GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Geobacter daltonii FRC-32

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_012647880.1 GEOB_RS13900 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000022265.1:WP_012647880.1
          Length = 247

 Score =  141 bits (355), Expect = 1e-38
 Identities = 83/240 (34%), Positives = 132/240 (55%), Gaps = 11/240 (4%)

Query: 21  FGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQP 80
           +G + A++   I + QG I  LIG NGAGKTT+ N +S       G ++F+ EP+Q L P
Sbjct: 11  YGKVHALKNVSIHLGQGEIVTLIGANGAGKTTILNTISGVTPAAGGEILFEKEPVQALSP 70

Query: 81  HQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQEQA 140
            +I + G+ +  +  +    LSV +N+ L A  +            Q   K   +  +Q 
Sbjct: 71  DRIVRLGIAQVPEGRQVFKPLSVEDNLDLGAYLR----------HRQREAKSRIRQDKQE 120

Query: 141 MFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICD 200
           +F L    L ++  + AG LSGG++++L +GRA+MT PKL+LLDEP+ G+ P ++ +I  
Sbjct: 121 IFTLFP-RLEERRKQPAGTLSGGEQQMLAIGRAMMTRPKLMLLDEPSMGLAPLVVQEIFR 179

Query: 201 RILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVLEAYLGK 260
            I    RQ G T L++E N    ++L DR +VL  G+ + +G  + +  N  V  AYLG+
Sbjct: 180 VIDNLRRQHGTTILLVEQNAKAALNLADRGYVLETGKVILEGLSSNLLENKDVQRAYLGR 239


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: 163
Number of extensions: 9
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: 247
Length adjustment: 24
Effective length of query: 236
Effective length of database: 223
Effective search space:    52628
Effective search space used:    52628
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 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