GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Caldicellulosiruptor hydrothermalis 108

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>NCBI__GCF_000166355.1:WP_013403450.1
          Length = 343

 Score =  132 bits (332), Expect = 1e-35
 Identities = 82/260 (31%), Positives = 133/260 (51%), Gaps = 12/260 (4%)

Query: 1   MARI-TLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLL 59
           M RI  L  I H+ G + K+     L  V+     G  + ++GPSG GK+TL+  I+ L 
Sbjct: 1   MIRIKNLTKIYHSNGIDIKA-----LDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLE 55

Query: 60  QPSHGRILFDGKDVTNLSTQS-----RNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEA 114
           +P+HG I  DG ++T LS        + +  +FQ   +  + TV  N+AFPL   G+ + 
Sbjct: 56  KPTHGSIEIDGVEMTKLSPTELKEMRKKVGIIFQHFNLLSSRTVKGNVAFPLEIAGLDKK 115

Query: 115 DVDRRVRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPH 174
            +D RV+++LE++ L +        L+  QKQ++ + R L  N    +L DE  + +DP 
Sbjct: 116 TIDNRVKELLELVGLTNKTDSYPSQLSGGQKQRVGIARALANNP-KVLLCDEATSALDPE 174

Query: 175 MKWVLRSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSH 234
               + + LK ++++FG T+V VTH+         KV VM  GQIV+ G   E+F  P  
Sbjct: 175 TTLSILNLLKEINREFGITIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKT 234

Query: 235 TFVGYFIGSPGMNFMPARIE 254
                F+ S   + +P  ++
Sbjct: 235 KIAQNFLRSLTFSELPEELK 254


Lambda     K      H
   0.321    0.137    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: 247
Number of extensions: 14
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: 356
Length of database: 343
Length adjustment: 29
Effective length of query: 327
Effective length of database: 314
Effective search space:   102678
Effective search space used:   102678
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