GapMind for Amino acid biosynthesis

 

Alignments 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 Aug 03 2021. The underlying query database was built on Aug 03 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