Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_086508841.1 BZY95_RS04820 3-oxoacyl-ACP reductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_002151265.1:WP_086508841.1 Length = 250 Score = 130 bits (328), Expect = 2e-35 Identities = 92/253 (36%), Positives = 135/253 (53%), Gaps = 24/253 (9%) Query: 4 RLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGL---------AGKPVEARKL 54 RL G++AL+T A QGIGLA A A+ GARV + L AG E L Sbjct: 10 RLDGRSALVTGASQGIGLACACALAQAGARVTLVARNAERLEEVVAALRAAGHEAEGLAL 69 Query: 55 DVRDDAAIK-ALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAF 113 DV+D AA + ALA D+L N AG I + +EED+ +LNV+A Y + + Sbjct: 70 DVQDQAATRRALAGR--RFDILVNNAGTNRPKPIDQVTEEDYAAVMELNVRATYFLTQTV 127 Query: 114 LPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAIC 173 + M GGS+IN+SS V G NR Y ASKAAV G+T+++A + RG+R N +C Sbjct: 128 IAEM--PAGGSVINVSSQMGHV-GAKNRSLYCASKAAVEGMTRAMAVELGPRGIRVNTLC 184 Query: 174 PGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSF 233 P + +P + Q G + A +A+ P+ R+G+ E++ ++L S ++ Sbjct: 185 PTFIETPMTQPFF----QEPG-----FREAVLAQIPLERLGQIEDVMGPVVFLASPAANL 235 Query: 234 TTGHAHVIDGGWS 246 TG A ++DGGW+ Sbjct: 236 ITGSALMVDGGWT 248 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: 150 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: 250 Length adjustment: 24 Effective length of query: 223 Effective length of database: 226 Effective search space: 50398 Effective search space used: 50398 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