Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Phaeo:GFF1301 Length = 257 Score = 138 bits (347), Expect = 1e-37 Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 12/253 (4%) Query: 3 QRLAGKTALITAAGQGIGLATAELFAREGARVIATDI---RIDGLA---GKPVEARKLDV 56 +RL+GK ALIT A +GIG A AE +A EGARV+ DI R + A G A +LDV Sbjct: 2 KRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVELDV 61 Query: 57 RDDAAI-KALAAEI---GAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRA 112 D A+I +AL+ + G +D+L N A A ++E + E + FD+NV M++A Sbjct: 62 TDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQA 121 Query: 113 FLPAMLDKG-GGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNA 171 M+ +G GG IINM+S A +G P Y A+KAAVI LT+S + I+ G+ NA Sbjct: 122 AAQQMITQGTGGKIINMASQAGR-RGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNA 180 Query: 172 ICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDES 231 I PG V + A+ +G +A P GR+G ++ +A++L S+++ Sbjct: 181 IAPGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASEDA 240 Query: 232 SFTTGHAHVIDGG 244 + + +DGG Sbjct: 241 DYVVAQTYNVDGG 253 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: 136 Number of extensions: 12 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: 247 Length of database: 257 Length adjustment: 24 Effective length of query: 223 Effective length of database: 233 Effective search space: 51959 Effective search space used: 51959 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