GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Desulfovibrio vulgaris Miyazaki F

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 8500845 DvMF_1583 ABC transporter related (RefSeq)

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Miya:8500845
          Length = 240

 Score =  195 bits (496), Expect = 6e-55
 Identities = 109/252 (43%), Positives = 155/252 (61%), Gaps = 16/252 (6%)

Query: 9   LPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV 68
           + +L    L   FGG+ A+ +   +V QG I  LIGPNGAGKTTLFN ++ F  P +G+V
Sbjct: 1   MSMLEIRKLSMFFGGLAALHDVNFDVRQGEILALIGPNGAGKTTLFNCVNGFYTPSEGQV 60

Query: 69  IFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128
           +F G+PI  L+PH++ Q G+ RTFQV + LSR+SV +N+L +A  +              
Sbjct: 61  LFKGQPISGLKPHKVCQMGIARTFQVVKPLSRMSVFDNVLASAFLRN------------- 107

Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188
                K  Q+ A  +L   GL     + + GL  G+RK LE+ RAL T P+ +LLDE  A
Sbjct: 108 --PTRKGAQDVADEVLHFTGLWDDRDQLSKGLPLGKRKRLEIARALATQPEFLLLDESFA 165

Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248
           G+NP  +D   D I+   +Q G+T +IIEH+M VIM++ DR+ VL  GQ +A+GTPA+I 
Sbjct: 166 GLNPAELDVSID-IIRGIKQQGITVMIIEHHMKVIMAISDRIVVLNFGQKIAEGTPAQIS 224

Query: 249 TNSQVLEAYLGK 260
            + QV+EAYLG+
Sbjct: 225 ADRQVVEAYLGE 236


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: 161
Number of extensions: 8
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: 240
Length adjustment: 24
Effective length of query: 236
Effective length of database: 216
Effective search space:    50976
Effective search space used:    50976
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 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