GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Lactobacillus silagei IWT126

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_089136363.1 CES79_RS03835 methionine ABC transporter ATP-binding protein

Query= TCDB::Q88P35
         (384 letters)



>NCBI__GCF_002217945.1:WP_089136363.1
          Length = 345

 Score =  142 bits (358), Expect = 1e-38
 Identities = 84/255 (32%), Positives = 138/255 (54%), Gaps = 11/255 (4%)

Query: 4   LELRNVNKTYGSGLPDT-----LKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQIT 58
           +E ++V+KT+  G   T     + D+ +S+  GE   ++G SG GKSTL+  I GLE  T
Sbjct: 10  IEFKHVSKTF-KGTATTKEVHAVHDVSISVDRGEIFGVIGYSGAGKSTLIRMINGLETPT 68

Query: 59  GGAILIDEQDVSGMSPKD-----RDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAID 113
            G++ +D QD++ +  +        I M+FQ+Y L  T ++ +NI   LK+ K+P+  I 
Sbjct: 69  EGSVKVDNQDITQLKKEPLAQLRHKIGMIFQNYNLLKTATIYQNITIPLKLEKIPKDEIQ 128

Query: 114 EEVARVAKLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVE 173
           +   +  K++ +       P+QLSGGQ QRVA+ RALA  P I L DE  S LD +    
Sbjct: 129 QRAEKYLKIVGLWDRRNSYPSQLSGGQSQRVAVARALAHEPTILLSDEATSALDPETTSS 188

Query: 174 MRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVA 233
           +   +K ++Q+L  T   +TH+     ++ DKVA+M+ G + + G    ++  P  +   
Sbjct: 189 ILDLLKDINQKLGLTIFIITHELDVVKSICDKVAIMEAGNVVEQGRTIDVFTGPKQEVTR 248

Query: 234 SFIGSPPMNFIPVRL 248
            F+GS  +  +P  L
Sbjct: 249 QFLGSNDLAGVPASL 263


Lambda     K      H
   0.320    0.137    0.391 

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: 243
Number of extensions: 15
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: 384
Length of database: 345
Length adjustment: 29
Effective length of query: 355
Effective length of database: 316
Effective search space:   112180
Effective search space used:   112180
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: 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