Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate PfGW456L13_3458 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= reanno::Phaeo:GFF1301 (257 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3458 Length = 251 Score = 140 bits (353), Expect = 3e-38 Identities = 94/257 (36%), Positives = 141/257 (54%), Gaps = 12/257 (4%) Query: 3 RLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVELDVT 62 +L+GKR ++TG ARGIGAA +A+ EGA VV +D A + G A + D+ Sbjct: 2 QLAGKRIIVTGGARGIGAAVVKAFVEEGAHVV--SLDLGEAASITGDGGGWAHSRVCDIA 59 Query: 63 DQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQAA 122 D S+D A + E GLD+L++ A + A +T + +++ F +N GT F+ A Sbjct: 60 DSQSVDAAFAWASEQLNGLDVLVHAAGIAPNASADSITLDEWEKVFAVNTRGT-FLTNRA 118 Query: 123 AQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAIA 182 A +++ +G+GG+IIN AS AG G+P + Y A+K AV++ T++ GI VNAIA Sbjct: 119 AYELL-KGSGGRIINFASAAGVLGQPGKAHYAASKGAVLAWTRTVAREWGPLGITVNAIA 177 Query: 183 PGVVDGEHWDGV-DAFFAKYEGKAPGQKKAEVAQSVPY-GRMG-TAADLTGMAVFLASED 239 P + W + DA A + Q A +A VP G++G A DL + VFLA + Sbjct: 178 PAM-----WTPMYDATRASMSAEQLQQHDAYMAGQVPIGGKLGEPARDLAPVLVFLAGDG 232 Query: 240 ADYVVAQTYNVDGGQWM 256 + +V QT +DGG M Sbjct: 233 SRFVTGQTLVIDGGMMM 249 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: 139 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: 251 Length adjustment: 24 Effective length of query: 233 Effective length of database: 227 Effective search space: 52891 Effective search space used: 52891 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 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