GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Ochrobactrum rhizosphaerae PR17

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_094578795.1 CEV32_RS19735 alcohol dehydrogenase AdhP

Query= BRENDA::P07913
         (341 letters)



>NCBI__GCF_002252475.1:WP_094578795.1
          Length = 344

 Score =  137 bits (345), Expect = 4e-37
 Identities = 106/343 (30%), Positives = 161/343 (46%), Gaps = 12/343 (3%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKA    +  + + + +VP+P+ G   + + I+ + +C TD+H    D W  K  P P +
Sbjct: 5   MKAAVVREFGKPLTIDEVPIPQPGDGQIQVAIQASGVCHTDLHAAEGD-WPVKPNP-PFI 62

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHIT-CGHCRNCRGGRTHLCRNTIGVGVNRPG 119
            GHE VG V  +G+ VK  K GDRV      T CGHC +C GG   LC   +  G +  G
Sbjct: 63  PGHEGVGFVSAVGKGVKHVKEGDRVGIPWLYTACGHCVHCLGGWETLCEEQLNTGYSVNG 122

Query: 120 CFAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSF--DLVGEDVLVSGAGPIGI 177
            FA+Y+V        +P NI  +  A     G  V+  L       G+ V++SG G +G 
Sbjct: 123 GFADYVVADPNFVGHLPKNIEFNEIAPILCAGVTVYKGLKVTDTKPGDWVVISGIGGLGH 182

Query: 178 MAAAVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGL 237
           MA   AK +G  NV   D+++ +L+LAR++G T  VN    N      +     G    L
Sbjct: 183 MAVQYAKAMGL-NVAAVDIDDKKLDLARRLGATVTVNAKTHNDPAAYIKKETDGGAQGVL 241

Query: 238 EMSGAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYK 297
             + +P AF   +     GG IA+ G+P  D  +    ++  G+ ++G     +  T   
Sbjct: 242 VTAVSPKAFEQAIGMAARGGTIALNGLPAGDFPLSIFNMVLNGVTVRG----SIVGTRLD 297

Query: 298 MAALIQSGLDLSPIITHRF-SIDDFQKGFDAMRSGQ-SGKVIL 338
           +   I    D     T R   ID+    FD MR+GQ  G+V++
Sbjct: 298 LQESIDFAADGKVKATIRTDKIDNINAIFDEMRAGQIEGRVVM 340


Lambda     K      H
   0.322    0.140    0.433 

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: 303
Number of extensions: 23
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: 341
Length of database: 344
Length adjustment: 29
Effective length of query: 312
Effective length of database: 315
Effective search space:    98280
Effective search space used:    98280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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