GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Shewanella sp. ANA-3

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 7023443 Shewana3_0673 ABC transporter related (RefSeq)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__ANA3:7023443
          Length = 243

 Score =  140 bits (354), Expect = 2e-38
 Identities = 79/234 (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  NR++ +  L+ +  
Sbjct: 66  DDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRKELNRDQREEELEHLLE 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 LKSRGLGVLITDHNVRETLDVCEHAYIVSHGNLIAEGTPAEILDNQQVRAVYLG 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: 112
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 (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