GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Shewanella oneidensis MR-1

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 201027 SO1865 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__MR1:201027
          Length = 302

 Score =  107 bits (266), Expect = 4e-28
 Identities = 74/228 (32%), Positives = 112/228 (49%), Gaps = 23/228 (10%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           L+   GL K +G  KA+    + +  G+   L+GPNGAGKTTLF+LL  ++ P  G V  
Sbjct: 3   LVQCQGLSKHYGNKKALNNVSLTLEAGAPIALVGPNGAGKTTLFSLLCGYLTPSAGTVRI 62

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLS-RLSVLENMLLAAQKQTGENFWQVQLQPQVV 129
            GE      P+     G +       TL   L+++  +   A+ Q               
Sbjct: 63  LGE-----APNSPTLLGQIAALPQDATLDPNLTIISQLSFFARLQG-------------- 103

Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189
             + KQ  ++A+ +L  V LA+ A +    LS G  K + + +AL+ +PKL+LLDEP AG
Sbjct: 104 -MDSKQANQEALRVLNLVDLAEVAQQKPPSLSHGMSKRVAIAQALIGSPKLVLLDEPTAG 162

Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237
           ++P     I  R L        TF+I  HN+D +  LCD+V  L +G+
Sbjct: 163 LDPANAKKI--RELVRILSPTTTFVISSHNLDELEKLCDQVLYLDKGE 208


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: 145
Number of extensions: 5
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: 302
Length adjustment: 26
Effective length of query: 234
Effective length of database: 276
Effective search space:    64584
Effective search space used:    64584
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 17 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