GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Paraburkholderia phymatum STM815

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_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000020045.1:WP_012402388.1
          Length = 594

 Score =  178 bits (452), Expect = 2e-49
 Identities = 98/250 (39%), Positives = 151/250 (60%), Gaps = 3/250 (1%)

Query: 10  PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69
           PLL      K FGG+ AV +   EV  G I GLIGPNGAGK+T FNL++  ++   G + 
Sbjct: 345 PLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGAIT 404

Query: 70  FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129
           F GE I  L   +I ++G+ RTFQ  + L  ++VLEN+ +    +     W  +   ++ 
Sbjct: 405 FRGERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGHLRGRAGVW--RSVARLN 462

Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189
             EE +L  +A   +  VGL +  Y+ AG L+ G++++LE+ RAL  +P L+LLDEPAAG
Sbjct: 463 GAEEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALCCDPTLLLLDEPAAG 522

Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249
           +  +    +   +L   R++GM+ L++EH+MD +M+L DR+ V+  G  +A+G P ++Q 
Sbjct: 523 LRYQEKQQLA-TLLRKLREEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQDVQN 581

Query: 250 NSQVLEAYLG 259
           +  VLEAYLG
Sbjct: 582 DPAVLEAYLG 591


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: 325
Number of extensions: 12
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: 594
Length adjustment: 31
Effective length of query: 229
Effective length of database: 563
Effective search space:   128927
Effective search space used:   128927
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: 50 (23.9 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