Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PfGW456L13_3499 Short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3499 Length = 255 Score = 154 bits (390), Expect = 1e-42 Identities = 92/246 (37%), Positives = 137/246 (55%), Gaps = 6/246 (2%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65 K V+GASRGIG A A+ A+QGA V++ S G +A+ I A GG A A+ Sbjct: 12 KIAFVSGASRGIGEAIAKLLAQQGAHVIV----SSRKLEGCQHVADAIIAAGGKATAIAC 67 Query: 66 DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICP-FHSFLDMPRELYLKTVGTNLNGAYFT 124 +++ ++ A E FG +D+LVNNA P F + LD + KTV N+ G +F Sbjct: 68 HIGEMEQISQVFAGIKEQFGRLDILVNNAATNPQFCNVLDTDLSAFQKTVDVNIRGYFFM 127 Query: 125 VQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRC 184 A + M+E G GG+II V+SI+ + G Q Y+ TKA ++++ + A +GIRC Sbjct: 128 SVEAGKLMRENG-GGSIINVASINGVSPGIFQGIYSVTKAAVINMTKVFAKECAQFGIRC 186 Query: 185 NAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGAS 244 NA+LPG T + + ++PL R+ +P ++AG +++LASD + Y TG S Sbjct: 187 NALLPGLTDTKFASALVKNEAILNTALQQIPLKRVADPSEMAGAVLYLASDASSYTTGVS 246 Query: 245 LLVDGG 250 L VDGG Sbjct: 247 LNVDGG 252 Lambda K H 0.319 0.136 0.383 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: 163 Number of extensions: 8 Number of successful extensions: 4 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: 256 Length of database: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 Effective search space: 53592 Effective search space used: 53592 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: 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