Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate RR42_RS34980 RR42_RS34980 oxidoreductase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Cup4G11:RR42_RS34980 Length = 251 Score = 324 bits (830), Expect = 1e-93 Identities = 169/251 (67%), Positives = 199/251 (79%), Gaps = 4/251 (1%) Query: 1 MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIR---IDGLAGKP-VEARKLDV 56 MTQRLAGK AL+TAAGQGIG ATAE + REGARVIA DI ++ LAG+P +LDV Sbjct: 1 MTQRLAGKLALVTAAGQGIGRATAEAYLREGARVIAADIDARLLEALAGQPGCTTLRLDV 60 Query: 57 RDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLPA 116 D AA++A A + GA+D+LFN AGFVH G ILEC E +DF+ +LNV+AMY M+RAFLPA Sbjct: 61 TDGAAVQAAAKQAGALDILFNGAGFVHHGTILECDEAAFDFSMNLNVRAMYSMMRAFLPA 120 Query: 117 MLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPGT 176 M+ + GSI+NM+S A S+KG PNRF Y A+KAAVIG+TKSVAAD+I G+RCNAICPGT Sbjct: 121 MVARRRGSIVNMASVAGSIKGAPNRFVYGATKAAVIGMTKSVAADYIGHGIRCNAICPGT 180 Query: 177 VASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFTTG 236 V SPSL QRI QA+ G +L V+AAFVARQPMGRIG EIAALA+YLGSDES+FTTG Sbjct: 181 VESPSLRQRIADQARDGGRSLAEVEAAFVARQPMGRIGSAAEIAALAVYLGSDESAFTTG 240 Query: 237 HAHVIDGGWSN 247 A VIDGGWSN Sbjct: 241 TAQVIDGGWSN 251 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: 236 Number of extensions: 6 Number of successful extensions: 2 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