GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF3453 PS417_17675 ABC transporter
          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.

Links

Downloads

Related tools

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 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