GapMind for catabolism of small carbon sources

 

Aligments 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_4400 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein

Query= TCDB::O50181
         (259 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4400 Arginine/ornithine
           ABC transporter, periplasmic arginine/ornithine binding
           protein
          Length = 258

 Score =  338 bits (868), Expect = 5e-98
 Identities = 163/257 (63%), Positives = 201/257 (78%)

Query: 1   MKKLALLGALALSVLSLPTFAADKPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALCEE 60
           M K  LLGALAL   S    A +  +RIGIEAAYPPFS KTP+G ++GFD DIGNALCEE
Sbjct: 1   MNKTELLGALALCAFSFLAHADEDSLRIGIEAAYPPFSFKTPEGNVSGFDYDIGNALCEE 60

Query: 61  MKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKEGA 120
           MKV+C+WV QEFDG+IP+LKVRKIDA+LSSM+IT++R +SVDF+ KYY+TP +F MK G 
Sbjct: 61  MKVKCEWVIQEFDGMIPSLKVRKIDAVLSSMSITEDRMKSVDFSKKYYHTPGKFAMKAGN 120

Query: 121 SLNDPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLDAVVA 180
            +NDP  DLKGKK GV R ST DR+A+ +L  AGV VVRY+SQ EA +DL +GRLDA +A
Sbjct: 121 LINDPLVDLKGKKIGVQRSSTYDRFATEQLEKAGVVVVRYSSQNEAFLDLASGRLDATLA 180

Query: 181 DSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDALRAN 240
           D VN ++ F+KT AG+G+A  GP + D KYFG G GIAVRKGDS    + +AAIDA+RAN
Sbjct: 181 DIVNTDESFIKTPAGQGFALTGPDINDPKYFGRGAGIAVRKGDSANVARLSAAIDAIRAN 240

Query: 241 GKYKQIQDKYFSFDVYG 257
           GKY+Q+  KYF+FD+YG
Sbjct: 241 GKYQQVMAKYFAFDIYG 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: 261
Number of extensions: 9
Number of successful extensions: 1
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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