Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate CA265_RS08650 CA265_RS08650 short-chain dehydrogenase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Pedo557:CA265_RS08650 Length = 248 Score = 123 bits (308), Expect = 4e-33 Identities = 77/250 (30%), Positives = 132/250 (52%), Gaps = 16/250 (6%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKLDVRDD----A 60 L GK AL+T GIG ATA+ +GA VI T R D + E + + D Sbjct: 4 LTGKKALVTGGNSGIGYATAKELKAQGAEVIITGRRKDAVDKAAAELGVIGLVADQSQIT 63 Query: 61 AIKALAAEIGAV----DVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLPA 116 AI+ LA+++ ++ D+LF AG V +I E +E+ +D F +N K Y + F+P Sbjct: 64 AIEGLASDVESIFNKIDILFINAGVVEQSSIAEATEKSFDTIFGINFKGAYFTLSKFIPL 123 Query: 117 MLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPGT 176 M D G S++ +SS + + G + Y++SK+A+ + + A + R +R N++ PG Sbjct: 124 MND--GSSVVFLSSNTAHMDGAKSSI-YTSSKSALNSVMRIAAVELAPRQIRVNSVSPGP 180 Query: 177 VASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFTTG 236 +A+ + + + + Q G + ++R P+G+IGK E++A + + D +++ TG Sbjct: 181 IATEIMNKMGLNEEQLNG-----INQWLISRSPLGKIGKSEDVAKMVAFFCGDAATYITG 235 Query: 237 HAHVIDGGWS 246 V+DGG S Sbjct: 236 AEIVMDGGMS 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: 113 Number of extensions: 3 Number of successful extensions: 2 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 17 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