GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Desulfovibrio vulgaris Hildenborough

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 209489 DVU0550 high-affinity branched-chain amino acid ABC transporter, ATP binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>MicrobesOnline__882:209489
          Length = 262

 Score =  180 bits (456), Expect = 3e-50
 Identities = 97/255 (38%), Positives = 156/255 (61%), Gaps = 5/255 (1%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L    + K+FGG++A+ E  + V  G I  LIGPNGAGKTT FN ++    P +G V+ 
Sbjct: 4   VLDVRSISKNFGGLRALNEVDLRVDAGEIVALIGPNGAGKTTFFNCITGIYVPTEGEVVV 63

Query: 71  D---GEPIQQ--LQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQ 125
                EP++    +P+Q+ + GM RTFQ  R    ++VLEN+++    +T        L+
Sbjct: 64  TRPGSEPVRVNGQKPNQVTELGMARTFQNIRLFQNMTVLENVMIGCHCRTRSGILGALLR 123

Query: 126 PQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDE 185
                 EE+++ +++  LL+SV L +   E A  L  G ++ LE+ RAL TNP L+LLDE
Sbjct: 124 DAKTRGEEQEIIDKSYELLKSVHLQQHYKEQARNLPYGAQRRLEIARALATNPFLLLLDE 183

Query: 186 PAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPA 245
           PAAG+NP+   ++   +L    +  ++ L+IEH+M+++MSL DR++V+  G  +A+GTP 
Sbjct: 184 PAAGMNPQETLELKGLVLEIRERLNLSVLLIEHDMNMVMSLSDRIYVMEYGSKIAEGTPE 243

Query: 246 EIQTNSQVLEAYLGK 260
           E+  N +V++AYLG+
Sbjct: 244 EVSRNPRVIKAYLGE 258


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: 170
Number of extensions: 6
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: 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 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