GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Pseudomonas putida KT2440

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate PP_0282 PP_0282 L-arginine ABC transporter - periplasmic binding subunit

Query= TCDB::Q9HU31
         (250 letters)



>FitnessBrowser__Putida:PP_0282
          Length = 250

 Score =  391 bits (1004), Expect = e-114
 Identities = 196/250 (78%), Positives = 216/250 (86%), Gaps = 2/250 (0%)

Query: 1   MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60
           M  YKK LLAAAATL  + +A AA+KLR+G E AYPPFN  DASG  VGFD DIG ALCA
Sbjct: 1   MHTYKKFLLAAAATLVMSANAMAAEKLRMGIEAAYPPFNNKDASGNVVGFDKDIGDALCA 60

Query: 61  KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120
           KMK EC VVTSDWDGIIPALNAKKFDF+V+S+SITDERKQAVDFT+PYY+NKLQF+APK+
Sbjct: 61  KMKVECSVVTSDWDGIIPALNAKKFDFLVSSLSITDERKQAVDFTNPYYSNKLQFIAPKN 120

Query: 121 VDFKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLA 180
           VDFKTDK+SLKGKVIG QRAT+AGT+LEDN  D V IKLYDTQENAYLDL SGR+DG+LA
Sbjct: 121 VDFKTDKESLKGKVIGTQRATLAGTYLEDNYPD-VEIKLYDTQENAYLDLVSGRIDGILA 179

Query: 181 DKFVQYDWLKSDAGKEFEFKGEPVFDNDKIGIAVRKGD-PLREKLNAALKEIVADGTYKK 239
           DK+VQY+WLKS  G  FEFKGEPV D+DKIGIAVRKGD  LR+ LN AL EI ADGTYKK
Sbjct: 180 DKYVQYEWLKSKDGSNFEFKGEPVMDSDKIGIAVRKGDTKLRDDLNKALAEIKADGTYKK 239

Query: 240 INDKYFPFSI 249
           INDKYFPFSI
Sbjct: 240 INDKYFPFSI 249


Lambda     K      H
   0.317    0.135    0.392 

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: 311
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: 250
Length of database: 250
Length adjustment: 24
Effective length of query: 226
Effective length of database: 226
Effective search space:    51076
Effective search space used:    51076
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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