GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaE in Kocuria flava HO-9041

Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate WP_058857311.1 AS188_RS01210 phenylacetate-CoA oxygenase/reductase subunit PaaK

Query= metacyc::MONOMER-15950
         (357 letters)



>NCBI__GCF_001482365.1:WP_058857311.1
          Length = 388

 Score =  276 bits (705), Expect = 9e-79
 Identities = 156/374 (41%), Positives = 222/374 (59%), Gaps = 20/374 (5%)

Query: 2   SKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICT 61
           + F+SL + +VR  T D+V +AF VP EL + + +  GQ++ +R ++ G EVRRSYSIC 
Sbjct: 14  ASFNSLEVSQVRRLTADSVEVAFAVPPELVEDYDYLPGQYVALRAEIGGHEVRRSYSICA 73

Query: 62  GVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVEL-------------- 107
               GE+RVAIK+  GG FS +ANE LKAG RL+VM P G F  +L              
Sbjct: 74  EPRPGEIRVAIKKDIGGVFSTWANEQLKAGDRLDVMNPQGAFTSKLRLTSLNDPEKLAAE 133

Query: 108 DAARHGNY--LAVAAGSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLK 165
           + A++ +   +A AAGSGITPI++I K  L     S   L+Y NRS+   +F E+L DLK
Sbjct: 134 EVAKNSSVHLVAFAAGSGITPIMAIAKAVLRASETSTFDLVYANRSAMDVMFAEELGDLK 193

Query: 166 NRYLQRLNLIFLFSREQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETV 225
           ++Y  RL +  + SREQ+   L +GRIDADK  ++    + V   D  F+CGP  + +  
Sbjct: 194 DKYPSRLAVHHVLSREQRISPLMSGRIDADKLNEILDEVVQVDRTDEWFLCGPFELVQLC 253

Query: 226 RDQLKANGMAAERIHFELFAAA--GSAQKREARESAAQDSSVSQ-ITVISDGRELSFELP 282
           RD L A G+  E I FELF      + Q ++ R   A  S  +  I    DG     E P
Sbjct: 254 RDTLAARGVPEESIRFELFTTGRPENPQGQQGRVVEADPSGENYGIEFTLDGLSSRIESP 313

Query: 283 RNS-QSILDAGNAQGAELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSC 341
           +++ +++L+A      ++P++C  GVC TC+ KVV GE EM+ N+ALE  EV AGYVL+C
Sbjct: 314 KSAHETVLNAALRVRPDVPFACAGGVCGTCRAKVVSGEFEMEENYALEKDEVDAGYVLTC 373

Query: 342 QTFPISDKVVLDFD 355
           QT P +D++V+DFD
Sbjct: 374 QTRPTTDELVVDFD 387


Lambda     K      H
   0.319    0.133    0.377 

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: 344
Number of extensions: 12
Number of successful extensions: 3
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: 357
Length of database: 388
Length adjustment: 30
Effective length of query: 327
Effective length of database: 358
Effective search space:   117066
Effective search space used:   117066
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: 49 (23.5 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