Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_019386674.1 P735_RS0103765 SDR family oxidoreductase
Query= reanno::Phaeo:GFF1301 (257 letters) >NCBI__GCF_000283015.1:WP_019386674.1 Length = 254 Score = 127 bits (318), Expect = 3e-34 Identities = 84/259 (32%), Positives = 131/259 (50%), Gaps = 14/259 (5%) Query: 1 MKRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVE-- 58 M +L+GK A+ITGA GIG A+ N+G V++ I+ Q+ A I E Sbjct: 1 MSKLNGKIAVITGATGGIGFQVAKRLGNDGFTVILNGIEDEAGAERVKQLEAEGIKAEYY 60 Query: 59 -LDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVE-VTREAYQRTFDINVSGTL 116 DVT + ++ +++ E +G +D+L+NNA E +T E Y+ +N+ T Sbjct: 61 GFDVTSEEAVTSNINKIGEKYGKIDVLVNNAGGLGGRSRFEDMTTEFYRFVMALNLDSTF 120 Query: 117 FMMQAAAQQMITQGTGGKIINMASQAG-RRGEPLVSVYCATKAAVISLTQSAGLNLISHG 175 F +AA + +G IIN S AG G P VY +KAAV ++T++ +L +G Sbjct: 121 FASRAAIP-FLKKGENASIINYTSIAGWNAGGPGAGVYGTSKAAVHAITRALAKDLAEYG 179 Query: 176 INVNAIAPGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFL 235 I VNA++PG +D + F K + A ++ GR+G ++ + FL Sbjct: 180 IRVNAVSPGTIDTD--------FHKQIKSTKPEVFASWKNNIMLGRLGQPENVASVVSFL 231 Query: 236 ASEDADYVVAQTYNVDGGQ 254 ASEDA ++ A+T V GGQ Sbjct: 232 ASEDASFITAETIQVTGGQ 250 Lambda K H 0.317 0.130 0.365 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: 144 Number of extensions: 8 Number of successful extensions: 3 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: 257 Length of database: 254 Length adjustment: 24 Effective length of query: 233 Effective length of database: 230 Effective search space: 53590 Effective search space used: 53590 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 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