Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_008538445.1 HMPREF9454_RS05535 SDR family oxidoreductase
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >NCBI__GCF_000245775.1:WP_008538445.1 Length = 271 Score = 84.3 bits (207), Expect = 3e-21 Identities = 77/278 (27%), Positives = 118/278 (42%), Gaps = 47/278 (16%) Query: 33 SLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPWWRV 92 +L+G+ VTGG SGIG A+V AF + GA V D+ + E + L P Sbjct: 5 ALEGKTAVVTGGASGIGKAVVQAFLDNGANVVVCDMNPQTPEYDLHEGSGEFLYVP---- 60 Query: 93 CDVRDVQALQACMADAAAELGSDFAVLVNN---------VASDDRHTLESVTPEYYDERM 143 DV +++A + A+ G +LVNN V DD + + +D+ Sbjct: 61 TDVTKADSVKAMVEAGKAKFGK-LDILVNNAGINIPRLLVDKDDPYGKYELDENVFDKVS 119 Query: 144 AINERPAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAK 203 A+N + + QA+ + G G +IN+ S G YA K++VN TR AK Sbjct: 120 AVNIKGVYLCAQALGHEFVKNGEGVIINMSSESGLEGSEGQSIYAATKNAVNSFTRSWAK 179 Query: 204 TLGQDRIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLP-------DKLRP------ 250 LG+ +R+ V+PG L+A G + LA + L ++LR Sbjct: 180 ELGKHHVRVVGVAPG----------ILEATGLRTLAYEESLAYTRGITVEQLRAGYTNTK 229 Query: 251 ----------HDIARMVLFLASDDAAMCTAQEFKVDAG 278 ++A MV+FL+S A+ F V G Sbjct: 230 TTPLGRDGKLTEVADMVMFLSSHRASYVHGVTFNVAGG 267 Lambda K H 0.320 0.133 0.405 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: 144 Number of extensions: 6 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: 280 Length of database: 271 Length adjustment: 25 Effective length of query: 255 Effective length of database: 246 Effective search space: 62730 Effective search space used: 62730 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 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