Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 144 bits (363), Expect = 2e-39 Identities = 86/248 (34%), Positives = 134/248 (54%), Gaps = 21/248 (8%) Query: 7 GKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEAR------KLDVRDDA 60 G+ ++T QGIG A FA EGA+ + D+ D G+ + A + DV D A Sbjct: 20 GRVCIVTGGAQGIGEACVRRFAAEGAKPVIVDV--DDARGQALAAELGALYVRCDVGDKA 77 Query: 61 AIKALAAEI----GAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLPA 116 + AL A++ G +DVL N AG A + LE +E D+D +N+K + + +A A Sbjct: 78 QVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVGQAVARA 137 Query: 117 MLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPGT 176 M+ GGG+I+NMSS + V +PN +Y+ SK V LT+ +A + +R NA+ PGT Sbjct: 138 MVTSGGGAIVNMSS-VNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAVAPGT 196 Query: 177 VASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFTTG 236 +A+ + ++ T D + ++R PM R+G+P EIA + +L SD +S+ TG Sbjct: 197 IATELAAKAVL--------TSDEAKRKIMSRTPMKRLGQPSEIADVVAWLASDAASYVTG 248 Query: 237 HAHVIDGG 244 +DGG Sbjct: 249 EIVTVDGG 256 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: 154 Number of extensions: 12 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: 267 Length adjustment: 24 Effective length of query: 223 Effective length of database: 243 Effective search space: 54189 Effective search space used: 54189 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: 47 (22.7 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