GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Shewanella loihica PV-4

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 5210884 Shew_3310 ABC transporter-related protein (RefSeq)

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__PV4:5210884
          Length = 243

 Score =  149 bits (375), Expect = 7e-41
 Identities = 87/250 (34%), Positives = 135/250 (54%), Gaps = 15/250 (6%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L A  L KS+     VQ+  + V  G I GL+GPNGAGKTT F ++   ++ DKGR+  
Sbjct: 5   ILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKGRIFI 64

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
           D + +     H  A++G+    Q A    +LSV +N++   Q ++  N            
Sbjct: 65  DDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQTRSDLN------------ 112

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
                 +E+   LLE   +      +   LSGG+R+ +E+ RAL  NPK ILLDEP AGV
Sbjct: 113 --NDGREEELEHLLEEFHITHIRDSHGMALSGGERRRVEIARALAANPKFILLDEPFAGV 170

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
           +P  + DI  +I+   +  G+  LI +HN+   + +C++ ++++ G  +A+GTPAEI  N
Sbjct: 171 DPISVIDI-KKIIEQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDN 229

Query: 251 SQVLEAYLGK 260
            QV   YLG+
Sbjct: 230 QQVRAVYLGE 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: 142
Number of extensions: 6
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: 243
Length adjustment: 24
Effective length of query: 236
Effective length of database: 219
Effective search space:    51684
Effective search space used:    51684
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 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