Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate WP_012412770.1 NPUN_RS33465 3-oxoacyl-ACP reductase
Query= SwissProt::Q9HK58 (254 letters) >NCBI__GCF_000020025.1:WP_012412770.1 Length = 246 Score = 140 bits (354), Expect = 2e-38 Identities = 87/249 (34%), Positives = 141/249 (56%), Gaps = 4/249 (1%) Query: 1 MLDFKGKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHK 60 M GK A+ITG SRGIGRAIAL LA GA+I+++YA + +A+EV+ K GV+A Sbjct: 1 MSSLSGKVAIITGASRGIGRAIALKLAGNGASIVVNYAGNAVKAEEVVAEIEKLGVEAIA 60 Query: 61 VKVDQSDPYESIRFAEKAIETFGKVHILVDNAGICPFEDFFRISVDLFEKVWKVNVESHY 120 ++ D S + R E+ +E FGKV ILV+NAGI ++ ++S + F+ ++ +NV+ + Sbjct: 61 IQADISKVPDIQRLFEQTLEHFGKVDILVNNAGIAFYKPITQVSEEDFDAIFAINVKGTF 120 Query: 121 FITQRIAKNMIENKINGRILLISSISAHVGGEFQTHYTTTKSALNGFMHSIAIVLGKYGI 180 F Q+ A+++ E GRI+ SS + + + Y TK A+ +A LG I Sbjct: 121 FACQQAAQHLSE---GGRIINFSSSTTVMMLPTYSAYVGTKGAVEQITRVLAKELGAKAI 177 Query: 181 LVNSLEPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDDNTYVTG 240 VN + PG T++ +E QE+ + + G+LG +++ FL SD+ ++TG Sbjct: 178 AVNVISPGPTDTELFREG-KTQEQIDRLAQMAAFGKLGDVQEIADVVAFLASDEARWITG 236 Query: 241 TELLADGGM 249 + +GG+ Sbjct: 237 QNIRVNGGI 245 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: 157 Number of extensions: 8 Number of successful extensions: 2 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: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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