GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF in Shewanella oneidensis MR-1

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q8DQH7
         (236 letters)



>lcl|FitnessBrowser__MR1:203044 SO3960 ABC transporter, ATP-binding
           protein (NCBI ptt file)
          Length = 243

 Score =  138 bits (348), Expect = 9e-38
 Identities = 78/234 (33%), Positives = 128/234 (54%), Gaps = 3/234 (1%)

Query: 4   LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63
           LK +NL+  Y   Q V+DVS  V  G+VV L+G NGAGKTT    + GLV+   G I   
Sbjct: 6   LKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHIFID 65

Query: 64  GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK--NREENQANLKKVFS 121
             ++   P       G+  +P+   +F  LTV +N+      +K  N ++ +  L+++  
Sbjct: 66  DDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRKELNSDQREEALEQLLE 125

Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQD 181
            F     R +Q   +LSGGE++ + + RAL + PK +LLDEP  G+ PI + +I  II+ 
Sbjct: 126 EFHITHIRDSQ-GMSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKKIIEQ 184

Query: 182 IQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
           ++ +G  VL+ + N  + L + +  Y++  G ++  GT  E+  +++VR  YLG
Sbjct: 185 LKSRGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTPAEILDNQQVRAVYLG 238


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: 115
Number of extensions: 5
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: 243
Length adjustment: 23
Effective length of query: 213
Effective length of database: 220
Effective search space:    46860
Effective search space used:    46860
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 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