Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_009122055.1 BUB52_RS10260 gluconate 5-dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >NCBI__GCF_900129655.1:WP_009122055.1 Length = 267 Score = 103 bits (256), Expect = 5e-27 Identities = 76/252 (30%), Positives = 119/252 (47%), Gaps = 8/252 (3%) Query: 33 SLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPWWRV 92 SL+G+ VTG GIG AI +AFAEQGA++ F D+ +E + A+ G+ + V Sbjct: 8 SLEGKVALVTGASYGIGFAIASAFAEQGAKICFNDINQELVDKGIAAYAEKGIQAHGY-V 66 Query: 93 CDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINERPAFF 152 CDV D A+QA +A E+GS +LVNN R + + + + + I+ F Sbjct: 67 CDVTDEPAVQAMVATIEKEVGS-VDILVNNAGIIRRIPMHEMEAADFRKVIDIDLNAPFI 125 Query: 153 AIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQDRIRI 212 +AV+P M + G G +IN+ S + YA AK + LTR + G+ I+ Sbjct: 126 VSKAVLPAMMKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEYGEYNIQC 185 Query: 213 NTVSPGWVMTERQIKL-WLDAEGEKE-----LARNQCLPDKLRPHDIARMVLFLASDDAA 266 N + PG++ T + L A+G + + L P ++ +FLAS+ + Sbjct: 186 NGIGPGYIATPQTAPLREKQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVFLASEASN 245 Query: 267 MCTAQEFKVDAG 278 VD G Sbjct: 246 AVNGHILYVDGG 257 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: 150 Number of extensions: 10 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: 280 Length of database: 267 Length adjustment: 25 Effective length of query: 255 Effective length of database: 242 Effective search space: 61710 Effective search space used: 61710 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