GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Pseudomonas fluorescens FW300-N2E2

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834
          Length = 256

 Score =  146 bits (369), Expect = 4e-40
 Identities = 91/261 (34%), Positives = 141/261 (54%), Gaps = 8/261 (3%)

Query: 1   MSAELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGAD 60
           MSA ++  R   + +  +L L+    RNAL   M  A   A+  +ERD  +  +VITG D
Sbjct: 1   MSAPVVVER---NGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGD 57

Query: 61  NFFCAGGNLNRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLA 120
           + F AG +LN L++  A+    Q   +DL   W    + S KP+IAAV G A GAG  LA
Sbjct: 58  SVFAAGADLNLLVDKGAQ----QVAELDLGQYWAPVAK-SQKPLIAAVSGFALGAGCELA 112

Query: 121 LACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHEL 180
           + CD++VA + A+F    ARVG+ P  GG+  L +A+ + +A+ +L+ G+ + A R  +L
Sbjct: 113 MMCDILVADNSARFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQL 172

Query: 181 GVVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVAS 240
           G+V++L   G+A   A+  A     + P ++  IK ++     Q L   L  E   F+  
Sbjct: 173 GLVSELVTEGSALARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLL 232

Query: 241 LHHREGLEGISAFLEKRAPVY 261
              ++  EG+ AFL+KR P Y
Sbjct: 233 FDTQDKTEGMRAFLDKRPPRY 253


Lambda     K      H
   0.317    0.132    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: 149
Number of extensions: 5
Number of successful extensions: 2
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: 262
Length of database: 256
Length adjustment: 24
Effective length of query: 238
Effective length of database: 232
Effective search space:    55216
Effective search space used:    55216
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