Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate AZOBR_RS07955 AZOBR_RS07955 tartronate semialdehyde reductase
Query= reanno::psRCH2:GFF2390 (296 letters) >FitnessBrowser__azobra:AZOBR_RS07955 Length = 302 Score = 164 bits (415), Expect = 2e-45 Identities = 108/289 (37%), Positives = 151/289 (52%), Gaps = 9/289 (3%) Query: 1 MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60 M++GFIGLG MG PMA +L AGH L V+D+N A E+L+ GA S +AQ A++ Sbjct: 1 MNVGFIGLGIMGRPMAGHLADAGHTLFVYDINPAP-EDLLAKGATACGSSREVAQ-KADI 58 Query: 61 IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120 + TM+P HV+ G NG+ AG +++D S+I P + A+ E G LDAP Sbjct: 59 VFTMVPDTPHVQAALFGPNGVAEGLSAGKIVVDMSSISPIETKAFAQRINELGCDYLDAP 118 Query: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGI 180 VSGG GA A +LT MVGG D F+ +P+ MGKNI G G+GQ KVAN +++ + Sbjct: 119 VSGGEVGAKAASLTIMVGGPDKAFETVKPLFEKMGKNITLVGGNGDGQTTKVANQIVVAL 178 Query: 181 SMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFG 240 ++ V EA+ G D A V G SS V R + GF Sbjct: 179 TIEAVGEALLFASKAGADP---AKVRQALMGGFASSRILE----VHGERMVKRTFDPGFR 231 Query: 241 SDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAII 289 +L KDL LA A+ + + A Q+L+ + +AQG D S ++ Sbjct: 232 IELHQKDLNLALSGARALGVSLPNTATCQELFNACAAQGGKAWDHSGMV 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: 249 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: 302 Length adjustment: 27 Effective length of query: 269 Effective length of database: 275 Effective search space: 73975 Effective search space used: 73975 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