GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pseudarthrobacter sulfonivorans Ar51

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001484605.1:WP_058929663.1
          Length = 345

 Score =  221 bits (562), Expect = 2e-62
 Identities = 115/250 (46%), Positives = 163/250 (65%), Gaps = 2/250 (0%)

Query: 10  PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69
           P++ A  + +SFGGI AV    +E+ +  IT LIGPNGAGKTTLFNLL+ F  P+ G+  
Sbjct: 37  PIVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKWQ 96

Query: 70  FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129
           F+G  +  + P+++A+ GMVRTFQ+ + + +L+V+ENM L   +Q GE   +  L   + 
Sbjct: 97  FEGNSLAGISPYKVARMGMVRTFQLTKVMGKLTVMENMRLGGSEQPGERLSKA-LFKGLW 155

Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189
              EK++  QA  LLE   L  K  +YA  LSGGQRKLLEM R+LM  PKL++LDEP AG
Sbjct: 156 GGREKEITAQANVLLEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRPKLVMLDEPMAG 215

Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249
           VNP L   + D I    + +GMT L +EH+M+++  + D V V+AEG+ +A+G P E+  
Sbjct: 216 VNPALTQSLLDHIKNL-KAEGMTVLFVEHDMNMVRHIADWVVVMAEGKIVAEGPPGEVMK 274

Query: 250 NSQVLEAYLG 259
           N  V++AYLG
Sbjct: 275 NPAVIDAYLG 284


Lambda     K      H
   0.319    0.136    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: 205
Number of extensions: 10
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: 260
Length of database: 345
Length adjustment: 27
Effective length of query: 233
Effective length of database: 318
Effective search space:    74094
Effective search space used:    74094
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 (21.7 bits)
S2: 48 (23.1 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