Align SDR family oxidoreductase (characterized, see rationale)
to candidate RR42_RS34980 RR42_RS34980 oxidoreductase
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS34980 Length = 251 Score = 315 bits (808), Expect = 4e-91 Identities = 159/250 (63%), Positives = 192/250 (76%) Query: 5 TGRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVT 64 T RLAGK L+TAA QGIGRA+ E + REGARVIA DI LE LA G T LDVT Sbjct: 2 TQRLAGKLALVTAAGQGIGRATAEAYLREGARVIAADIDARLLEALAGQPGCTTLRLDVT 61 Query: 65 DDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGM 124 D A++A + G +D+LFN AG+V G ILECD+ A+DFS NLN +AM+ +RA LP M Sbjct: 62 DGAAVQAAAKQAGALDILFNGAGFVHHGTILECDEAAFDFSMNLNVRAMYSMMRAFLPAM 121 Query: 125 LAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTI 184 +A++ GSIVN+AS A S+KG NRF YGA+KAAV+G+TKSVAAD++ GIRCNAICPGT+ Sbjct: 122 VARRRGSIVNMASVAGSIKGAPNRFVYGATKAAVIGMTKSVAADYIGHGIRCNAICPGTV 181 Query: 185 ESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTGS 244 ESPSL QRI+ QA++ G+S EV AAFVARQPMGRIG A E+AALA+YL SDES FTTG+ Sbjct: 182 ESPSLRQRIADQARDGGRSLAEVEAAFVARQPMGRIGSAAEIAALAVYLGSDESAFTTGT 241 Query: 245 IHMIDGGWSN 254 +IDGGWSN Sbjct: 242 AQVIDGGWSN 251 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: 205 Number of extensions: 4 Number of successful extensions: 1 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: 251 Length adjustment: 24 Effective length of query: 230 Effective length of database: 227 Effective search space: 52210 Effective search space used: 52210 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