GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_3856 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)

Query= TCDB::Q9HU31
         (250 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3856
           Lysine-arginine-ornithine-binding periplasmic protein
           precursor (TC 3.A.1.3.1)
          Length = 251

 Score =  390 bits (1003), Expect = e-113
 Identities = 186/251 (74%), Positives = 218/251 (86%), Gaps = 1/251 (0%)

Query: 1   MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60
           M+ Y+K LLAAA +L F+  A A +KL++G E AYPPFN  DASGQ VGFD DIG ALCA
Sbjct: 1   MQTYRKFLLAAAVSLVFSTSAMAVEKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCA 60

Query: 61  KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120
           KMK ECEVVTS+WDGIIPAL AKKFDF+++S+S+ DERKQAVDFTDPYY+NKLQF+APK+
Sbjct: 61  KMKVECEVVTSNWDGIIPALMAKKFDFLISSLSVNDERKQAVDFTDPYYSNKLQFIAPKN 120

Query: 121 VDFKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLA 180
           VDFK DK+SLKGKVIGAQR+T+AGTWLED +   +T KLYDTQENAYLDL+SGR+D +LA
Sbjct: 121 VDFKVDKESLKGKVIGAQRSTLAGTWLEDELGSDITAKLYDTQENAYLDLTSGRVDAILA 180

Query: 181 DKFVQYDWLKSDAGKEFEFKGEPVFDNDKIGIAVRKG-DPLREKLNAALKEIVADGTYKK 239
           DK+V YDWLK++AG+ +EFKG+PV + DKI IAVRKG D LR KLNAALKEI+ADGTYKK
Sbjct: 181 DKYVNYDWLKTEAGRAYEFKGDPVVEGDKIAIAVRKGNDELRNKLNAALKEILADGTYKK 240

Query: 240 INDKYFPFSIY 250
           INDKYFPFSIY
Sbjct: 241 INDKYFPFSIY 251


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: 309
Number of extensions: 10
Number of successful extensions: 2
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: 251
Length adjustment: 24
Effective length of query: 226
Effective length of database: 227
Effective search space:    51302
Effective search space used:    51302
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 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