GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Azospirillum thiophilum BV-S

Align methylmalonyl-CoA epimerase (EC 5.1.99.1) (characterized)
to candidate WP_045586149.1 AL072_RS14955 VOC family protein

Query= BRENDA::Q8RCQ6
         (150 letters)



>NCBI__GCF_001305595.1:WP_045586149.1
          Length = 179

 Score = 76.6 bits (187), Expect = 2e-19
 Identities = 44/138 (31%), Positives = 72/138 (52%), Gaps = 4/138 (2%)

Query: 13  QIGIVVRDIEESLQNYAEFFGVEKPQWFWTDDYSKAHTKFNGRPTKARAKLAFFELGPLQ 72
           Q G VVRDIE ++  ++   G+    WF+ +     +  + G   +    +A    GPLQ
Sbjct: 10  QAGYVVRDIEAAMDYWSRTLGIGP--WFYNERVPIRNYSYRGESYEVHNSVALANSGPLQ 67

Query: 73  LELIEP-DENPSTWREFLDKNGEGIHHIAFVVKDMDRKVEELYRKGMKVIQKGDF-EGGR 130
           +ELI+  ++ PS +R+FL     G+ H+A+  +D D  ++ L  +G K +  G+  E GR
Sbjct: 68  MELIQTRNDAPSMYRDFLQAGNTGLQHVAYWTEDYDADLDRLLGQGFKPVMSGEVGEKGR 127

Query: 131 YAYIDTLRALKVMIELLE 148
           + Y DT      +IEL E
Sbjct: 128 FIYFDTEYHPGTVIELSE 145


Lambda     K      H
   0.320    0.139    0.415 

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: 76
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: 150
Length of database: 179
Length adjustment: 18
Effective length of query: 132
Effective length of database: 161
Effective search space:    21252
Effective search space used:    21252
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 (21.8 bits)
S2: 43 (21.2 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