GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Cupriavidus basilensis 4G11

Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate RR42_RS28555 RR42_RS28555 3-hydroxyisobutyrate dehydrogenase

Query= BRENDA::Q8ZLV8
         (296 letters)



>FitnessBrowser__Cup4G11:RR42_RS28555
          Length = 299

 Score =  189 bits (479), Expect = 9e-53
 Identities = 105/292 (35%), Positives = 159/292 (54%), Gaps = 7/292 (2%)

Query: 3   MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVI 62
           M + FIGLG MG PM++NLLKAG++L V D NP A++ + A GA  A +A+  A + D +
Sbjct: 1   MHIAFIGLGNMGAPMARNLLKAGHALTVFDLNPTALSALQADGAAVAPSARKAAAEADFV 60

Query: 63  ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPV 122
           ITMLP + HV+   LG  G++ G +PG  L+D S+I P   R ++   K +G  + DAPV
Sbjct: 61  ITMLPAATHVRATYLGPEGVLAGVRPGVPLVDSSTIDPATIRALAAEAKRQGNPIADAPV 120

Query: 123 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALN 182
           SGG   A  GTL+ MVG +  +F++   ++  M  ++VH GD G G V K+ N +I+ ++
Sbjct: 121 SGGTGGAQAGTLTFMVGAEPTLFEQLKPVLSCMGRNIVHCGDTGTGQVAKICNNLILGIS 180

Query: 183 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAP-------MVMDRNFKPGFRI 235
           +  +SEA+ L  K G++  ++   +          D   P           R +  GF  
Sbjct: 181 MIGVSEAMALGVKLGIDAGVLAGIVNTSTGRCWAADTCNPYPGVIETAPASRGYSGGFGA 240

Query: 236 DLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYE 287
           DL +KDL  A D +  V   L L A   ++ QA+   G G+ D S +   Y+
Sbjct: 241 DLMLKDLGLATDAARSVRQPLFLGALAQQIYQAVSQAGDGHLDFSGVIRQYQ 292


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: 251
Number of extensions: 6
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: 299
Length adjustment: 26
Effective length of query: 270
Effective length of database: 273
Effective search space:    73710
Effective search space used:    73710
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.

Links

Downloads

Related tools

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