Aligments for a candidate for prpE in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for prpE in Pseudomonas putida KT2440

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate PP_3553 PP_3553 AMP-binding domain protein

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Putida:PP_3553
          Length = 540

 Score =  416 bits (1068), Expect = e-120
 Identities = 223/536 (41%), Positives = 318/536 (59%), Gaps = 5/536 (0%)

Query: 10  EGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGF 69
           +G+ P    +  LTPL F+ER    + +  AV++   R  +   Y      ASAL  RG 
Sbjct: 6   QGLMPAAVNHVALTPLSFIERTAAVYGNYPAVIHGAIRRNWQETYQRCRRLASALAGRGI 65

Query: 70  SREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY 129
            R D ++ +  N P  LE+ FGVP  G VL  +N RL  + +A+++ H ++K ++ D  +
Sbjct: 66  GRGDTVAVMLPNTPTMLEAHFGVPMTGAVLNTLNVRLDAEAIAFMLQHGEAKVLITDREF 125

Query: 130 LNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSM 189
            ++++E    +     L+ D D+P   E  R   ++ Y  L+  G  +       +E+  
Sbjct: 126 -HAVIEGALALLEHPPLVVDVDDPEYGE-GRAVSQLDYEALLNEGDPEFAWEWPDDEWQA 183

Query: 190 ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWAT 249
           I+L YTSGTTG PKGV++HHRGA+LNA+   +   M    VYLWTLPMFH   W + W  
Sbjct: 184 ISLNYTSGTTGNPKGVVYHHRGAYLNALGNQMTWAMGHRPVYLWTLPMFHCNGWCYPWTI 243

Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309
            A+  T+V L +VD   I  L+ + +V+H+C AP V   L +  +       + V  +VA
Sbjct: 244 TALAGTHVFLRRVDPQKILTLIREHKVSHLCGAPIVLNALVNMPEAAKAAIEHPVQAMVA 303

Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369
           GAAP    + A++++G  + H YGLTE YGP ++C W  EWD+L LEE+A++K+RQG+ Y
Sbjct: 304 GAAPPAKVIGAVEQMGIKVTHTYGLTEVYGPVTVCAWHDEWDALSLEERARIKSRQGVRY 363

Query: 370 VSFE--MDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427
            + +  M       +PVP DG T+GE+ MRG+ V  GY KNPE TAE+FR GWFH+GD A
Sbjct: 364 PTLDGLMVADPQTLQPVPRDGDTLGEIFMRGNTVMKGYLKNPEATAEAFRGGWFHTGDLA 423

Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487
           V H DGYIEI DR KD+I +GGE +S+I VE  L +   V   AV   PDEKWGE   A 
Sbjct: 424 VWHADGYIEIKDRLKDIIISGGENISTIEVEDALYKHSAVLEAAVVARPDEKWGETPCAF 483

Query: 488 IELQEGVKLTEE-EVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKA 542
           + L+ G + T E ++  +C+E LA F+ PK V FG +P T+TGK+QKYVLR+ AKA
Sbjct: 484 VALKPGREDTREADITSWCREHLAGFKVPKTVVFGELPKTSTGKIQKYVLRDRAKA 539


Lambda     K      H
   0.319    0.136    0.411 

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: 778
Number of extensions: 40
Number of successful extensions: 4
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: 549
Length of database: 540
Length adjustment: 35
Effective length of query: 514
Effective length of database: 505
Effective search space:   259570
Effective search space used:   259570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources