GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Stenotrophomonas chelatiphaga DSM 21508

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_083492030.1 ABB28_RS12765 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001431535.1:WP_083492030.1
          Length = 261

 Score = 80.9 bits (198), Expect = 2e-20
 Identities = 66/236 (27%), Positives = 113/236 (47%), Gaps = 24/236 (10%)

Query: 22  GGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGE-PIQQLQP 80
           G +K +    + +AQG  T L+GPNG GK+T   L++  + P       DG  P++ L  
Sbjct: 12  GQVKVLHGLSLRIAQGQHTALLGPNGCGKSTFIKLITRELYP---LAHADGHVPVKVLGQ 68

Query: 81  HQIAQQGMVRTFQVARTLSRLSVLENML---------LAAQKQTGENFWQVQLQPQVVVK 131
           ++         +QV R  S+L ++   L         L  ++     F+   + P     
Sbjct: 69  NR---------WQVDRLRSQLGIVTGDLSNNLADMPGLTVEQAVLTGFFASYVLPAFREI 119

Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191
            +         L  S  LA     YA  LS G+ + + + RAL+  P  +LLDEP+ G++
Sbjct: 120 SQDMRDRARATLAMSGALALHGRTYA-ELSAGETRRVLIARALVNRPHALLLDEPSTGLD 178

Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247
                 + D + +  RQ G+T +++ H+++ I+   +RV +L +G+ LADGT AE+
Sbjct: 179 LVARQQLVDTMQSLARQ-GITLVLVTHHVEEIIPEIERVVLLRDGRVLADGTRAEL 233


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: 131
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: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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