GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natA in Herbaspirillum seropedicae SmR1

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 HSERO_RS08285 HSERO_RS08285 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08285 HSERO_RS08285 amino acid
           ABC transporter ATP-binding protein
          Length = 258

 Score =  198 bits (503), Expect = 1e-55
 Identities = 98/250 (39%), Positives = 156/250 (62%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L  S L   FGG+ AV    + V +  +  +IGPNGAGKTT+FN +S F RP  G ++ 
Sbjct: 8   MLEVSNLSMRFGGLLAVDGVSLAVQEREVFAIIGPNGAGKTTVFNCISGFYRPTSGEIML 67

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
           DG  I +   HQ+AQQG+VRTFQ  R    ++V+EN+L+A  +Q   N     L+     
Sbjct: 68  DGASIARQPSHQVAQQGLVRTFQNIRLFKSMTVVENLLVAQHQQVNTNLLSGLLKTPAYR 127

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
           K E++  ++A + L+ +GL   A   AG LS G ++ +E+ R ++T P+L+LLDEPAAG+
Sbjct: 128 KSEQEALQRAAYWLDQLGLTALANREAGTLSYGLQRRVEIARCMITKPRLLLLDEPAAGL 187

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
           NP+   ++   I    R+ G+  L+IEH+M +IM + DR+ V+  G+ +  GTP +++++
Sbjct: 188 NPQEKQELSQLIDRLRREHGVAVLLIEHDMSLIMGISDRILVMEHGKPIVTGTPEQVRSD 247

Query: 251 SQVLEAYLGK 260
            +V++AYLG+
Sbjct: 248 ERVIKAYLGE 257


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: 168
Number of extensions: 6
Number of successful extensions: 1
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: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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