GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cmtB in Moritella dasanensis ArB 0140

Align Mannitol-specific phosphotransferase enzyme IIA component (characterized, see rationale)
to candidate WP_017223100.1 A923_RS0118070 fused PTS fructose transporter subunit IIA/HPr protein

Query= uniprot:Q45420
         (145 letters)



>NCBI__GCF_000276805.1:WP_017223100.1
          Length = 385

 Score =  106 bits (264), Expect = 4e-28
 Identities = 57/136 (41%), Positives = 78/136 (57%)

Query: 6   LKKENIVLHARVENKTEAIRLAGQILVNNGYVEDSYIDKMFEREALTSTYMGNFIAIPHG 65
           L   +I L     NK  AI+   Q L N  YVE SY+D M  REA  STY+GN IAIPHG
Sbjct: 4   LSTNDIQLKQSASNKQHAIKALAQSLANKTYVEASYVDGMLAREAQHSTYLGNGIAIPHG 63

Query: 66  TEDAKQFVKHSGISIIQIPDGVDFGDGNIVKLLIGIAGKNNEHLEILSKIAIVCSEVENV 125
           T D +  V  +G+ +   P GVD+G+G +V L I IA K++EHL IL ++  V S     
Sbjct: 64  TVDTRDLVNKTGVQLHHYPQGVDWGEGQVVYLAIAIAAKSDEHLAILKQLTHVLSADGIE 123

Query: 126 ETMIKAATEEEILSIL 141
           + +    + E I+++L
Sbjct: 124 QQLQDCDSAEAIIAVL 139


Lambda     K      H
   0.316    0.135    0.365 

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: 122
Number of extensions: 4
Number of successful extensions: 1
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: 145
Length of database: 385
Length adjustment: 23
Effective length of query: 122
Effective length of database: 362
Effective search space:    44164
Effective search space used:    44164
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: 41 (21.6 bits)
S2: 46 (22.3 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