GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Salinicoccus carnicancri Crm

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_083854810.1 C792_RS0100870 ATP-binding cassette domain-containing protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000330705.1:WP_083854810.1
          Length = 261

 Score =  100 bits (248), Expect = 4e-26
 Identities = 71/233 (30%), Positives = 109/233 (46%), Gaps = 24/233 (10%)

Query: 11  LLAASGLCKSFGG----IKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKG 66
           L+      KSF G     KAV    + +    I G+IG +GAGK+TL   ++    PD G
Sbjct: 17  LIDIKAATKSFAGKNGDFKAVDSITLSIQNKEIFGIIGESGAGKSTLMRFINALETPDSG 76

Query: 67  RVIFDGEPIQQLQPHQIA--QQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQL 124
           +VI DG  +  L    +   Q+ +   FQ    L   +V +N+ L               
Sbjct: 77  QVIVDGTDVVTLGKKDLRKHQKDISMIFQHFNLLGNKTVEDNIRL--------------- 121

Query: 125 QPQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLD 184
            P  + K +  L    +  +E VGL  K   Y   LSGGQ++ + + RAL+T PK++L D
Sbjct: 122 -PLTLHKYKTPLSVDEV--IEFVGLDDKRDSYPAELSGGQKQRVGIARALVTRPKILLCD 178

Query: 185 EPAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237
           EP + ++    D+I D +     +  MT +I+ H + VI  LC R  V+  G+
Sbjct: 179 EPTSALDENTTDEIVDVLGRAQEEFDMTVVIVTHELGVIKQLCRRAAVMERGR 231


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: 154
Number of extensions: 8
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: 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