Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_084936983.1 HA51_RS22390 SDR family oxidoreductase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_002095475.1:WP_084936983.1 Length = 246 Score = 318 bits (815), Expect = 7e-92 Identities = 160/247 (64%), Positives = 197/247 (79%), Gaps = 3/247 (1%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVTDDD 67 L GK VLITAA QGIG AS FA +GA V+ +DI+ T L++L ++ + LDVTD Sbjct: 3 LHGKRVLITAAGQGIGLASARYFAEQGANVVGSDINITALQDLQNVT---PYRLDVTDRA 59 Query: 68 AIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGMLAK 127 AI+A V ++G VDVLFNCAG V +GN+L C ++ W F+ +LN AMFH I+A LPGMLA+ Sbjct: 60 AIRAAVEELGPVDVLFNCAGVVHSGNLLACTEQEWQFALDLNVSAMFHMIQAFLPGMLAQ 119 Query: 128 KAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTIESP 187 K GSI+N++S ASSVKGVANRFAY A+KAAV+GLT+SVAADF++ GIRCNAICPGT++SP Sbjct: 120 KKGSIINMSSVASSVKGVANRFAYSATKAAVIGLTRSVAADFIADGIRCNAICPGTVDSP 179 Query: 188 SLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTGSIHM 247 SL QRI+TQA+ GKSEDEV AAFVARQP+GRIG EE+A LA YLASD SN+TTG+ + Sbjct: 180 SLRQRIATQAQAEGKSEDEVYAAFVARQPIGRIGTVEEIAYLAAYLASDASNYTTGTAQV 239 Query: 248 IDGGWSN 254 IDGGWSN Sbjct: 240 IDGGWSN 246 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: 200 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: 254 Length of database: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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 24 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