Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Echvi_2940 Echvi_2940 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Cola:Echvi_2940 Length = 251 Score = 167 bits (423), Expect = 2e-46 Identities = 108/256 (42%), Positives = 148/256 (57%), Gaps = 21/256 (8%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKL---------- 54 + KT LIT GIGLA + FA EG V D D G+ V A +L Sbjct: 1 MKNKTILITGGASGIGLAMTKRFAEEGGNVYFIDY--DQKTGEKV-AEELTSKGHRVTFL 57 Query: 55 --DVRDDAAIKALAAEI-GAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIR 111 DV +K + I G++DVL N AG H GN+ +EED+D + +NVK +Y Sbjct: 58 QGDVSQTEEMKQTISSISGSIDVLVNNAGISHVGNLENTAEEDFDRLYQVNVKGIYNCSL 117 Query: 112 AFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNA 171 A LP M +KGG SIINM+S AS++ G+P+RFAYS +K AV +T S+A D++ +R N+ Sbjct: 118 ASLPKMKEKGG-SIINMASVASTM-GLPDRFAYSMTKGAVFSMTLSMARDYVEYNIRVNS 175 Query: 172 ICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDES 231 I PG V +P ++ + + + AA QP+GR+GKPEEIAA+A+YL SDE+ Sbjct: 176 IAPGRVHTPFVDGFLAKNYPGKEKEMFDKLAA---TQPIGRMGKPEEIAAMAVYLSSDEA 232 Query: 232 SFTTGHAHVIDGGWSN 247 SF TG + IDGG+ N Sbjct: 233 SFLTGGNYPIDGGFVN 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: 169 Number of extensions: 9 Number of successful extensions: 5 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: 251 Length adjustment: 24 Effective length of query: 223 Effective length of database: 227 Effective search space: 50621 Effective search space used: 50621 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