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 Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate PP_4487 PP_4487 acetyl-CoA synthetase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Putida:PP_4487
          Length = 696

 Score =  951 bits (2459), Expect = 0.0
 Identities = 446/652 (68%), Positives = 536/652 (82%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS    + +   +A   L +   Y+AMYQQS+  PD FW EQ + +DWIKP+ KVK TSF
Sbjct: 44  MSAAPLYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSF 103

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
              +V IKW+ DGTLN+++NCLDRHL+E GD+ AIIWEGDD S+ ++I+Y+ELH  VC+F
Sbjct: 104 DDHHVDIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEHRNITYRELHEQVCKF 163

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN L    + +GDVV IYMPM+PEA VAMLACARIGA+HSV+FGGFSPEA+AGRIID  S
Sbjct: 164 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKS 223

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           ++VIT+DEGVR GR  PLK NVD AL NP  +SV+ ++V KRTGG I W + RD+W+ DL
Sbjct: 224 KVVITADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDL 283

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
           ++ AS     +EM AE+ LFILYTSGSTGKPKGVLHTTGGYLVYAALT + VFDY PG++
Sbjct: 284 MKVASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEV 343

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGWVTGHSY++YGPLA GATTL+FEGVPN+P   R++++VDKH+VNILYTAPTA
Sbjct: 344 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTA 403

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRA+MAEG  A+EG D SSLR+LGSVGEPINPEAW WY+K +G E+CP+VDTWWQTETGG
Sbjct: 404 IRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGG 463

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
            +I+PLPGAT LK GSATRPFFGV PALVDN GN ++GA EG+LVI DSWPGQ+R+L+GD
Sbjct: 464 ILISPLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGD 523

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           H+RF  TYF TF+ MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESA+VAH 
Sbjct: 524 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHS 583

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           K+AEAAVVG+PH+IKGQ IY YVTLN G E S +L  E++NWVRKEIGP+A+PDV+ W  
Sbjct: 584 KVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASEQLRLELKNWVRKEIGPIASPDVIQWAP 643

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652
            LPKTRSGKIMRRILRKIA G+   LGD STLADPGVV+ L++  +A+ + S
Sbjct: 644 GLPKTRSGKIMRRILRKIATGEYDALGDISTLADPGVVQHLIDTHKAMNLAS 695


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: 1570
Number of extensions: 66
Number of successful extensions: 1
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: 696
Length adjustment: 39
Effective length of query: 613
Effective length of database: 657
Effective search space:   402741
Effective search space used:   402741
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.

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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
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