GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Pontibacillus litoralis JSM 072002

Align methylmalonyl-CoA epimerase (EC 5.1.99.1) (characterized)
to candidate WP_036834967.1 N784_RS11140 VOC family protein

Query= metacyc::MONOMER-17285
         (139 letters)



>NCBI__GCF_000775615.1:WP_036834967.1
          Length = 142

 Score = 79.3 bits (194), Expect = 2e-20
 Identities = 46/128 (35%), Positives = 72/128 (56%), Gaps = 4/128 (3%)

Query: 5   IDHIGLVVADLDAAIDFYRTAYDVTEWERI--ELPERHALIGVARFGDVLIELIAPTSDQ 62
           +DHIG+ V DL  +IDFY      T  +R   E     + I +        EL+APT++ 
Sbjct: 5   LDHIGVAVRDLQGSIDFYERVLGATLVDRYRSEAEGVESEIAIMDIQGARTELLAPTNNT 64

Query: 63  AS-FARFLREKGPGMHHIAYRVDDIYAALATLQARGLPLIDREPRPGIHDTLVAFVHPKA 121
            S  ARFL++KG G+HH+AY+VDD+  ALA L+ +G+  +    R   H   + +++P A
Sbjct: 65  TSPIARFLKQKGKGVHHVAYQVDDLDEALAQLERQGVRTLPHTLRTNKHGRRLIYLNP-A 123

Query: 122 GGQGVLVE 129
             +G ++E
Sbjct: 124 DTEGTIIE 131


Lambda     K      H
   0.326    0.142    0.432 

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: 68
Number of extensions: 4
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: 139
Length of database: 142
Length adjustment: 15
Effective length of query: 124
Effective length of database: 127
Effective search space:    15748
Effective search space used:    15748
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 42 (20.8 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