Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate 7025539 Shewana3_2690 short chain dehydrogenase (RefSeq)
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__ANA3:7025539 Length = 255 Score = 130 bits (326), Expect = 3e-35 Identities = 96/258 (37%), Positives = 132/258 (51%), Gaps = 26/258 (10%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIR-------IDGLAGKPVEARKL--D 55 L GK A+IT A GIG ATA+ FAREGA+++ R +D + + EA L D Sbjct: 4 LQGKVAIITGASSGIGYATAKRFAREGAKLVLGARRGAILASLVDEIITQGGEAIYLAGD 63 Query: 56 VRDDAAIKALAA----EIGAVDVLFNCAGFVHAGNILE--CSEEDWDFAFDLNVKAMYRM 109 V D+ L A + G +D+ FN G + S +W+ N+ + + Sbjct: 64 VTDEVYASDLVALAVEQYGGLDIAFNNVGINGELGVDSDALSRAEWENTLTTNLTSAFLA 123 Query: 110 IRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRC 169 + LP ML +G GSII SS G P AY+ASKA +IGLT+S+A ++ RG+R Sbjct: 124 AKYQLPQMLKRGAGSIIFTSSFVGYTIGFPQTAAYAASKAGMIGLTQSLAVEYGARGIRV 183 Query: 170 NAICPGTVASP-SLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGS 228 NA+ PG +P E +A A L A++ R+ P EIA ALYL S Sbjct: 184 NALLPGGTDTPMGREFANTPEAMAFVKNLHALK----------RLADPAEIAQSALYLAS 233 Query: 229 DESSFTTGHAHVIDGGWS 246 D +SFTTG A ++DGG S Sbjct: 234 DAASFTTGIALLVDGGVS 251 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: 152 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 223 Effective length of database: 231 Effective search space: 51513 Effective search space used: 51513 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