GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas simiae WCS417

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF3453 PS417_17675 ABC transporter

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__WCS417:GFF3453
          Length = 249

 Score =  185 bits (470), Expect = 7e-52
 Identities = 112/254 (44%), Positives = 154/254 (60%), Gaps = 12/254 (4%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           +LE   L + +G   AVNGVNLKVE   + ++IGPNGAGKT++F+CLTG  Q T G I  
Sbjct: 4   LLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAIHF 63

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL-LVAQHRHLNTNFLAGLFKTPAF 123
           DG+ +   P H     G+ R+FQ   LF+ ++  ENL L AQ R        G      +
Sbjct: 64  DGKNLMRKPAHGRVGLGMARSFQLTSLFQNLSVRENLRLAAQGRD-------GARALNFW 116

Query: 124 RR--SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181
           RR  S+RE +E A   LE + LT  A+  AG L++GQQR LE+   + ++P++LMLDEP 
Sbjct: 117 RRVDSKREHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLLMLDEPT 176

Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241
           +G+   +   +  LI+ L  +H  TVLLIEH+M +VMSIS  I V++ G  L +GTPE +
Sbjct: 177 SGMGIDDIPIMTQLISDLGRDH--TVLLIEHNMSIVMSISQRITVMSHGQILVEGTPEFV 234

Query: 242 RDNPDVIKAYLGEA 255
           R +  V  AYLGEA
Sbjct: 235 RADERVRTAYLGEA 248


Lambda     K      H
   0.320    0.137    0.391 

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: 175
Number of extensions: 10
Number of successful extensions: 3
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: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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: 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