Alignments for a candidate for prpE in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Pseudomonas putida KT2440

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate PP_2351 PP_2351 propionyl-CoA synthetase

Query= reanno::Phaeo:GFF1175
         (629 letters)



>FitnessBrowser__Putida:PP_2351
          Length = 629

 Score =  697 bits (1800), Expect = 0.0
 Identities = 332/625 (53%), Positives = 432/625 (69%)

Query: 1   MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60
           MSY   Y    ++P  FW E A  ++W   P   L D  DG + WFAD R+N+CY A+D 
Sbjct: 1   MSYQHSYAHSISDPAAFWAEQAAHLAWHRKPALTLQDNADGTHRWFADGRLNSCYLALDH 60

Query: 61  HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120
            +EQGRGEQ A+IYDSP+T  ++  +Y +LR+ VA LAG LR  GV KGD VIIYMPM+P
Sbjct: 61  QIEQGRGEQLALIYDSPVTGVQQTYTYNQLRDEVARLAGLLRQLGVNKGDGVIIYMPMVP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180
           +A  AMLACAR+GAVHSVVFGGFAANELA+RIDDA P  ++ ASCGLE  R + YKPL+D
Sbjct: 121 QAAMAMLACARIGAVHSVVFGGFAANELALRIDDARPTLLLTASCGLEFDRVIAYKPLVD 180

Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
            A+ LA H+P   ++ QR Q  AEL+ GRD++W       EP   V ++   P YI+YTS
Sbjct: 181 RALQLARHQPRNVLVLQRPQAHAELLPGRDLDWQAALADAEPVAPVELDAGDPLYIMYTS 240

Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTG+PKG++R   G  VAL + M++IY +  GDV+W  SDVGWVVGHS I YGPL+ G 
Sbjct: 241 GTTGKPKGIVRENGGNAVALCYAMRHIYGMQAGDVWWGISDVGWVVGHSLIVYGPLMSGC 300

Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360
           TT+ +EGKPI TPDA  +WRV+ +++V + F APTA RA+++EDP+G+ ++K+DLS L+Q
Sbjct: 301 TTVFYEGKPIRTPDASAYWRVVEQYRVNALFCAPTAMRAIRKEDPEGDLIRKHDLSSLRQ 360

Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420
           ++LAGE+ D  T  W +     PV DHWWQTETGW + A  +G+E    K GS    +PG
Sbjct: 361 LFLAGEKLDSSTHEWLERVSGKPVHDHWWQTETGWPVTAPCVGLEGSAAKPGSSNRAVPG 420

Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480
           Y V +LD+ GH +     G+I + LPLPPG   TLW   +R+ ++YL T+PGYY TGD G
Sbjct: 421 YNVRVLDDEGHLLGANHQGSIVIALPLPPGCSQTLWGDHERYLQAYLRTYPGYYHTGDGG 480

Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540
             D+DG++YIM RTDDVINV+GHRLSTG ME+++A HP VAECAVIGV D +KGQ P+  
Sbjct: 481 YLDDDGFVYIMGRTDDVINVSGHRLSTGEMEDLVARHPAVAECAVIGVHDEIKGQVPLAL 540

Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600
           + L  G       ++ ++V  VRE+IGP+A F    +V RLPKTRSGKILR  +  IADG
Sbjct: 541 VVLKDGEGIAEAQLLVELVGSVREEIGPLACFNRVRLVKRLPKTRSGKILRAVLRKIADG 600

Query: 601 TDWKMPATIDDPAILDEITTALQGL 625
            D+  P+T+DDPA+L EI   L  L
Sbjct: 601 QDYVPPSTLDDPAVLGEIEAVLADL 625


Lambda     K      H
   0.318    0.137    0.428 

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: 1264
Number of extensions: 55
Number of successful extensions: 3
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: 629
Length of database: 629
Length adjustment: 38
Effective length of query: 591
Effective length of database: 591
Effective search space:   349281
Effective search space used:   349281
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis