GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Escherichia coli BW25113

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 14791 b0654 glutamate and aspartate transporter subunit (NCBI)

Query= TCDB::Q8YPM8
         (308 letters)



>FitnessBrowser__Keio:14791
          Length = 246

 Score =  116 bits (290), Expect = 6e-31
 Identities = 84/261 (32%), Positives = 127/261 (48%), Gaps = 22/261 (8%)

Query: 45  LGIQFGFDFLKQQASFDIGETLIAYKPTDTYSLALWVGLINSLRIAFVGIILTTIVGILA 104
           + I + +    QQA F  G T        TY   +W G   ++ ++    I+  +VG   
Sbjct: 1   MSIDWNWGIFLQQAPF--GNT--------TYLGWIWSGFQVTIALSICAWIIAFLVGSFF 50

Query: 105 GIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFAVFLGLPRADNKISLGGFIGLSQN 164
           GI R   N  +  +  +YVE+FRN PL++Q   WY  +   LP    KI +     L  N
Sbjct: 51  GILRTVPNRFLSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPE---KIGMWFKAELDPN 107

Query: 165 GLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRL 224
              + +F  S     L LGL  +T A + E VR  IQS+ +GQ  A  ++GL      R 
Sbjct: 108 ---IQFFLSS----MLCLGL--FTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRY 158

Query: 225 VIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLT 284
           V+ P A RVI+PP+TS+ +NL KNS++A  IG  D+   A    + +  A E    + L 
Sbjct: 159 VLLPNAYRVIVPPMTSEMMNLVKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLA 218

Query: 285 YLSLSLTISLIMNAFNRTVQI 305
           Y+ ++  I L+M    R V++
Sbjct: 219 YVLINAFIMLVMTLVERKVRL 239


Lambda     K      H
   0.328    0.143    0.430 

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: 186
Number of extensions: 7
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: 308
Length of database: 246
Length adjustment: 25
Effective length of query: 283
Effective length of database: 221
Effective search space:    62543
Effective search space used:    62543
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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