GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Marinomonas arctica 328

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_111606038.1 DK187_RS03925 LPS export ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_003259225.1:WP_111606038.1
          Length = 241

 Score =  138 bits (348), Expect = 8e-38
 Identities = 84/239 (35%), Positives = 133/239 (55%), Gaps = 7/239 (2%)

Query: 1   MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60
           M++L+ ++L+  Y   Q V+DVS  V  GE V L+G NGAGKTT    + G+V   +G I
Sbjct: 1   MAILEAKHLAKSYKKRQVVKDVSIAVESGEAVGLLGPNGAGKTTCFYMIVGMVANDAGGI 60

Query: 61  EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQAN----L 116
              GQ+I           G+  +P+   +F  ++V +N+   A L+  +E N+A     L
Sbjct: 61  FIDGQDITHDAMHTRAQKGIGYLPQEASIFRKMSVEDNIL--AILETRKELNKAQQEERL 118

Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176
           +++   F     R N   A LSGGE++ + + RAL   PK +LLDEP  G+ PI + +I 
Sbjct: 119 EELLEEFHINHIRTNLGMA-LSGGERRRVEIARALAMNPKFILLDEPFAGVDPISVGDIK 177

Query: 177 DIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
            II+ +Q+ G  VL+ + N  + L I D+ Y++  G I+ SG    + ++E+V+K YLG
Sbjct: 178 LIIKHLQESGIGVLITDHNVRETLDICDKAYIVGNGYIIASGDANTVINNEQVKKVYLG 236


Lambda     K      H
   0.315    0.134    0.358 

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: 129
Number of extensions: 3
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: 236
Length of database: 241
Length adjustment: 23
Effective length of query: 213
Effective length of database: 218
Effective search space:    46434
Effective search space used:    46434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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