GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pandoraea thiooxydans ATSB16

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_047212682.1 PATSB16_RS03645 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001931675.1:WP_047212682.1
          Length = 252

 Score =  210 bits (534), Expect = 3e-59
 Identities = 114/248 (45%), Positives = 157/248 (63%), Gaps = 1/248 (0%)

Query: 12  LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71
           L+  GL   +G    + +  +EV+   + G+IGPNGAGK+TLF +LS FIRP+ GR+ F 
Sbjct: 3   LSTHGLVLRYGDFTVLDDVSMEVSVAGLHGMIGPNGAGKSTLFAVLSGFIRPNAGRISFA 62

Query: 72  GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131
           G  ++ L P + A+ G+ RTFQV R    LSV EN+ +AA+ Q GE+  ++   P  V  
Sbjct: 63  GTMLEHLSPVERARTGVGRTFQVPREFKHLSVRENLQVAARHQPGESMLKLLFAPSAVRM 122

Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191
            E+ + E+    LE + L K A ++AGGLS GQ+KLLE+GR LMT PK ILLDEP AGVN
Sbjct: 123 AERAIAERVERTLEFLKLTKVADQHAGGLSSGQKKLLELGRVLMTEPKFILLDEPYAGVN 182

Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNS 251
           P LID+I  RI   N Q G+ FLIIEHN++ +  L D ++V+  G+ +A GTP  +    
Sbjct: 183 PVLIDEISTRIRELNTQ-GIGFLIIEHNLEALNRLVDDLYVMDRGRLIAHGTPQTVLNEP 241

Query: 252 QVLEAYLG 259
            V  AY+G
Sbjct: 242 AVRAAYIG 249


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: 162
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: 252
Length adjustment: 24
Effective length of query: 236
Effective length of database: 228
Effective search space:    53808
Effective search space used:    53808
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