GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Dinoroseobacter shibae DFL-12

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate 3608351 Dshi_1753 Enoyl-CoA hydratase/isomerase (RefSeq)

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__Dino:3608351
          Length = 258

 Score = 93.2 bits (230), Expect = 5e-24
 Identities = 77/256 (30%), Positives = 121/256 (47%), Gaps = 12/256 (4%)

Query: 11  TESESTLVLTLSNPGARNALHPDMYAAGIEALDSVE-RDPSIRAVVITGADNFFCAGGNL 69
           T  +   VLTL+ P   NAL+  M A   E  D+V+      R +V+TGA   FC+G +L
Sbjct: 9   TIEDDAAVLTLNRPDVMNALNSQMRA---EITDAVKLAGAEARVLVMTGAGRAFCSGQDL 65

Query: 70  NRLLENRAKDPSVQAQSIDLLAEWISALRL---SSKPVIAAVDGAAAGAGFSLALACDLI 126
                +RA   ++  +   L  E++  LR       P IAAV+G AAGAG +LALA D++
Sbjct: 66  G----DRANAANLDLERT-LRDEYVPMLRAIFDCPVPTIAAVNGPAAGAGANLALAADVV 120

Query: 127 VAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKL 186
           +A + A F+ ++ R+GL PD GG+++L + +    A    +    I A +    G++ + 
Sbjct: 121 IATESAVFLQAFTRIGLIPDAGGTYWLPRQMGFAKAMGAALFADKITARQADAWGMIWEA 180

Query: 187 TKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREG 246
                      A A  L K    +   +K  +  +    L   L  E          R+ 
Sbjct: 181 VPDAEFEAVWRARAAHLAKGPTAAYEAVKQALRDSFNNDLDGQLALEAKLQGKMGETRDF 240

Query: 247 LEGISAFLEKRAPVYK 262
            EG+ AFLEKR+  ++
Sbjct: 241 KEGVLAFLEKRSASFE 256


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: 130
Number of extensions: 7
Number of successful extensions: 4
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: 258
Length adjustment: 24
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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.

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