GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Marinobacter adhaerens HP15

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate GFF55 HP15_55 enoyl-CoA hydratase/isomerase

Query= BRENDA::Q5SLK3
         (254 letters)



>FitnessBrowser__Marino:GFF55
          Length = 266

 Score =  164 bits (414), Expect = 2e-45
 Identities = 96/256 (37%), Positives = 146/256 (57%), Gaps = 9/256 (3%)

Query: 5   ERQDGVLVLTLNRPEKLNAITGEL-LDALYAALKEGEEDREVRALLLTGAGRAFSAGQDL 63
           ER   V V+ +N PE  NA+T E  ++ +     E + D+ +RA++LTG G+AF AG ++
Sbjct: 8   ERLGNVAVVRMNSPETHNALTTESQINEIVDLCAEVKADKSIRAMVLTGTGKAFCAGGNI 67

Query: 64  TEFGDRKPDY--------EAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDL 115
            +   R+  +        + +     ++   L  L+ P++ AVNG A GAG+ LA   D+
Sbjct: 68  KDMQKRQGIFAGSPYDLRDVYRNGIQKIPLCLYELDIPVIAAVNGHAIGAGLDLACMCDI 127

Query: 116 RLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHR 175
           R+A+  A F  +FV++G+VP  G ++LLPR+VG+ KA  +      + AE+AL+ GLV +
Sbjct: 128 RIASNNAKFAESFVKLGIVPGDGGAWLLPRIVGIPKASLMAFTGETIGAEQALSWGLVEQ 187

Query: 176 VVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQD 235
           V   ++L  EAL LA+ +A+ P  A  L K+LL E   + L   L L A  Q  A  TQD
Sbjct: 188 VCAPDELDAEALGLAQRIAENPGHALRLCKRLLREGQHMRLDSLLELSAAYQSLAHHTQD 247

Query: 236 HEEGVRAFREKRPPRF 251
           H+E V +F EKR P F
Sbjct: 248 HQEAVDSFVEKRKPNF 263


Lambda     K      H
   0.318    0.135    0.371 

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: 151
Number of extensions: 7
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: 254
Length of database: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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