Alignments for a candidate for prpE in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pseudomonas stutzeri RCH2

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF2396 Psest_2444 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__psRCH2:GFF2396
          Length = 544

 Score =  213 bits (541), Expect = 2e-59
 Identities = 152/502 (30%), Positives = 242/502 (48%), Gaps = 25/502 (4%)

Query: 47  RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRL 106
           RY Y+         AS L + G    D +S ++ N     E FF VP  G VL   N RL
Sbjct: 40  RYDYACLAARSAQAASMLGKLGIGPGDCVSSLAWNTHRHYELFFAVPGIGAVLHTANPRL 99

Query: 107 SPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMT 166
           S +++ Y INH+ S+ ++ D  +   +  ++ ++      +E    PS+      +  + 
Sbjct: 100 SDEQIVYTINHAGSQVLLFDSSFAACVARLRPRLGNIRHFIELAAQPSSG----LQDVLG 155

Query: 167 YRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMD 226
           Y +L+   +  PL  P  +E +   L YTSGTTG PKGV++ HR   L+AMA  L     
Sbjct: 156 YEQLI--AAEQPLDWPQFDENAGAVLCYTSGTTGDPKGVLYSHRSVVLHAMAAGLSGAFG 213

Query: 227 LNSVYLWTLP---MFHAASWGFSWATVAVGATNVC-LDKVDYPLIYRLVEKERVTHMCAA 282
           L S +   +P   ++H  +WG  +A    G   V   DK+D   +  L++ E VT     
Sbjct: 214 L-SAFDCIMPCSSLYHGTAWGIPFAAAINGCKFVLPCDKMDGASLQELIKTEGVTLSGGV 272

Query: 283 PTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQ-EIGGYMCHVYGLTETYGPH 341
           PT++     +++R+     +   +++ G+A   A  +  Q + G  +C ++G+TET  P 
Sbjct: 273 PTIWTMYLAHLERSGEDSGSLARLVIGGSAVPRAMAETFQTKYGVAVCQLWGMTET-SPL 331

Query: 342 SICEWRREWDSLPLEEQAK------LKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVV 395
            +        +  L E+ +      +  RQG      E+ + D  G+ +P DG + G + 
Sbjct: 332 GVVAT----PTPKLAERGQQATNDTIWTRQGRLQFGIELKIVDEEGRELPCDGVSSGSLK 387

Query: 396 MRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSI 455
           +RG      YY++ +   +   DGWF +GD A +  DG++ I DR KD+I +GGE VSSI
Sbjct: 388 VRGPWTVERYYRSEKSALDE--DGWFDTGDIATLDADGFMRITDRSKDVIKSGGEWVSSI 445

Query: 456 LVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECP 515
            +E      PGVK  AV G    KW E     IE     ++T E ++   +  +  +  P
Sbjct: 446 DIENVAAACPGVKVAAVVGVFHPKWEERPVLVIEPHADAEVTVETILAHLEPNIVKWWMP 505

Query: 516 KIVEFGPIPMTATGKMQKYVLR 537
             V F  +P+TATGK+ K VLR
Sbjct: 506 DAVIFDAVPLTATGKIDKKVLR 527


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: 656
Number of extensions: 30
Number of successful extensions: 5
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: 544
Length adjustment: 36
Effective length of query: 513
Effective length of database: 508
Effective search space:   260604
Effective search space used:   260604
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.

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

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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:

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
the source code
instructions for running GapMind on your computer

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