Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate PP_4299 PP_4299 tartronate semialdehyde reductase
Query= reanno::psRCH2:GFF2390 (296 letters) >FitnessBrowser__Putida:PP_4299 Length = 297 Score = 166 bits (419), Expect = 8e-46 Identities = 108/289 (37%), Positives = 150/289 (51%), Gaps = 12/289 (4%) Query: 3 IGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAELII 62 IGFIG G MG PMA NL KAGH L + + AA +L+ AGA+ + +P +AQ AE II Sbjct: 4 IGFIGTGIMGKPMAQNLQKAGHSLFISTHHDAAPADLIAAGAVALANPKEVAQ-EAEFII 62 Query: 63 TMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAPVS 122 M+P V+ V G NG+ ++ID S+I P + + A+ G LDAPVS Sbjct: 63 VMVPDTPQVESVLFGENGVAEGVGPNKVVIDMSSISPTATKAFAEKIKATGAAYLDAPVS 122 Query: 123 GGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGISM 182 GG GA A TL+ MVGG F+ P+ AMGKNI G G+GQ AKVAN +++ +++ Sbjct: 123 GGEVGAKAATLSIMVGGCPNAFERTLPLFEAMGKNITRVGGNGDGQTAKVANQIIVALNI 182 Query: 183 IGVAEAMALGVALGMDAKTLAGVI--NTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFG 240 VAEA+ G D + + +S + G D GF Sbjct: 183 QAVAEALLFAAKNGADPAKVREALMGGFASSKILEVHAERMIKGTFD---------PGFR 233 Query: 241 SDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAII 289 +L KDL LA + AK++ + + AQQ++ + A G G D SA+I Sbjct: 234 INLHQKDLNLALQGAKELGINLPNTSNAQQVFNTCQALGGGNWDHSALI 282 Lambda K H 0.318 0.134 0.392 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: 240 Number of extensions: 12 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: 296 Length of database: 297 Length adjustment: 26 Effective length of query: 270 Effective length of database: 271 Effective search space: 73170 Effective search space used: 73170 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