Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate AZOBR_RS22360 AZOBR_RS22360 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__azobra:AZOBR_RS22360 Length = 296 Score = 170 bits (431), Expect = 3e-47 Identities = 100/285 (35%), Positives = 152/285 (53%), Gaps = 7/285 (2%) Query: 5 VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64 + FIGLG MG PM +NLLKAG++++ D + A AGA A+ A A + +V++T Sbjct: 4 IAFIGLGNMGAPMMRNLLKAGHTVLAFDLSEAACTAARDAGATIATGPGAAAGEAEVVVT 63 Query: 65 MLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVSG 124 MLP HV+EV +GII AKPG++ ID S++ ++R ++ A +A G M+DAPVSG Sbjct: 64 MLPAGKHVREVYTAPDGIIAKAKPGSLFIDSSTVDVDSARFVAAAAEAAGHAMVDAPVSG 123 Query: 125 GEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNIA 184 G A TL+ MVGG F + ++ AM ++VHTG G G K+ N +I+ +++ Sbjct: 124 GVGGAEAATLTFMVGGSDTAFRRAEPILSAMGKAIVHTGGPGNGQAAKICNNMILGISML 183 Query: 185 AMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPM-------VMDRNFKPGFRIDL 237 +SEA LA K G+ ++ L + P+ +R+++PGF L Sbjct: 184 GVSEAFALAEKLGLGSQKLFDVASKSSGQCWSLTSYCPVPGPVPTSPANRDYQPGFAAAL 243 Query: 238 HIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282 +KDL A++ G+ LPL +M G G D S + Sbjct: 244 MLKDLKLAVEAGQSTGSPLPLGGEAAQMYALFCNAGFGGKDFSGI 288 Lambda K H 0.316 0.132 0.367 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: 234 Number of extensions: 8 Number of successful extensions: 2 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: 296 Length adjustment: 26 Effective length of query: 270 Effective length of database: 270 Effective search space: 72900 Effective search space used: 72900 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 (21.6 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