GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacD in Burkholderia phytofirmans PsJN

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate BPHYT_RS19730 BPHYT_RS19730 dihydroxy-acid dehydratase

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS19730 BPHYT_RS19730
           dihydroxy-acid dehydratase
          Length = 577

 Score = 1160 bits (3002), Expect = 0.0
 Identities = 577/577 (100%), Positives = 577/577 (100%)

Query: 1   MADSNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCN 60
           MADSNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCN
Sbjct: 1   MADSNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCN 60

Query: 61  AHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDG 120
           AHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDG
Sbjct: 61  AHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDG 120

Query: 121 VILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGT 180
           VILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGT
Sbjct: 121 VILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGT 180

Query: 181 MTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLA 240
           MTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLA
Sbjct: 181 MTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLA 240

Query: 241 GRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE 300
           GRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE
Sbjct: 241 GRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE 300

Query: 301 LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNA 360
           LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNA
Sbjct: 301 LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNA 360

Query: 361 ANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEEL 420
           ANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEEL
Sbjct: 361 ANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEEL 420

Query: 421 HAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSG 480
           HAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSG
Sbjct: 421 HAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSG 480

Query: 481 TAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP 540
           TAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP
Sbjct: 481 TAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP 540

Query: 541 KRGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577
           KRGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH
Sbjct: 541 KRGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577


Lambda     K      H
   0.318    0.135    0.401 

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: 1311
Number of extensions: 54
Number of successful extensions: 3
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: 577
Length of database: 577
Length adjustment: 36
Effective length of query: 541
Effective length of database: 541
Effective search space:   292681
Effective search space used:   292681
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: 53 (25.0 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