Alignments for a candidate for prpE in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Azohydromonas australica DSM 1124

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028997690.1 H537_RS0109260 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000430725.1:WP_028997690.1
          Length = 656

 Score = 1014 bits (2623), Expect = 0.0
 Identities = 483/649 (74%), Positives = 557/649 (85%), Gaps = 1/649 (0%)

Query: 12  RVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAP 71
           +++ P    A  A +  MEAYQAL  EAE DYEG+W R A+ELL W +PFT+VLD SNAP
Sbjct: 7   KLYQPDAETAKSAYVAGMEAYQALVAEAEADYEGYWGRLAKELLSWKQPFTQVLDSSNAP 66

Query: 72  FYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLK 131
           F+KWF DG+LNASYNCLDRN++NG  DK AI+FEAD G VT+VTY++L  + CR AN LK
Sbjct: 67  FFKWFADGKLNASYNCLDRNVENGKGDKTAIIFEADGGEVTKVTYKDLLERTCRLANALK 126

Query: 132 ALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALIT 191
           A G++KGDRVVIY+ MS++GV AMQACAR+GATHSVVFGGFSA+SL++R+ D GA  +IT
Sbjct: 127 AQGVKKGDRVVIYIAMSIDGVAAMQACARIGATHSVVFGGFSAQSLRDRIEDTGAKLIIT 186

Query: 192 ADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQP 251
           AD Q+RGGK LPLKAI D+AL+LGGC++V+ V+V +R+G  VA TEGRD WM++  AGQ 
Sbjct: 187 ADHQVRGGKQLPLKAIVDEALSLGGCDSVQKVLVVKRSGAGVAMTEGRDVWMDEALAGQD 246

Query: 252 DTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTA 311
             CE E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLL A +T KWTFD+K DD+FWCTA
Sbjct: 247 AVCEPEWVEAEHPLFLLYTSGSTGKPKGVQHSTGGYLLHAALTTKWTFDLKDDDVFWCTA 306

Query: 312 DIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLI 371
           DIGWVTGHTYI YGPLA G T++VFEGVPTYP+AGRFW MI  HKV++FYTAPTAIRSLI
Sbjct: 307 DIGWVTGHTYITYGPLALGGTEIVFEGVPTYPDAGRFWKMIQDHKVTVFYTAPTAIRSLI 366

Query: 372 KAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGH 431
           KAAE++E +HPK YDLSSLR+LG+VGEPINP AW WY++++G  RCPIVDTFWQTETGGH
Sbjct: 367 KAAESNEAVHPKSYDLSSLRILGSVGEPINPAAWEWYHQHVGGGRCPIVDTFWQTETGGH 426

Query: 432 MITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDP 491
           MITPLPGATPLVPGSCTLP PGI AA+VDETG +VP G GGILVVK+PWP+MIRTIWGDP
Sbjct: 427 MITPLPGATPLVPGSCTLPFPGIQAAVVDETGKEVPWGQGGILVVKKPWPSMIRTIWGDP 486

Query: 492 ERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVS 551
           ERF+KSY+PE+  G+LYLAGDG+IRD  TGYFTI GRIDDVLNVSGHRMGTMEIESALVS
Sbjct: 487 ERFKKSYYPEDFKGQLYLAGDGAIRDAKTGYFTITGRIDDVLNVSGHRMGTMEIESALVS 546

Query: 552 -NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPK 610
              LVAEAAVVGRPDD TGEAICAFVVLKR RP+G+EA  IA +LR+ + KEIGPIAKPK
Sbjct: 547 CTELVAEAAVVGRPDDTTGEAICAFVVLKRPRPSGDEAKAIAKQLRDHIAKEIGPIAKPK 606

Query: 611 DIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           DIRFGDNLPKTRSGKIMRRLLRS+AK E +TQDTSTLENPAIL+QL QA
Sbjct: 607 DIRFGDNLPKTRSGKIMRRLLRSVAKNEAVTQDTSTLENPAILDQLGQA 655


Lambda     K      H
   0.319    0.136    0.422 

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: 1524
Number of extensions: 75
Number of successful extensions: 2
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: 660
Length of database: 656
Length adjustment: 38
Effective length of query: 622
Effective length of database: 618
Effective search space:   384396
Effective search space used:   384396
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: 54 (25.4 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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