GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaE in Dinoroseobacter shibae DFL-12

Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate 3610441 Dshi_3822 phenylacetate-CoA oxygenase/reductase, PaaK subunit (RefSeq)

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



>FitnessBrowser__Dino:3610441
          Length = 356

 Score =  355 bits (910), Expect = e-102
 Identities = 184/358 (51%), Positives = 241/358 (67%), Gaps = 6/358 (1%)

Query: 1   MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60
           M++FH L++ +VR   RDAV +    P +  D F F QGQ+L  R   DG E+RRSYSIC
Sbjct: 1   MARFHPLSVTDVRKTIRDAVVVTLK-PVDGGD-FGFIQGQYLTFRRSFDGTELRRSYSIC 58

Query: 61  TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120
            G +DG L+V IKRV GG FS +AN+SL  G  LE M P G FH  LD     NYLA A 
Sbjct: 59  AGRDDGVLQVGIKRVEGGAFSTWANDSLAPGMTLEAMAPMGSFHTPLDPHTPRNYLAFAG 118

Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180
           GSGITPILSI+KT L  EP SR+TL+Y NR   + +FRE+LEDLKN ++ RL +I +   
Sbjct: 119 GSGITPILSILKTVLAREPGSRLTLVYANRGVNTIMFREELEDLKNLHMGRLTVIHVLES 178

Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240
           + Q++DL+ GR+D  KC  LF+ WID+ ++D AFICGP+ M   +   L+A+GM  +RI 
Sbjct: 179 DAQEIDLFTGRVDGAKCDALFAHWIDIDSIDTAFICGPEPMMLGIAAALRAHGMTDDRIK 238

Query: 241 FELFAAAGSAQKREARESAA---QDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGA 297
           FELFA+    +      +AA    ++  +  TV  DG   SF + ++ QSILDA  A   
Sbjct: 239 FELFASGQPGRLPRKPGAAAGHDPEARATAATVTMDGAARSFAMDKD-QSILDAALANAL 297

Query: 298 ELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFD 355
           + PY+CKAGVCSTCKCKV+EGEVEM +N ALEDYEVA GYVLSCQ++P++D+VV+ +D
Sbjct: 298 DAPYACKAGVCSTCKCKVLEGEVEMIANHALEDYEVARGYVLSCQSYPVTDRVVVTYD 355


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: 376
Number of extensions: 16
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: 356
Length adjustment: 29
Effective length of query: 328
Effective length of database: 327
Effective search space:   107256
Effective search space used:   107256
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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