Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_057509319.1 ABB28_RS14605 6-phosphogluconate dehydrogenase (decarboxylating)
Query= reanno::pseudo3_N2E3:AO353_05985 (294 letters) >NCBI__GCF_001431535.1:WP_057509319.1 Length = 301 Score = 55.8 bits (133), Expect = 1e-12 Identities = 56/197 (28%), Positives = 81/197 (41%), Gaps = 11/197 (5%) Query: 1 MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQG---A 57 M IA IGLG MGA MA+ L + GH + D +A A A+ G + AT EA Sbjct: 1 MDIAMIGLGRMGANMAQRLQRGGHRVVGHDPMEAARARAAESGLEVFATLAEAVAALPVP 60 Query: 58 ELVITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMAD 117 +V M+PA V ++ +A+G +D + Q + A + A + D Sbjct: 61 RVVWLMVPAGDTVDQTLA---QLVPHLAEGDVVIDGGNSNYQDSVRRARSLADDDIFYLD 117 Query: 118 APVSGGTGGAAAGTLTFMVG----ATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICN 173 SGG G G + M+G A +L Q + R G G G K+ + Sbjct: 118 CGTSGGVWGLQEG-YSLMIGGDAAAVEQLATVFQALAPAADRGWARVGPSGAGHYTKMIH 176 Query: 174 NLLLAISMVGVSEAMAL 190 N + M +E AL Sbjct: 177 NGIEYGMMQAYAEGFAL 193 Lambda K H 0.317 0.132 0.382 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: 191 Number of extensions: 3 Number of successful extensions: 1 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: 294 Length of database: 301 Length adjustment: 26 Effective length of query: 268 Effective length of database: 275 Effective search space: 73700 Effective search space used: 73700 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: 48 (23.1 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