Alignments for a candidate for paaZ2 in Azoarcus sp. BH72

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Azoarcus sp. BH72

Align PaaZ protein involved in aerobic phenylacetate metabolism (characterized, see rationale)
to candidate WP_011764034.1 AZO_RS01515 phenylacetic acid degradation protein PaaN

Query= uniprot:Q5P3J4
         (554 letters)



>NCBI__GCF_000061505.1:WP_011764034.1
          Length = 554

 Score =  937 bits (2421), Expect = 0.0
 Identities = 457/554 (82%), Positives = 504/554 (90%)

Query: 1   MTHPLFEKHRATLDAAVQAIRTRGFWTPYPEMPSPKVYGETANEDGKRAVEACFGQDFPL 60
           MTHPL+ KH+ATL+AA+ AI TRG+WTPY EMPSPKVYGETA +DGKRA EAC G+DF L
Sbjct: 1   MTHPLYAKHQATLEAALAAIHTRGYWTPYAEMPSPKVYGETAADDGKRAFEACLGKDFEL 60

Query: 61  DQAGETGRLAPERSPYGTELGVRYPVCSPSALVEAAQAAQDGWQRLGAEGRVGVCLEILE 120
           DQ G +G  A ERSPYG  L VRYPVC PSAL+ AA+AA  GW+++GAEGRVGVCLEIL+
Sbjct: 61  DQPGRSGWAASERSPYGIALDVRYPVCEPSALIAAAEAAMPGWRKIGAEGRVGVCLEILD 120

Query: 121 RLNKRSFEIAHAVMLTSGQGWMMAFQAGGPHAQDRGLEAVAYAWDEMSRIPAETVWEKPQ 180
           RLNKRSFEIAHAVM+T+GQGWMMAFQAGGPHAQDRGLEAVAYAWD M  +PA TVWEKPQ
Sbjct: 121 RLNKRSFEIAHAVMMTTGQGWMMAFQAGGPHAQDRGLEAVAYAWDAMRGVPATTVWEKPQ 180

Query: 181 GKNPPLRMKKHFEIVGRGVALVIGCGTFPTWNTYPGFFAALATGNPVIVKPHEHAILPAA 240
           GKNPPL+M+KH+EIVGRGVALV+GCGTFPTWNTYPG FAALATGNPVIVKPH +AILPAA
Sbjct: 181 GKNPPLKMQKHYEIVGRGVALVVGCGTFPTWNTYPGLFAALATGNPVIVKPHSNAILPAA 240

Query: 241 ITVRIAREVLAEQGLDPNLVSLAVVTKREDTQALATHPAVKSIDFTGGNLFGEWLIDNAR 300
           +TV+IAREVLAE GLDP++VSLAVV KR DTQALATHPAVKSIDFTG N+FG+WLIDNAR
Sbjct: 241 MTVKIAREVLAEAGLDPSVVSLAVVEKRSDTQALATHPAVKSIDFTGSNVFGQWLIDNAR 300

Query: 301 QAQVYAELAGVNNVVVESTDAYKAMLRNLAFTLCLYSGQMCTTTQAILVPAGGIDTDQGH 360
           QAQVYAELAGVNNVV+ESTD YKAMLRNLAFTLCLYSGQMCTTTQAILVPAGGIDTDQGH
Sbjct: 301 QAQVYAELAGVNNVVIESTDNYKAMLRNLAFTLCLYSGQMCTTTQAILVPAGGIDTDQGH 360

Query: 361 KSFDEFASDLAAAIDKTLADPAVATAVLGAIQSADTLRRIDEAGEYGKVVLASRKLEHPE 420
           K +DE A+DL AAIDK L+DPAVATAVLGAIQS  TL RI+EAG+YG +VLAS+K+EHPE
Sbjct: 361 KRYDEVAADLGAAIDKFLSDPAVATAVLGAIQSDATLARINEAGQYGDIVLASKKIEHPE 420

Query: 421 FPNAEVRTPVLLTCDASDEKSYMVERFGPVSFVVRVADADAAVALSERIVREHGALTVGV 480
           FP AEVRTPVLL CDA+ EKSYM ERFGP++FVV+VAD  AAVALSERIVREHGALTVG+
Sbjct: 421 FPQAEVRTPVLLACDAAAEKSYMEERFGPIAFVVKVADGAAAVALSERIVREHGALTVGL 480

Query: 481 YSTKPQVLDAMTAATMHAGAALSINLTGAVFVNQSAAFSDYHGVGMNPAANASYADSAFV 540
           YSTK +V+DAMT AT+ AG ALSINLTG VFVNQSAAFSDYHGVGMNPAANASY+D+AFV
Sbjct: 481 YSTKAEVIDAMTEATLRAGVALSINLTGGVFVNQSAAFSDYHGVGMNPAANASYSDAAFV 540

Query: 541 ANRFRVVQRRYHVE 554
           ANRFRVVQRRYHVE
Sbjct: 541 ANRFRVVQRRYHVE 554


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: 978
Number of extensions: 19
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: 554
Length of database: 554
Length adjustment: 36
Effective length of query: 518
Effective length of database: 518
Effective search space:   268324
Effective search space used:   268324
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)
Rules (tab-delimited)
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