GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Pantoea rwandensis LMG 26275

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_084936660.1 HA51_RS21730 fumarylacetoacetate hydrolase family protein

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



>NCBI__GCF_002095475.1:WP_084936660.1
          Length = 278

 Score =  152 bits (385), Expect = 6e-42
 Identities = 94/267 (35%), Positives = 137/267 (51%), Gaps = 12/267 (4%)

Query: 19  SDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNP--------RLGPCVAGT 70
           S GI+R+          GA  P     L    V  L A S  P        R  P V   
Sbjct: 15  SYGIVREEGVIDVGSRLGAECPDLKSLLQRGAVSDLEAFSSLPADHPYSAIRFLPVVENP 74

Query: 71  GKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIV 130
           GK  C+G+NY+D   E   T+   P +F++   ++ G    L+ P  +++ D+E EL ++
Sbjct: 75  GKVFCVGMNYADKRKEFAETLDA-PTLFVRFADSLAGHEQPLLKPATTQEFDYEGELAVI 133

Query: 131 IGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDE 190
           IGK A  V  A+AL +VAGY    D + R  Q      +T GK+    G  GPW+ T DE
Sbjct: 134 IGKAAYQVKAADALQHVAGYSCFMDATVRDMQFT---WFTAGKNWQQTGGFGPWMTTADE 190

Query: 191 VADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMG 250
           + DPQ LA+   +N   +Q+ +T +MV+  A ++ Y+S F  L PGD+I TG+P GVG  
Sbjct: 191 IPDPQQLAIKTWLNEREVQNDTTASMVHPVAKIIEYISAFSPLSPGDVIITGSPGGVGKK 250

Query: 251 MKPPRYLKAGDVVELGIEGLGSQKQRV 277
             PP ++  GDV+E+ IE +G  +  V
Sbjct: 251 RTPPLFMFPGDVIEVEIEKIGRLRHTV 277


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: 234
Number of extensions: 15
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: 281
Length of database: 278
Length adjustment: 26
Effective length of query: 255
Effective length of database: 252
Effective search space:    64260
Effective search space used:    64260
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