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_2767 PP_2767 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__Putida:PP_2767
          Length = 277

 Score =  196 bits (499), Expect = 4e-55
 Identities = 115/264 (43%), Positives = 162/264 (61%), Gaps = 11/264 (4%)

Query: 6   MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65
           M+  PLL +E +++ F G+ A++D+ FS   GEI A+IGPNGAGK++L N I G Y    
Sbjct: 1   MSNLPLLELEGISLSFKGVKAISDIGFSVAEGEICALIGPNGAGKSSLLNIINGVYRAQQ 60

Query: 66  GRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRAS 125
           GR+      G++    R+     + +  +ARTFQNI LF GMSVL+N++  ++ K  R+S
Sbjct: 61  GRIRFA---GQQ---RRVMHPHAAARDGIARTFQNIALFKGMSVLDNVLTGRNLKR-RSS 113

Query: 126 GFSIAGLLG-LPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMC 184
               A  +G  P     +R A +     ++ +R+  + D   G LPYG Q+R+E+ARA+ 
Sbjct: 114 WLEQALRIGRAPGEDDRQRAAAERV---IEFLRIQPWRDEIVGTLPYGLQKRIELARALA 170

Query: 185 TEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDY 244
            EP +L LDEP AG+N  E  E++  +  I  E  + V+LIEHD+ VVM IS HVVVLDY
Sbjct: 171 AEPRLLLLDEPMAGMNAEEKREMSRFIVEINREFGMTVVLIEHDIGVVMGISHHVVVLDY 230

Query: 245 GRKISDGDPAFVKNDPAVIRAYLG 268
           GRKI DG P  V+ +P VI AYLG
Sbjct: 231 GRKIGDGSPEQVRRNPDVIAAYLG 254


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: 186
Number of extensions: 8
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: 277
Length adjustment: 26
Effective length of query: 268
Effective length of database: 251
Effective search space:    67268
Effective search space used:    67268
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