GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Pseudomonas putida KT2440

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate PP_4864 PP_4864 High-affinity branched-chain amino acid transport ATP-binding protein BraF

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__Putida:PP_4864
          Length = 291

 Score =  261 bits (666), Expect = 2e-74
 Identities = 141/292 (48%), Positives = 195/292 (66%), Gaps = 27/292 (9%)

Query: 6   MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65
           M+   +L+V++L M+FGG+ A++DVS      +I A+IGPNGAGKTT+FNC+TGFY  + 
Sbjct: 1   MSDDIILSVDNLMMQFGGIKALSDVSLKVRRNQIFALIGPNGAGKTTVFNCLTGFYKASG 60

Query: 66  GRLTLR----HADGKEFLLERMP--------------------GYRISQKASVARTFQNI 101
           GR+ L     H +  + L ER                      G  +  +A +ARTFQNI
Sbjct: 61  GRIELNVRGSHTNVIQLLGERFQAADFVSPARFANRMYYKMFGGTHLVNRAGLARTFQNI 120

Query: 102 RLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEF 161
           RLF  MSV+ENL+VAQH  + R     +AG+L   +Y + E +A+D A YWL+ V L++ 
Sbjct: 121 RLFKEMSVVENLLVAQHMWVNRNL---LAGVLNTKAYRKAESDALDHAFYWLEVVDLVDC 177

Query: 162 ADWEAGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIG 221
           A+  AG L YG QRRLEIARAMCT P ++CLDEPAAGLNP+E+  L+ ++  +RDEH I 
Sbjct: 178 ANRLAGELSYGQQRRLEIARAMCTRPKIICLDEPAAGLNPQETEALSRMIRVLRDEHDIT 237

Query: 222 VLLIEHDMSVVMTISDHVVVLDYGRKISDGDPAFVKNDPAVIRAYLGEEEDE 273
           V+LIEHDM +VM+ISDH+VVLD+G  I++G P  ++++P VI AYLG +E+E
Sbjct: 238 VVLIEHDMGMVMSISDHIVVLDHGNVIAEGAPQDIRHNPTVIAAYLGADEEE 289


Lambda     K      H
   0.319    0.137    0.397 

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: 234
Number of extensions: 5
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: 294
Length of database: 291
Length adjustment: 26
Effective length of query: 268
Effective length of database: 265
Effective search space:    71020
Effective search space used:    71020
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: 48 (23.1 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