GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02383 H281DRAFT_02383 amino acid/amide ABC transporter membrane protein 2, HAAT family /amino acid/amide ABC transporter ATP-binding protein 1, HAAT family

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Burk376:H281DRAFT_02383
          Length = 594

 Score =  181 bits (460), Expect = 2e-50
 Identities = 101/249 (40%), Positives = 153/249 (61%), Gaps = 3/249 (1%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           LL  +   K FGG+ AV +   EV  G I GLIGPNGAGK+T FNL++  ++   G + F
Sbjct: 346 LLTVNKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGEITF 405

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
            GE I  L   +I ++G+ RTFQ  + L  ++VLEN+ + A  +     W+  ++   V 
Sbjct: 406 RGERIDALSSREIVKRGIGRTFQHVKLLPGMTVLENVAIGAHLRGHAGVWRSIVRLNSV- 464

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
            EE +L  +A   +  VGL +  Y+ AG L+ GQ+++LE+ RAL  +P L+LLDEPAAG+
Sbjct: 465 -EEARLMAEAARQIRRVGLEQHMYDEAGSLALGQQRILEIARALCCDPTLLLLDEPAAGL 523

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
             +    + D +L   + +GM+ L++EH+MD +M+L DR+ V+  G  +A+G P E+Q +
Sbjct: 524 RYQEKLQLAD-LLRRLKAEGMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQEVQQD 582

Query: 251 SQVLEAYLG 259
             VLEAYLG
Sbjct: 583 PAVLEAYLG 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 Sep 17 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