GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Algoriphagus aquaeductus T4

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_111391596.1 CLV31_RS04135 LPS export ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_003253485.1:WP_111391596.1
          Length = 245

 Score =  139 bits (349), Expect = 7e-38
 Identities = 83/249 (33%), Positives = 133/249 (53%), Gaps = 16/249 (6%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L A  L K + G + V +  ++V QG I GL+GPNGAGKTT F ++   I+P++G++  
Sbjct: 2   MLRAEHLVKIYKGRRVVNDISVQVEQGEIVGLLGPNGAGKTTSFYMIVGLIQPNEGKIFL 61

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
           + + I  L  ++ A+ G+    Q A    +LSV EN+L                  ++  
Sbjct: 62  ENQEITSLPMYKRAKLGIGYLAQEASVFRKLSVEENILAVL---------------EMTN 106

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
             + Q +E+   LLE   L          LSGG+R+  E+ RAL  +PK +LLDEP AGV
Sbjct: 107 LPKAQQKEKVEMLLEEFSLTHVRKNLGMVLSGGERRRTEIARALAVDPKFVLLDEPFAGV 166

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
           +P  +++I   I+   +   +  LI +HN++  +S+ DR +++ EG+ L  GT  E+  +
Sbjct: 167 DPIAVEEI-QTIVAKLKTKNIGILITDHNVNETLSITDRAYLMFEGRLLKAGTAEELAAD 225

Query: 251 SQVLEAYLG 259
            QV   YLG
Sbjct: 226 EQVRRVYLG 234


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: 135
Number of extensions: 5
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: 245
Length adjustment: 24
Effective length of query: 236
Effective length of database: 221
Effective search space:    52156
Effective search space used:    52156
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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