GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Marinomonas arctica 328

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_111606971.1 DK187_RS08770 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>NCBI__GCF_003259225.1:WP_111606971.1
          Length = 250

 Score =  117 bits (292), Expect = 3e-31
 Identities = 70/239 (29%), Positives = 123/239 (51%), Gaps = 5/239 (2%)

Query: 18  VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRA 77
           VL L+    +NA+  DMY A   AL S E +  ++  ++ G    F +G ++N  + + A
Sbjct: 15  VLCLNRTDKKNAITLDMYQALTNALRSAEHNDQVKVTMLYGLGGDFSSGNDINEFV-HIA 73

Query: 78  KDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVMS 137
           + P    + ++ +  ++  L    KP+IA V+G A G G ++ L CDL++A+ +A+    
Sbjct: 74  QTP----EKMEAIMAFLQVLSCYKKPLIAGVEGRAVGVGATMLLHCDLVLASREARLQFP 129

Query: 138 YARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAAV 197
           + ++GL P+   S  L Q +  Q A E+L+ G+ + A + HE+G+VN L + G A   A+
Sbjct: 130 FVQLGLVPEAASSHLLPQLVGHQKAFEILVLGEVVSATQAHEMGLVNHLCEEGEAYKLAL 189

Query: 198 AWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEK 256
            +A  +  +   +VA  K L+   G   +   L+ E   F   L   E  +  +AFL +
Sbjct: 190 FYAQRIAALPVEAVALSKDLLKFRGQDDVQMALMREGRIFKDRLRSTEAHQAFTAFLSR 248


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: 115
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: 250
Length adjustment: 24
Effective length of query: 238
Effective length of database: 226
Effective search space:    53788
Effective search space used:    53788
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 24 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