GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Streptacidiphilus oryzae TH49

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_051938939.1 BS73_RS00335 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000744815.1:WP_051938939.1
          Length = 262

 Score =  198 bits (504), Expect = 8e-56
 Identities = 109/254 (42%), Positives = 156/254 (61%), Gaps = 13/254 (5%)

Query: 6   SPPLPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDK 65
           +P  PLL    + + FGG++A+    + V  G++TGLIGPNG+GKTTLFN+++ + RPD 
Sbjct: 4   TPARPLLRIEDVHRDFGGLRALAGCSLAVETGTVTGLIGPNGSGKTTLFNVVTGYDRPDS 63

Query: 66  GRVIFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQ 125
           GRV  DG+ I    P  + + G+ RTFQ+ R   RLS+L+N+ + A           + +
Sbjct: 64  GRVRLDGQEITGAAPDAVGRLGLARTFQLTRVFDRLSLLDNLRVGAAAVP-------RAR 116

Query: 126 PQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDE 185
            Q + +E + L+     LL+ VGL   A   AG LS GQRKL+E+   L   P+++LLDE
Sbjct: 117 RQALYRESRCLE-----LLDVVGLVDHADRRAGELSYGQRKLVELATVLAQQPRIVLLDE 171

Query: 186 PAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPA 245
           PA GVNP LI  I   I   NR  G TFL++EHNM+ +M +CD V V+  G+ +A G P 
Sbjct: 172 PAGGVNPGLIARIGGLIRELNR-SGTTFLVVEHNMEFVMGVCDTVAVMERGEVIAQGEPE 230

Query: 246 EIQTNSQVLEAYLG 259
            I+T+ +VL+AYLG
Sbjct: 231 AIRTDPRVLDAYLG 244


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: 189
Number of extensions: 9
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: 262
Length adjustment: 25
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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 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