Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate WP_012674847.1 SULAZ_RS01425 KR domain-containing protein
Query= SwissProt::Q9HK58 (254 letters) >NCBI__GCF_000021545.1:WP_012674847.1 Length = 239 Score = 117 bits (293), Expect = 2e-31 Identities = 81/253 (32%), Positives = 141/253 (55%), Gaps = 18/253 (7%) Query: 2 LDFKGKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHKV 61 ++ KGK A+ITGGS+ IGRAI +GLAK+G N++I Y S + EA E+ +GV+++ + Sbjct: 1 MEIKGKTALITGGSKRIGRAITIGLAKEGCNVIIHYHSSEREAQELKTLVESFGVRSYLL 60 Query: 62 KVDQSDPYESIRFAEKAIETFGKVHILVDNAGI---CPFEDFFRISVDLFEKVWKVNVES 118 K D + + +R AE+++ V IL++NA + P + +++F + ++V++ Sbjct: 61 KADLTKEEDIVRIAEESVNI--GVDILINNASLYYKTPLDTATFKDLNIF---YSIHVKA 115 Query: 119 HYFITQRIAKNMIENKINGRILLISSISAHVGGEFQTHYTTTKSALNGFMHSIAIVLGKY 178 +++++ I K M E K GRI+ I SA + T YT +K AL + A Y Sbjct: 116 PFYLSKVIGKKMYEKK-EGRIVNIVDYSAILPYPDYTPYTVSKGALLTMTKAFAKEFAPY 174 Query: 179 GILVNSLEPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDDNTYV 238 +LVN + PG I ++ EDL ++E ++T++ R G +++ +L+ D + Sbjct: 175 -VLVNGILPGPI---VSPEDLQDKE---IPLKKTLLKRWGGEQEVFKAVKYLIETD--FT 225 Query: 239 TGTELLADGGMLI 251 TG + +GG LI Sbjct: 226 TGALIPVEGGRLI 238 Lambda K H 0.318 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: 167 Number of extensions: 13 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: 254 Length of database: 239 Length adjustment: 24 Effective length of query: 230 Effective length of database: 215 Effective search space: 49450 Effective search space used: 49450 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 (21.7 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