG 244 +S+ TG V+DGG Sbjct: 271 SASYVTGQTLVVDGG 285 Lambda K H 0.320 0.133 0.381 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: 165 Number of extensions: 12 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: 247 Length of database: 290 Length adjustment: 25 Effective length of query: 222 Effective length of database: 265 Effective search space: 58830 Effective search space used: 58830 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 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