GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapQ in Herbaspirillum seropedicae SmR1

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ

Query= TCDB::Q52813
         (400 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS17565 HSERO_RS17565
           glutamate/aspartate ABC transporter permease GltJ
          Length = 241

 Score = 87.4 bits (215), Expect = 4e-22
 Identities = 46/130 (35%), Positives = 73/130 (56%)

Query: 268 EFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIII 327
           +F+   L L  +TA+ + E VR GI  +P+GQ  A  ALGL        V++P A+RI++
Sbjct: 106 QFVMAMLCLGMFTAARVCEQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMRIVL 165

Query: 328 PPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLF 387
           PPLTS++LN+ KNS++A  IG  +L A G  +++ + Q  E      + Y+ ++I     
Sbjct: 166 PPLTSEFLNIFKNSAVASTIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICVMSL 225

Query: 388 MNWFNAKMAL 397
           M     K +L
Sbjct: 226 MRILERKTSL 235



 Score = 52.8 bits (125), Expect = 1e-11
 Identities = 27/78 (34%), Positives = 43/78 (55%)

Query: 83  SSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNI 142
           S+  TY   LL G+  T+ + ++    A ++G  +GI R   N  ++     YVE+FRN+
Sbjct: 15  STGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRALSGFAACYVELFRNV 74

Query: 143 PPLLVIFFWYLGVLSVLP 160
           P L+ IF WY  +  +LP
Sbjct: 75  PLLVQIFIWYFAMPELLP 92


Lambda     K      H
   0.327    0.141    0.432 

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: 284
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 400
Length of database: 241
Length adjustment: 27
Effective length of query: 373
Effective length of database: 214
Effective search space:    79822
Effective search space used:    79822
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: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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