GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Pseudomonas fluorescens FW300-N1B4

Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate Pf1N1B4_924 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein

Query= TCDB::O50181
         (259 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_924
          Length = 258

 Score =  309 bits (791), Expect = 4e-89
 Identities = 155/258 (60%), Positives = 193/258 (74%), Gaps = 2/258 (0%)

Query: 1   MKKLALLGALALSVLSLPT-FAADKPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALCE 59
           MKK  L+  LALS+L+  + FAA+K +RIGIEAAYPPF+ KT  G++ GFD DIGNALC 
Sbjct: 1   MKKFPLITGLALSLLACSSLFAAEKDLRIGIEAAYPPFASKTDKGEIVGFDYDIGNALCA 60

Query: 60  EMKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKEG 119
           +MKV+C WVE EFDGLIP+LKV+KID  LSSMTI ++RK+SVDFT+KYY T +R VMK+G
Sbjct: 61  QMKVKCVWVEGEFDGLIPSLKVKKIDMALSSMTINEDRKKSVDFTHKYYFTSSRLVMKDG 120

Query: 120 ASLNDPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLDAVV 179
           A ++D  A LKGK  GV R +T DRYA+    P G+ V RY + +E  MDL AGRLDA+ 
Sbjct: 121 AVVDDQYASLKGKNIGVQRATTTDRYATEVFEPKGINVKRYGNNEEIYMDLAAGRLDAIF 180

Query: 180 ADSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDALRA 239
           AD++ L D FL    GKGYAFVGP+L D KY GEG GIAVRKG+++L    N AID +RA
Sbjct: 181 ADTIPLSD-FLAMPRGKGYAFVGPELKDPKYVGEGAGIAVRKGNTQLVADLNKAIDEIRA 239

Query: 240 NGKYKQIQDKYFSFDVYG 257
           NG+Y++I  KYF  D+YG
Sbjct: 240 NGEYQKISQKYFKSDIYG 257


Lambda     K      H
   0.316    0.135    0.381 

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: 238
Number of extensions: 8
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: 259
Length of database: 258
Length adjustment: 24
Effective length of query: 235
Effective length of database: 234
Effective search space:    54990
Effective search space used:    54990
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 (21.6 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