GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Acidithiobacillus ferrooxidans ATCC 23270

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_012536544.1 AFE_RS06880 fumarylacetoacetate hydrolase family protein

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



>NCBI__GCF_000021485.1:WP_012536544.1
          Length = 227

 Score =  103 bits (258), Expect = 3e-27
 Identities = 76/225 (33%), Positives = 107/225 (47%), Gaps = 20/225 (8%)

Query: 51  VETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPND 110
           V TL A+S NP          +  C+G NY+DHA E G+    EP  FMK  SAI+  N 
Sbjct: 10  VVTLDAMSSNP------FPVRRIFCVGQNYADHAREMGSAPDTEPFFFMKPASAILRNNS 63

Query: 111 DLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEA-LDYVAGYCTVHDVSERAFQ---TERH 166
            L  P G+     EVEL + + K  K++   +   DYV GY    D++ R  Q    E+ 
Sbjct: 64  VLPYPPGTTDLQPEVELVVALHKGGKHIPTGKVDDDYVFGYAVGLDMTRRDLQRAAREKG 123

Query: 167 GQWTKGKSCDTFGPTGPWLVTKDEVADPQDLA-MWLKVNGETMQDGSTKTMVYGAAHLVS 225
             W   K+ D   P     +T +  +       + LKVNG+  Q      M++    +V 
Sbjct: 124 QPWEMAKAFDHSAPC--TAITPEFYSGTIARGKVELKVNGQIRQSADVGDMLWKIPQIVH 181

Query: 226 YLSQFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGL 270
           +LS  + L PGD++ TGTP GVG  +K       GDV+E  + GL
Sbjct: 182 FLSNQVELFPGDLLFTGTPAGVGPVVK-------GDVIEATVAGL 219


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: 192
Number of extensions: 12
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: 227
Length adjustment: 24
Effective length of query: 257
Effective length of database: 203
Effective search space:    52171
Effective search space used:    52171
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: 46 (22.3 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