Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PP_2723 PP_2723 Uncharacterized oxidoreductase YhdF
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Putida:PP_2723 Length = 285 Score = 146 bits (368), Expect = 5e-40 Identities = 91/246 (36%), Positives = 131/246 (53%), Gaps = 5/246 (2%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L GK L+TGA +GIGRA AI A+ GADVAI Y + AQ ++A G++ + + G Sbjct: 40 LAGKIALITGADSGIGRAVAIAYAREGADVAIAYLNEHDDAQETARWVKAAGRQCLLLPG 99 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFL-DMPVDVVERTFKVNLHGAYFM 122 D+A Q D V K V FG++D++V+NA H L D+ D +TF N+ + + Sbjct: 100 DLAQKQHCHDIVDKTVAQFGRIDILVNNAAFQMAHESLDDIDDDEWVKTFDTNITAIFRI 159 Query: 123 VQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRC 182 Q A M + GGSI+ SS+++ Y TK + + A LGK GIR Sbjct: 160 CQRALPSMPK---GGSIINTSSVNSDDPSPSLLAYAATKGAIANFTAGLAQLLGKQGIRV 216 Query: 183 NSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242 NSV PG I T + + D+ R + + P+GR G P ++A V L SD A+Y++G+ Sbjct: 217 NSVAPGPIWTPLIPATMPDEAVRNF-GSGYPMGRPGQPVEVAPIYVLLGSDEASYISGSR 275 Query: 243 LLVDGG 248 V GG Sbjct: 276 YAVTGG 281 Lambda K H 0.318 0.133 0.379 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: 160 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: 254 Length of database: 285 Length adjustment: 25 Effective length of query: 229 Effective length of database: 260 Effective search space: 59540 Effective search space used: 59540 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