Align 3-hydroxyisobutyrate dehydrogenase, mitochondrial; HIBADH; EC 1.1.1.31 (characterized)
to candidate CA265_RS01080 CA265_RS01080 6-phosphogluconate dehydrogenase
Query= SwissProt::P31937 (336 letters) >FitnessBrowser__Pedo557:CA265_RS01080 Length = 285 Score = 141 bits (356), Expect = 2e-38 Identities = 91/291 (31%), Positives = 150/291 (51%), Gaps = 12/291 (4%) Query: 40 TPVGFIGLGNMGNPMAKNLMKHGYPLIIYDVFPDACKEFQDAGEQVVSSPADVAEKADRI 99 T +G+IGLGNMG PMA+ L+ GY +++Y+ D ++ G + +P D+ D + Sbjct: 4 TKIGWIGLGNMGIPMAEQLINAGYAVMVYNRSKDKEASLKEMGASIAQTPQDLITTTDVV 63 Query: 100 ITMLPTSINAIEAYSGANGILKKVKKGSLLIDSSTIDPAVSKELAKEVEKMGAVFMDAPV 159 I M+ + ++G G+L+ G ++I+ ST+ P++SKE+A + G ++DAPV Sbjct: 64 IVMVSDDAAIAQIFNGEGGLLRVETSGKIIINMSTVSPSISKEMAALCKANGNFYLDAPV 123 Query: 160 SGGVGAARSGNLTFMVGGVEDEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNMLLAIS 219 SG V A +G L MVGG ED F + +L MG G G G +AK+ N LLA+ Sbjct: 124 SGSVKQAETGQLVIMVGGEEDVFNQVKPILEKMGKLAKLVGENGAGNSAKLAINSLLALY 183 Query: 220 MIGTAEAMNLGIRLGLDPKLLAKILNMSSGRCWSSDTYNPVPGVMDGVPSANNYQGGFGT 279 G AE + + G+ L +++N ++ + + + G D + A++Y+ F Sbjct: 184 AQGLAETVLFANKQGIKTSDLLELINNAA----IGNIFTKIKG--DAI-IADHYKAAFAL 236 Query: 280 TLMAKDLGLAQDSATSTKSPILLGSLAHQIYRMMCAKGYSKKDFSSVFQFL 330 + KDL LA+ A SP L A + AK Y ++D ++ + L Sbjct: 237 KHIVKDLNLAK--AEGISSP--LAKTALNTFGDAAAK-YGEEDIIAIIKQL 282 Lambda K H 0.318 0.133 0.384 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: 230 Number of extensions: 5 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: 336 Length of database: 285 Length adjustment: 27 Effective length of query: 309 Effective length of database: 258 Effective search space: 79722 Effective search space used: 79722 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 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