GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Tistlia consotensis USBA 355

Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= uniprot:A0A161GM94
         (322 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  161 bits (408), Expect = 2e-44
 Identities = 101/294 (34%), Positives = 157/294 (53%), Gaps = 1/294 (0%)

Query: 26  MLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85
           ML  A+ I  + +L+   FL+  N+  +       GI +  M + + +G  DLSVGSV  
Sbjct: 36  MLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDLSVGSVAG 95

Query: 86  CAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLA 145
            +G+V  + ++D   + + I   ++ G  VGL++GI+I   R+ A + TL  M I R LA
Sbjct: 96  LSGIVLGLALKDY-PIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGMMAIGRSLA 154

Query: 146 YIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGGN 205
           YIF+   A+              +FG+P  +L     +L     L YT  GR   AIG N
Sbjct: 155 YIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGGRTIYAIGSN 214

Query: 206 QEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLGG 265
           +EAA  AG+ V    I+ + V G + A+A     +++ S  P+ G G EL  I+A V+GG
Sbjct: 215 KEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGMELDAIAAVVIGG 274

Query: 266 VSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRL 319
            SL GG G I   + GVLI+ +I N +NL  +  F+Q    GSI+++A++++RL
Sbjct: 275 ASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVERL 328


Lambda     K      H
   0.330    0.144    0.420 

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: 257
Number of extensions: 16
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: 322
Length of database: 335
Length adjustment: 28
Effective length of query: 294
Effective length of database: 307
Effective search space:    90258
Effective search space used:    90258
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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