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_04060 H281DRAFT_04060 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Burk376:H281DRAFT_04060
          Length = 257

 Score =  187 bits (476), Expect = 1e-52
 Identities = 100/248 (40%), Positives = 155/248 (62%), Gaps = 1/248 (0%)

Query: 12  LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71
           L+  G+ K FGG++A+ +  +E+  G I GLIGPNGAGKTT FN+++    PD G    D
Sbjct: 7   LSVKGVNKRFGGLQALSDVGLEIKAGQIYGLIGPNGAGKTTFFNVITGLYTPDSGDFKLD 66

Query: 72  GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131
           G+       +Q+A+ G+ RTFQ  R    ++ LEN+++    +T         Q     K
Sbjct: 67  GQNYTPTAVYQVAKAGIARTFQNIRLFGGMTALENVMVGRHVRTKHGLLGAVFQTPAERK 126

Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191
           EE++++E+A+ LLE VG+A+ A   +  LS G ++ LE+ RAL T+PKL+ LDEPAAG+N
Sbjct: 127 EEREIKERAIELLEYVGIAQYADYTSRNLSYGHQRRLEIARALATDPKLLALDEPAAGMN 186

Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNS 251
                ++  R+L   R DG T L+IEH++ ++M LC+++ VL  G+ +A G P ++Q + 
Sbjct: 187 ATEKVEL-TRLLDKIRADGKTILLIEHDVKLVMGLCNQMTVLDYGKVIAQGLPQDVQKDP 245

Query: 252 QVLEAYLG 259
           +V+EAYLG
Sbjct: 246 KVIEAYLG 253


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: 172
Number of extensions: 5
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: 260
Length of database: 257
Length adjustment: 24
Effective length of query: 236
Effective length of database: 233
Effective search space:    54988
Effective search space used:    54988
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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