Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_063836871.1 BS73_RS00110 SDR family oxidoreductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_000744815.1:WP_063836871.1 Length = 345 Score = 165 bits (418), Expect = 1e-45 Identities = 100/256 (39%), Positives = 144/256 (56%), Gaps = 21/256 (8%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGL---------AGKPVEARKLD 55 L GKTA +T AG GIG A A A EGARV A DIR+ +G A + D Sbjct: 4 LTGKTAFVTGAGSGIGQACALRLAEEGARVAAVDIRLPAAEETAKRIEASGGTAVAVECD 63 Query: 56 VRDD----AAIKALAAEIGAVDVLFNCAGFVHA-GNILECSEEDWDFAFDLNVKAMYRMI 110 V AA+ +GA+ V+ N AG + A G+++ CSE+DWD +NVK+MY + Sbjct: 64 VSSGRQVAAAVSRTVEALGALHVIVNAAGILAAEGDVVACSEDDWDRVMGVNVKSMYLIG 123 Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170 + +P +L GGGSI+N++S +P+ AY ASK AV+ LT+ +A + +G+R N Sbjct: 124 KHGVPEILRAGGGSIVNIAS-VFGFTALPDECAYDASKGAVLNLTRQMAVQYAKQGIRVN 182 Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDE 230 A+CP +P L+ A G ++A +A PMGR+ +PEEIA+ +L SD+ Sbjct: 183 ALCPSDCDTPLLD------ALLAGGDVEAEKAELAKPIPMGRLARPEEIASGVAFLASDD 236 Query: 231 SSFTTGHAHVIDGGWS 246 ++F TG A +DGG S Sbjct: 237 AAFVTGVALPVDGGSS 252 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: 234 Number of extensions: 10 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: 247 Length of database: 345 Length adjustment: 26 Effective length of query: 221 Effective length of database: 319 Effective search space: 70499 Effective search space used: 70499 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: 48 (23.1 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