GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Lactobacillus silagei IWT126

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_089136363.1 CES79_RS03835 methionine ABC transporter ATP-binding protein

Query= reanno::psRCH2:GFF857
         (371 letters)



>NCBI__GCF_002217945.1:WP_089136363.1
          Length = 345

 Score =  140 bits (354), Expect = 4e-38
 Identities = 77/244 (31%), Positives = 128/244 (52%), Gaps = 11/244 (4%)

Query: 4   VTLRDICKSYDGTPITRHI------DLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITS 57
           +  + + K++ GT  T+ +       + ++ GE    +G SG GKSTL+R+I GLE  T 
Sbjct: 10  IEFKHVSKTFKGTATTKEVHAVHDVSISVDRGEIFGVIGYSGAGKSTLIRMINGLETPTE 69

Query: 58  GDLLIDNQRVNDLPPKD-----RSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKR 112
           G + +DNQ +  L  +        +GM+FQ+Y L    T+ +N+   LKL  + K EI++
Sbjct: 70  GSVKVDNQDITQLKKEPLAQLRHKIGMIFQNYNLLKTATIYQNITIPLKLEKIPKDEIQQ 129

Query: 113 RVEAVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQM 172
           R E   +I+ L       P  LSGGQ QRVA+ R +  EP + L DE  S LD      +
Sbjct: 130 RAEKYLKIVGLWDRRNSYPSQLSGGQSQRVAVARALAHEPTILLSDEATSALDPETTSSI 189

Query: 173 RIEIARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAG 232
              +  ++Q++  T+  +TH+     ++ DK+ ++ AG + + G+ + ++  PK      
Sbjct: 190 LDLLKDINQKLGLTIFIITHELDVVKSICDKVAIMEAGNVVEQGRTIDVFTGPKQEVTRQ 249

Query: 233 FLGS 236
           FLGS
Sbjct: 250 FLGS 253


Lambda     K      H
   0.322    0.139    0.405 

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: 255
Number of extensions: 13
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: 371
Length of database: 345
Length adjustment: 29
Effective length of query: 342
Effective length of database: 316
Effective search space:   108072
Effective search space used:   108072
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 (21.9 bits)
S2: 49 (23.5 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