Alignments for a candidate for paaZ1 in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ1 in Amycolatopsis halophila YIM 93223

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_034268231.1 AMYHA_RS04460 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_000504245.1:WP_034268231.1
          Length = 679

 Score =  646 bits (1667), Expect = 0.0
 Identities = 345/678 (50%), Positives = 447/678 (65%), Gaps = 13/678 (1%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L S++SG W +       +H A +GE +  V++ G+DMAAA  +    G  ALR +TF +
Sbjct: 7   LRSYVSGDWHTPADAGTPVHDATTGEEIARVSTTGIDMAAALDYGRRVGGAALRELTFHQ 66

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           R A+LKA+A HL   ++  Y LSA+TGAT  DS  DI+GGIG LFTY+S G RELP+DT+
Sbjct: 67  RGALLKALASHLREHRDELYTLSAKTGATLGDSKFDIDGGIGVLFTYSSKGRRELPNDTV 126

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
           + E  + PLSK G F  +H+L+   GVAV INAFNFP WG LEK AP +L GMP+++KPA
Sbjct: 127 YAEGAVEPLSKGGTFVGQHILSPMRGVAVQINAFNFPVWGPLEKFAPAFLAGMPSLVKPA 186

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
           + TA LT  +V+ IV+SG++PEG++ L+CGSAGDLLDH+ +QDVV+FTGSA+T   LR  
Sbjct: 187 SQTAYLTHRLVELIVESGILPEGSLQLVCGSAGDLLDHVTAQDVVSFTGSASTASQLRAH 246

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           P+IV  ++ F  EADSLN  +LG D     PEF L+I+++V EMT KAGQKCTAIRR  V
Sbjct: 247 PSIVRNAVRFNAEADSLNLSILGPDAAQGTPEFDLYIKQLVTEMTVKAGQKCTAIRRAFV 306

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLG 363
           P  L++ V+ A   RL KV VG+P  +GV+MGAL + EQR +V+  +  L+  G  +   
Sbjct: 307 PAELMDDVAAAASERLAKVTVGNPTSDGVRMGALASLEQREEVRRSLKSLMDVGTVVYGD 366

Query: 364 -GQADLSAA----GAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418
             Q D+  A    GAF  P LL    P E    H  EAFGPVATL+P  +    ++LA  
Sbjct: 367 PEQVDVVDADVERGAFISPVLLRVDDP-ERAEPHQVEAFGPVATLIPYTSTEQVIELAAK 425

Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478
           G GSL G++VT D   AR+ +   A  HGR+ +L+ + AKESTGHGSPLP LVHGGPGRA
Sbjct: 426 GEGSLVGSVVTGDAAFAREVVLGVAPWHGRLLVLDTDDAKESTGHGSPLPGLVHGGPGRA 485

Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGD 538
           GGGEE+GGL  VKH+MQRTAVQ SPT+L  ++ QWV GA   E   HPFRK   EL+ GD
Sbjct: 486 GGGEEMGGLNGVKHHMQRTAVQASPTVLTKVTGQWVPGAPRTEG-THPFRKSLAELRVGD 544

Query: 539 SLLTPRRTMTEADIVNFACLSGDHFYAHMD-KIAAAESIFGERVVHGYFVLSAAAGLFVD 597
           +++   R +T  DI +FA  +GD FYAH D + AAA  +FG  V HGY V+S AAGLFV 
Sbjct: 545 TVVAGPRQVTREDIAHFAEFTGDTFYAHTDEEAAAANPLFGGIVAHGYLVVSFAAGLFVA 604

Query: 598 AGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFN 657
              GPV+ANYGLE+LRF+ PVK GD + V LT K+   +     E    G V W  +V N
Sbjct: 605 PEPGPVLANYGLENLRFLTPVKAGDELTVTLTAKQIIPR-----ENADYGEVRWDTDVTN 659

Query: 658 QHQTPVALYSILTLVARQ 675
                VA Y +LTLV+++
Sbjct: 660 ADGESVAKYDVLTLVSKE 677


Lambda     K      H
   0.319    0.134    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: 1117
Number of extensions: 53
Number of successful extensions: 5
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: 681
Length of database: 679
Length adjustment: 39
Effective length of query: 642
Effective length of database: 640
Effective search space:   410880
Effective search space used:   410880
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: 54 (25.4 bits)

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

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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

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