Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate RR42_RS21790 RR42_RS21790 short-chain dehydrogenase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Cup4G11:RR42_RS21790 Length = 252 Score = 151 bits (382), Expect = 1e-41 Identities = 97/260 (37%), Positives = 142/260 (54%), Gaps = 30/260 (11%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKP-----------VEARK 53 +AGK L T GIG A A FAR GAR++ D+ GLA VE K Sbjct: 1 MAGKVVLNTGGASGIGRAMAHGFARHGARLMLLDLDAQGLASAKAELEAAYPEVQVEIVK 60 Query: 54 LDVRDDAAIK----ALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRM 109 + D A++ A A G +D+L N AG LE + +DW A D+++ ++ Sbjct: 61 ASITDPDAVEQACAATEARFGRIDILLNNAGISMNKPSLELTPDDWRRAIDIDLSGVFFC 120 Query: 110 IRAFLPAMLDKGGGSIINMSSA---ASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRG 166 +A M+ +GGGSI++ +S ASS + R AY A+KA V+ LTKS+AA++ Sbjct: 121 TQAAARRMVRQGGGSILSTASMWGLASSAR----RLAYCAAKAGVVSLTKSLAAEWAEYN 176 Query: 167 VRCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYL 226 +R NA+CPG ++ +E + ++A +D A +AR P+ R G PEE+A +AL+L Sbjct: 177 IRVNAVCPGYTSTALMETLLASKA------IDG--EALLARTPLRRFGAPEEMAEVALFL 228 Query: 227 GSDESSFTTGHAHVIDGGWS 246 SD ++F TGHA V DGGW+ Sbjct: 229 ASDSAAFITGHALVSDGGWT 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: 148 Number of extensions: 11 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: 252 Length adjustment: 24 Effective length of query: 223 Effective length of database: 228 Effective search space: 50844 Effective search space used: 50844 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