GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Marinobacter adhaerens HP15

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate GFF4154 HP15_4094 enoyl-CoA hydratase/isomerase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__Marino:GFF4154
          Length = 264

 Score =  134 bits (336), Expect = 3e-36
 Identities = 81/257 (31%), Positives = 128/257 (49%)

Query: 1   MSAELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGAD 60
           M+  L+T+          LT + P A NA++  +  A + A++ +     +R +V+ GA 
Sbjct: 1   MTDTLVTTAFDAGTGVARLTFNRPEALNAINVPLAEAFLAAVEHINSLSGVRCIVLAGAG 60

Query: 61  NFFCAGGNLNRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLA 120
             F AGG+++ +     +        +D +   I  LR    PVIAAV G AAGAG SL 
Sbjct: 61  RAFMAGGDVSSMAGTSEQAGKAIGAILDAVNPAILLLRSMDAPVIAAVRGVAAGAGLSLT 120

Query: 121 LACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHEL 180
           L  DL++A +DAKF+++Y  +G  PD GGSW LA  L    A E+++ G+ + A    + 
Sbjct: 121 LMADLVIAEEDAKFLVAYNGIGAVPDCGGSWALAHKLGAGRAAELMLLGRTLNAGEAKDW 180

Query: 181 GVVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVAS 240
           G+VN++              +++ K    +    + L+  A    L+ HL AER  F+  
Sbjct: 181 GMVNEVVPASEFESRVNRMIEKVAKGPTRAFGAFRQLIDRANGDRLAAHLEAERVAFLEM 240

Query: 241 LHHREGLEGISAFLEKR 257
               +  EG+SAFL KR
Sbjct: 241 TRTEDFAEGVSAFLAKR 257


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: 136
Number of extensions: 6
Number of successful extensions: 1
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: 264
Length adjustment: 25
Effective length of query: 237
Effective length of database: 239
Effective search space:    56643
Effective search space used:    56643
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