GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Rhizobium etli CFN 42

Align BadK (characterized)
to candidate WP_011425014.1 RHE_RS08795 enoyl-CoA hydratase/isomerase family protein

Query= metacyc::MONOMER-943
         (258 letters)



>NCBI__GCF_000092045.1:WP_011425014.1
          Length = 259

 Score =  114 bits (285), Expect = 2e-30
 Identities = 87/260 (33%), Positives = 122/260 (46%), Gaps = 10/260 (3%)

Query: 1   MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60
           M+S  +  +    V I+T++RP+ LNAL+  ++ AL  A  A +A+  +   V+ G  + 
Sbjct: 1   MASGTVRVDVDRHVAILTISRPEKLNALDLDMLKALADAADAVEANPDLRVAVLTGEGKG 60

Query: 61  FAAGADIASMAAWS--YSDVYGSNFIT---RNWETIRQIRKPVLAAVAGLAYGGGCELAL 115
           F+AG DI    AW      V+G  ++    R +E +  +R P++AA+ G A GGG ELA 
Sbjct: 61  FSAGGDIK---AWGGMLPQVFGHAWVRHGHRIFERLATLRVPLIAALNGHALGGGLELAG 117

Query: 116 ACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYG 175
             DI +A    K  LPE  LG++PG  GTQRL R  G      M L      AEEA   G
Sbjct: 118 VADIRVAEEHIKIGLPETGLGMVPGWSGTQRLVRRFGAQAVRRMALGGEIFTAEEARLLG 177

Query: 176 LVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARF 235
           +V  VV            A  IAA    A+   K  L  A  +    G   E        
Sbjct: 178 IVDAVVPTGNSVAAARQYAGRIAARGPAAVEIAK--LMIASANGEDNGTAVEALGSILAA 235

Query: 236 ASADAREGIQAFLEKRAPCF 255
            + D +EG+ +F EKR   F
Sbjct: 236 KTGDLKEGVASFSEKRPATF 255


Lambda     K      H
   0.321    0.135    0.389 

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: 135
Number of extensions: 5
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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