Align SDR family oxidoreductase (characterized, see rationale)
to candidate PP_1951 PP_1951 Oxidoreductase, short chain dehydrogenase/reductase family
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Putida:PP_1951 Length = 275 Score = 137 bits (345), Expect = 2e-37 Identities = 97/268 (36%), Positives = 133/268 (49%), Gaps = 33/268 (12%) Query: 10 GKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLE----ELASIA-GVETHLLDVT 64 G V++T AA G+G A TE A GA+V D+++ L+ L S+ V +H+LDVT Sbjct: 11 GARVIVTGAASGLGLAFTEAMAESGAQVAMLDLNREALDAQFRRLRSLGYSVRSHVLDVT 70 Query: 65 D----DDAIKALVAKVGTVDVLF--------------NCAGYVAAGNILE-CDDKAWDFS 105 D DD A+ A G +D++F N AG N+LE D W Sbjct: 71 DRDAVDDTFNAVAAGFGGLDIVFANAGIDPGPGFAALNAAGEREPANMLEEYSDHRWRKV 130 Query: 106 FNLNAKAMFHTIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSV 165 +++ A+F++IRA M A ++GSI+ S ++ V AY A+KA L ++ Sbjct: 131 ISVSLDAVFYSIRAAARHMRANRSGSIIVTTSVSALRPAVTLGAAYAAAKAGAAQLVRAT 190 Query: 166 AADFVSQGIRCNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEE 225 A + S G+R NAI PG E T EVRA A PMGRI + EE Sbjct: 191 ALELASDGVRVNAIAPGPFE---------TDIGGGFMHNSEVRAKMAAGVPMGRIAEVEE 241 Query: 226 VAALALYLASDESNFTTGSIHMIDGGWS 253 + LALYLAS S+F TG +IDGG S Sbjct: 242 IKPLALYLASKASSFVTGQQFVIDGGLS 269 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: 142 Number of extensions: 6 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: 275 Length adjustment: 25 Effective length of query: 229 Effective length of database: 250 Effective search space: 57250 Effective search space used: 57250 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: 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