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 Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF2177 Psest_2220 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__psRCH2:GFF2177
          Length = 585

 Score =  344 bits (883), Expect = 6e-99
 Identities = 216/580 (37%), Positives = 309/580 (53%), Gaps = 55/580 (9%)

Query: 73  GTLNLAANCLDRH-------------LQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119
           G LNLA   +DRH             L+ NG R             + +SY +L R   R
Sbjct: 44  GGLNLAHEAVDRHAAGPRAGYCALRFLERNGSR-------------RELSYLQLKRQTNR 90

Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179
           FAN L +LG+ +G+ + +      E  + +L   + G V S +F  F PE +  R+   +
Sbjct: 91  FANVLAQLGVARGERLFVLCNRGVELYLGVLGGLKNGCVVSPLFAAFGPEPLETRLRLGD 150

Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHD 239
             +++TS+        +  +K V  A     +  ++HV++   +GG        DL  HD
Sbjct: 151 CSVLLTSE--------MLYRKKV--ARLRDRLPLLKHVLLYDESGGHTSIDGTLDL--HD 198

Query: 240 LVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGD 299
           L+  A ++ +     A+ P  + +TSG+TG PKG LH  G  L +  +T +Y  D HP D
Sbjct: 199 LLAAAGEEFKIAPTTADSPSLLHFTSGTTGTPKGALHVHGAALTHY-VTGRYALDLHPDD 257

Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPT 359
           IYWC+AD GWVTG SY +  PL  G T+++  G  +     R   +++K ++++ YTAPT
Sbjct: 258 IYWCSADPGWVTGTSYGILAPLLLGVTSVVDCGEFD---AERWYGILEKERISVWYTAPT 314

Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETG 419
           AIR LM  G +         LR + SVGEP+NPEA  W  + +G    P+ D WWQTETG
Sbjct: 315 AIRMLMKAGPELARRHFHPQLRFVASVGEPLNPEAVWWGKEVLG---LPIHDNWWQTETG 371

Query: 420 GFMITPLPGATELKAGSATRPFFGVQPALVDN--EGN-PLEGATE-GSLVITDSWPGQAR 475
           G MI  +P A  +K GS  +P  GV+ A+V +  +GN    G  E G L +   WPG  R
Sbjct: 372 GIMIANIP-AMPIKPGSMGKPLPGVEAAIVRHGEDGNLTFLGDDEIGELALKQPWPGMFR 430

Query: 476 TLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESA 535
           T  G  ER+ + +   +   Y SGD ARRD DGYYW  GR DDV+  +GH +G  E+ESA
Sbjct: 431 TYLGQEERYRRCFAGDW---YLSGDLARRDADGYYWFIGRSDDVIKSAGHLIGPFEVESA 487

Query: 536 LVAHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDV 595
           L+ H  +AEAAV+G P  + G+ + A+V+L  G E S  L+ E+    RK +G    P  
Sbjct: 488 LMEHSAVAEAAVIGKPDPLLGETVKAFVSLKRGREASEALHDELIGHARKRLGAAVAPKE 547

Query: 596 LHWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADP 635
           L +  SLP+TRSGK+MRR+L+    G     GD STL +P
Sbjct: 548 LEFLASLPRTRSGKLMRRLLKARELGLPE--GDISTLENP 585


Lambda     K      H
   0.317    0.135    0.421 

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: 1085
Number of extensions: 60
Number of successful extensions: 7
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: 652
Length of database: 585
Length adjustment: 37
Effective length of query: 615
Effective length of database: 548
Effective search space:   337020
Effective search space used:   337020
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: 53 (25.0 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
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