GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ2 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:

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:

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:

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:

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