Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate GFF2316 PGA1_c23480 putative D-beta-hydroxybutyrate dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >FitnessBrowser__Phaeo:GFF2316 Length = 257 Score = 100 bits (250), Expect = 2e-26 Identities = 82/258 (31%), Positives = 123/258 (47%), Gaps = 24/258 (9%) Query: 34 LQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAG-LPRPWWRV 92 L GR V VTGGGSG+GAA+ +FA GAR+ + E L + A+ G LP Sbjct: 9 LAGRHVVVTGGGSGVGAALARSFAGGGARLTLLG---RRIEPLQEVAAETGALPL----A 61 Query: 93 CDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINERPAFF 152 CDV + +A++A + D A + +V + N + + ++ +A+N F Sbjct: 62 CDVTEAEAVRAAL-DTARQQHGPVSVAIANAGAAPSKPFAKMDLADFEAALAVNLSGVFN 120 Query: 153 AIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPC---YAIAKSSVNGLTRGLAKTLGQDR 209 QA +P M+ G G +I + ST GYP Y AK V GLTR LA+ L + Sbjct: 121 LWQAALPDMKSAGWGRMIAVASTAGL---KGYPYVSGYCAAKHGVVGLTRSLAQELARSG 177 Query: 210 IRINTVSPGWVMT---ERQIKLWLDAEG--EKELARNQCLPDK----LRPHDIARMVLFL 260 I +N + PG++ T ER I + G E+E A++ + ++P ++A LFL Sbjct: 178 ITVNAICPGFIETPLLERSIATIVSTTGMSEEEAAKSLRAGNPQGRFIQPEEVADAALFL 237 Query: 261 ASDDAAMCTAQEFKVDAG 278 AS AA + G Sbjct: 238 ASSSAASINGSALPITGG 255 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: 139 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: 257 Length adjustment: 25 Effective length of query: 255 Effective length of database: 232 Effective search space: 59160 Effective search space used: 59160 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