Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_024981780.1 BXU11_RS13235 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_002017945.1:WP_024981780.1 Length = 248 Score = 130 bits (327), Expect = 2e-35 Identities = 83/254 (32%), Positives = 127/254 (50%), Gaps = 26/254 (10%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIAT-------------DIRIDGLAGKPVEA 51 L GK A+IT A +GIG AE+FA+ GA + T ++ G+ K ++ Sbjct: 4 LEGKVAIITGASRGIGKGIAEVFAKHGANIAFTYSSSVESALALENELNTMGIKAKGYQS 63 Query: 52 RKLDVRD-DAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMI 110 D + + A+ A+ G+VD+L N AG ++ SE D+D D+N+K+++ M Sbjct: 64 NAADFNEAQTFVDAVLADFGSVDILINNAGITKDNLMMRMSEADFDQVIDVNLKSVFNMT 123 Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170 +A L + GSIINMSS VKG + Y+ASKA VIG +KSVA + +R +RCN Sbjct: 124 KAIQKTFLKQRAGSIINMSSVV-GVKGNAGQTNYAASKAGVIGFSKSVALELGSRNIRCN 182 Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDE 230 I PG + + + D V + P+ R G +++A L+ SD Sbjct: 183 VIAPGFI-----------ETEMTAKLSDDVVKGWREGIPLKRGGSTDDVANACLFFASDM 231 Query: 231 SSFTTGHAHVIDGG 244 S++ TG + GG Sbjct: 232 SAYVTGQVLNVCGG 245 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: 145 Number of extensions: 5 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: 248 Length adjustment: 24 Effective length of query: 223 Effective length of database: 224 Effective search space: 49952 Effective search space used: 49952 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: 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