GapMind for catabolism of small carbon sources

 

Aligments for a candidate for LRA3 in Azospirillum brasilense Sp245

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate AZOBR_RS31430 AZOBR_RS31430 galactarate dehydratase

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS31430 AZOBR_RS31430 galactarate
           dehydratase
          Length = 507

 Score =  218 bits (555), Expect = 3e-61
 Identities = 146/404 (36%), Positives = 214/404 (52%), Gaps = 28/404 (6%)

Query: 5   AQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPLDAFDDPSAEREPP 63
           A++ T +G +R DGR   RN + +   V C+   AR I  QFR + L A+ +        
Sbjct: 105 AERATFQGIVRPDGRVATRNYIGILTTVNCSATAARMIADQFRGDALAAYPNIDGV---- 160

Query: 64  VHLIGFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRAS- 116
           V L    GC      +      + +     HPN  AVL + LGCE      LV+V   + 
Sbjct: 161 VALTHSYGCGMGSQGDAIDALRRTIAGYARHPNFAAVLVLGLGCEVNQIDKLVEVEGLTI 220

Query: 117 GRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSG 176
           G  ++ L IQE GGT +T++  V+ IR    ++   ++  +  S L++   CGGSDG SG
Sbjct: 221 GDTLQTLAIQESGGTAATVRASVERIRALLPRVNDVKRETVPASHLILALQCGGSDGYSG 280

Query: 177 ITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYY 236
           ITANPA+G A D LI  G T +  ET E+ G E  +  R+  PA+G+ +V  +     Y 
Sbjct: 281 ITANPALGHAVDLLIRNGGTAVLSETPEVYGAEHLLTRRSVNPAVGETLVERIRWWEDYT 340

Query: 237 SILG---HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTG-GLYLLDV 292
           S  G   + + + GN  GGLTT  EKSLGA AK+G + +V +++  + P TG GL  +D 
Sbjct: 341 SRTGGEMNNNPSPGNKKGGLTTILEKSLGAVAKAGTTNLVEVVRYAE-PITGPGLVFMDT 399

Query: 293 VPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNL 352
                   G+  +S   +    +A GA+V+ FTTGRGSV G   +P +K+  N A +R +
Sbjct: 400 P-------GYDPVSATGQ----VAGGANVLCFTTGRGSVFGCKPTPSLKLATNTALFRKM 448

Query: 353 SGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLG 396
             DMD+D G I  G  T++EVGR +F+  +  + G  +KSE LG
Sbjct: 449 PDDMDIDCGPIATGDATIEEVGRTIFQLILDTASGKKTKSEELG 492


Lambda     K      H
   0.318    0.137    0.408 

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: 657
Number of extensions: 35
Number of successful extensions: 5
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: 431
Length of database: 507
Length adjustment: 33
Effective length of query: 398
Effective length of database: 474
Effective search space:   188652
Effective search space used:   188652
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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