GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Pseudomonas putida KT2440

Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate PP_1143 PP_1143 3-hydroxyisobutyrate dehydrogenase family protein

Query= BRENDA::Q8ZLV8
         (296 letters)



>FitnessBrowser__Putida:PP_1143
          Length = 295

 Score =  197 bits (500), Expect = 3e-55
 Identities = 109/284 (38%), Positives = 168/284 (59%), Gaps = 2/284 (0%)

Query: 5   VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64
           +GF G+G+MG PM + LL AGY L V +R+P+  A ++AAGA  AS+   +    D+++ 
Sbjct: 8   LGFAGIGLMGLPMCRRLLAAGYPLTVWNRSPDKCAALVAAGARLASSPAELCRDSDMVLL 67

Query: 65  MLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAK-GVEMLDAPVS 123
            L ++  V+EV  GE GI +G + G +LID SS+ P A+RE++  L A  G+  LDAPVS
Sbjct: 68  CLADTAVVREVVFGEQGIAQGGRSGQLLIDFSSLEPTATREMAAELAALCGMAWLDAPVS 127

Query: 124 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNI 183
           GG P A  GTL++MVGG+ A   +   +++ +   V H G +GAG VTK  NQ+IVA N 
Sbjct: 128 GGTPGAEAGTLAIMVGGEAADLQRARPVLQVLGQRVTHMGAVGAGQVTKACNQMIVACNA 187

Query: 184 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKP-GFRIDLHIKDL 242
             ++E + LA ++GV+  L+ +A+ GG A S  L   AP + +  F+P  + +   +KDL
Sbjct: 188 LVIAEVVALAEQSGVDATLIAEALAGGFADSKPLQILAPQMAESRFEPIKWHVRTLLKDL 247

Query: 243 ANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYY 286
             A+  S   G+  PL+    ++M+   + G+   D + L   Y
Sbjct: 248 DGAVKFSREQGSATPLSGLAAQLMRLHGSQGYLQKDPATLVELY 291


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: 193
Number of extensions: 8
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: 295
Length adjustment: 26
Effective length of query: 270
Effective length of database: 269
Effective search space:    72630
Effective search space used:    72630
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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