GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Brucella inopinata BO1

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_008509284.1 BIBO1_RS15425 fumarylacetoacetate hydrolase family protein

Query= reanno::Smeli:SM_b21112
         (281 letters)



>NCBI__GCF_000182725.1:WP_008509284.1
          Length = 287

 Score =  142 bits (359), Expect = 6e-39
 Identities = 87/277 (31%), Positives = 135/277 (48%), Gaps = 7/277 (2%)

Query: 1   MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGN 60
           MK L +   G    G+L  DG++ DLS           +  +   LA L  E     +  
Sbjct: 1   MKFLSFSTCGGRHYGVLKEDGVV-DLSARHGSRWPTLREVIEAGALAQLAQEAAGLAADV 59

Query: 61  PRLGPC----VAGTGKFICIGLNYSDHAAE--TGATVPPEPIIFMKATSAIVGPNDDLVL 114
           P         +    K IC+G+N+ D   E   G   P  P +F++   +  G    L+ 
Sbjct: 60  PLSSITYEIPIPSPEKIICVGVNFPDRNEEYKDGQAAPANPSLFVRFPRSFTGHERPLMR 119

Query: 115 PRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKS 174
           P  S + D+E E+ I+IGK  + ++E +ALD++A     ++ + R +        T+GK+
Sbjct: 120 PPESPQLDYEGEIAIIIGKGGRRIAEKDALDHIAALTLCNEGTIRDWVRHAKFNVTQGKN 179

Query: 175 CDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLR 234
            D  G  GPWLV   + +   D+ +  +VNGE  Q   T  M++    +++Y+S F +L 
Sbjct: 180 FDATGSIGPWLVPYTDESQIADIQLTTRVNGEVRQQDRTSRMIFSFRKIINYVSTFTTLV 239

Query: 235 PGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLG 271
           PGD+I  GTP G G    PP +LK GDVVE+  EG+G
Sbjct: 240 PGDVIVCGTPTGAGARFDPPIWLKPGDVVEVEAEGIG 276


Lambda     K      H
   0.315    0.136    0.408 

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: 244
Number of extensions: 13
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: 281
Length of database: 287
Length adjustment: 26
Effective length of query: 255
Effective length of database: 261
Effective search space:    66555
Effective search space used:    66555
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: 42 (22.0 bits)
S2: 47 (22.7 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