Align SDR family oxidoreductase (characterized, see rationale)
to candidate Ga0059261_2637 Ga0059261_2637 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Korea:Ga0059261_2637 Length = 247 Score = 128 bits (321), Expect = 1e-34 Identities = 90/253 (35%), Positives = 129/253 (50%), Gaps = 21/253 (8%) Query: 5 TGRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASI-AGVETHLLDV 63 +GR AG+ ++T A GIGRA+ E A EGA+V DIS E LA T +D Sbjct: 6 SGRFAGRVAVVTGGAAGIGRAAAERMAAEGAQVSVWDISD---EALAGCDFAAHTAKVDQ 62 Query: 64 TDDDAIKA----LVAKVGTVDVLFNCAGYVAAGNILEC-DDKAWDFSFNLNAKAMFHTIR 118 +D+ + A + A++G +D+L AG LE AW +N F + Sbjct: 63 SDEAQVIAAAADVAARLGRLDILVVSAGITGPNTTLETYPSDAWQQVMAINLNGTFFCDK 122 Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNA 178 AV+P M A G IVNIAS A +G N AY SKA V+GLTKS+ + I NA Sbjct: 123 AVIPHMKANGYGRIVNIASVAGK-EGNPNASAYSTSKAGVIGLTKSLGKELAKDNITVNA 181 Query: 179 ICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDES 238 + P +++ +Q TQA +++ PMGR G +E AA+ +LAS+E+ Sbjct: 182 VTPAAVKTAIFDQ--MTQAHID---------FMLSKIPMGRFGTVDENAAMICFLASEEA 230 Query: 239 NFTTGSIHMIDGG 251 +F+TG++ GG Sbjct: 231 SFSTGAVFDTSGG 243 Lambda K H 0.316 0.129 0.359 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: 174 Number of extensions: 7 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: 254 Length of database: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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