GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Phaeobacter inhibens BS107

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate GFF249 PGA1_c02610 putative high-affinity branched-chain amino acid transport ATP-binding protein LivG

Query= uniprot:A0A159ZWS6
         (255 letters)



>FitnessBrowser__Phaeo:GFF249
          Length = 255

 Score =  218 bits (556), Expect = 7e-62
 Identities = 102/249 (40%), Positives = 166/249 (66%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           +L++E+ +++FGG++AVN ++ +V+E +V A++GPNGAGK+TVFN ++ FYQP  G +  
Sbjct: 3   LLEIEHATLKFGGVVAVNDLSFSVEEGEVYAIVGPNGAGKSTVFNLISRFYQPHSGRLSF 62

Query: 65  DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124
           DG  +       +A  G+ RTFQN+ LF   T ++NLL+ +HRH  +     LF TP  R
Sbjct: 63  DGRDLLQSKADAVADLGIARTFQNIELFDHATVLQNLLVGRHRHRRSTLMEELFFTPRVR 122

Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           + ER      E  +D ++L  + ++    L YG ++ +E+ R + + PR+L+LDEPA+GL
Sbjct: 123 REERRHRAAVEEVIDFLDLQAYRDKMIAGLPYGVRKVVELGRALASGPRLLLLDEPASGL 182

Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244
           + +ET D++  I  +R++  +TVL++EHDM LV S+SD ++ +  G  LA+GTP +++ N
Sbjct: 183 SVEETRDMRWWIDDIRKQMGITVLMVEHDMGLVSSVSDRVLALADGAKLAEGTPAEVQAN 242

Query: 245 PEVIKAYLG 253
           P VI+AYLG
Sbjct: 243 PAVIEAYLG 251


Lambda     K      H
   0.321    0.138    0.398 

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: 184
Number of extensions: 8
Number of successful extensions: 1
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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