GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Pseudomonas fluorescens FW300-N2E3

Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate AO353_04645 AO353_04645 ABC transporter substrate-binding protein

Query= TCDB::O50181
         (259 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_04645 AO353_04645 ABC
           transporter substrate-binding protein
          Length = 258

 Score =  322 bits (826), Expect = 4e-93
 Identities = 160/258 (62%), Positives = 202/258 (78%), Gaps = 2/258 (0%)

Query: 1   MKKLALLGALALSVLSLPT-FAADKPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALCE 59
           MKKL L+G LALS+L+  + FAA+K +RIGIEAAYPPF+ KT DG++ GFD DIGNALC 
Sbjct: 1   MKKLPLIGGLALSLLACSSLFAAEKTLRIGIEAAYPPFASKTSDGKITGFDYDIGNALCA 60

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

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

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

Query: 240 NGKYKQIQDKYFSFDVYG 257
           NG+Y++I+ KYF  D+YG
Sbjct: 240 NGEYQKIEAKYFKSDIYG 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: 246
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.

Links

Downloads

Related tools

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 paper from 2022 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