Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate Pf1N1B4_1220 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= reanno::psRCH2:GFF2390 (296 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1220 Length = 291 Score = 124 bits (312), Expect = 2e-33 Identities = 94/299 (31%), Positives = 145/299 (48%), Gaps = 30/299 (10%) Query: 1 MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60 M +GFIGLG MG PM NLLKAGH++ V++ ++A ++ L AGA PVDSP AQ AE+ Sbjct: 1 MELGFIGLGTMGVPMVLNLLKAGHRVKVWNRSSAPLDELARAGAQPVDSPALAAQ--AEV 58 Query: 61 IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120 +I+ML ++ V++ GL + AG + ++ ST+ A+E A E + AP Sbjct: 59 LISMLGDDVAIRSVFIDGKGLDGLA-AGSVHVNMSTVSVALAKEFAALHTERDVAYVSAP 117 Query: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCG-AAGNGQVAKVANNMLLG 179 V G AAAG L + G QP+ +G+ G A VAK++ N+++ Sbjct: 118 VLGRVDVAAAGNLNILASGPAQALARVQPLFDVLGRKTWPFGECAELACVAKLSANLMIA 177 Query: 180 ISMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYS--- 236 ++ +A+A L + G+ T +I T FP VP +GY Sbjct: 178 SAIESMAQASTLASSYGISRATFIEMI-----------TSTLFP-----VPVYQGYGQLM 221 Query: 237 -------GGFGSDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAI 288 GF L LKD+ LA EA + + P+ ++ + A G G D++++ Sbjct: 222 IDKHFEPAGFKLSLGLKDIRLALEAGEAAQVPLPFASVLKDNLLDGMAHGQGDQDWASL 280 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: 239 Number of extensions: 11 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: 291 Length adjustment: 26 Effective length of query: 270 Effective length of database: 265 Effective search space: 71550 Effective search space used: 71550 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