Alignments for a candidate for paaZ2 in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Dechloromonas agitata is5

Align PaaZ protein involved in aerobic phenylacetate metabolism (characterized, see rationale)
to candidate WP_027456475.1 K420_RS0101390 phenylacetic acid degradation protein PaaN

Query= uniprot:Q5P3J4
         (554 letters)



>NCBI__GCF_000519045.1:WP_027456475.1
          Length = 555

 Score =  836 bits (2159), Expect = 0.0
 Identities = 405/555 (72%), Positives = 468/555 (84%), Gaps = 2/555 (0%)

Query: 1   MTHPLFEKHRATLDAAVQAIRTRGFWTPYPEMPSPKVYGETANEDGKRAVEACFGQDFPL 60
           M+HPL EKHRATLD A+ AI TRG+W+ Y EMPSPK YGETA EDGK+A EA  G+ F L
Sbjct: 1   MSHPLLEKHRATLDGALNAIATRGYWSAYNEMPSPKTYGETAAEDGKKAFEAHLGRQFVL 60

Query: 61  DQAGETGRLAPERSPYGTELGVRYPVCSPSALVEAAQAAQDGWQRLGAEGRVGVCLEILE 120
           +Q G+TG    E+SPYG E+G++YPVC   AL+ A Q A  GWQ++GA GR G+CLEIL+
Sbjct: 61  EQPGQTGWAGGEQSPYGIEMGIQYPVCDHEALIAAGQQAMAGWQKVGAAGRTGICLEILD 120

Query: 121 RLNKRSFEIAHAVMLTSGQGWMMAFQAGGPHAQDRGLEAVAYAWDEMSRIPAETVWEKPQ 180
           RLNK+SFE+AHAVM+T+GQGWMMAFQAG PHAQDRGLEAVAYAW E S +PAETVW+KPQ
Sbjct: 121 RLNKQSFELAHAVMMTTGQGWMMAFQAGSPHAQDRGLEAVAYAWREQSFVPAETVWDKPQ 180

Query: 181 GKNPPLRMKKHFEIVGRGVALVIGCGTFPTWNTYPGFFAALATGNPVIVKPHEHAILPAA 240
           GKNPPL MKKHFEIVG+GV +V+GCGTFPTWNTYPG FAAL+TGN VIVKPH +AILPAA
Sbjct: 181 GKNPPLVMKKHFEIVGQGVGVVVGCGTFPTWNTYPGLFAALSTGNAVIVKPHSNAILPAA 240

Query: 241 ITVRIAREVLAEQGLDPNLVSLAVVTKREDTQALATHPAVKSIDFTGGNLFGEWLIDNAR 300
           ITVR  R VLAE G+DPNLV+L V + R  TQ L TH AVKSIDFTGGN+FG+WL+DN R
Sbjct: 241 ITVRTIRAVLAENGIDPNLVTLCVASDRATTQKLVTHSAVKSIDFTGGNVFGQWLVDNCR 300

Query: 301 QAQVYAELAGVNNVVVESTDAYKAMLRNLAFTLCLYSGQMCTTTQAILVPAGGIDTDQGH 360
           QA+VYAELAGVNN+V++STDAYK MLRNLAFTL LYSGQMCTT+QAI VPAGGIDT+ GH
Sbjct: 301 QARVYAELAGVNNIVIDSTDAYKPMLRNLAFTLSLYSGQMCTTSQAIFVPAGGIDTEDGH 360

Query: 361 KSFDEFASDLAAAIDKTLADPAVATAVLGAIQSADTLRRID--EAGEYGKVVLASRKLEH 418
           KS+D+  +DLA A+   LA P VA AVLGA+QSADTL+RI+  ++G  GKVVLAS KLE+
Sbjct: 361 KSYDDVCADLAKAVSGFLAKPEVAHAVLGAVQSADTLKRIEMADSGTLGKVVLASTKLEN 420

Query: 419 PEFPNAEVRTPVLLTCDASDEKSYMVERFGPVSFVVRVADADAAVALSERIVREHGALTV 478
           PEFP A VRTPVLL CDA+DE +YM ERFGP+SF+V+VAD  A +ALSERIV  HGALT 
Sbjct: 421 PEFPKATVRTPVLLACDAADEHAYMEERFGPISFIVKVADTAAGIALSERIVATHGALTA 480

Query: 479 GVYSTKPQVLDAMTAATMHAGAALSINLTGAVFVNQSAAFSDYHGVGMNPAANASYADSA 538
           G+YSTKP+V+DAMTAATM +  ALSINLTG VFVNQSAA+SDYHG G NPAANASYAD+A
Sbjct: 481 GIYSTKPEVIDAMTAATMRSKVALSINLTGGVFVNQSAAYSDYHGTGGNPAANASYADAA 540

Query: 539 FVANRFRVVQRRYHV 553
           FVANRF VVQRRYH+
Sbjct: 541 FVANRFVVVQRRYHI 555


Lambda     K      H
   0.319    0.133    0.395 

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: 917
Number of extensions: 25
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: 554
Length of database: 555
Length adjustment: 36
Effective length of query: 518
Effective length of database: 519
Effective search space:   268842
Effective search space used:   268842
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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